Assoc. Prof. Michal Otyepka, Ph.D.

2011

• V. Mlynsky, P. Banas, N. G. Walter, J. Sponer, and M. Otyepka, “QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility
  of Multiple Competing Reaction Mechanisms,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 115, iss. 47, pp. 13911-13924, 2011.
  [Bibtex]

  @article ISI:000297195400014,
  Author = Mlynsky, Vojtech and Banas, Pavel and Walter, Nils G. and Sponer, Jiri
     and Otyepka, Michal,
  Title = QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility
     of Multiple Competing Reaction Mechanisms,
  Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
  Year = 2011,
  Volume = 115,
  Number = 47,
  Pages = 13911-13924,
  Month = DEC 1,
  Abstract = The hairpin ribozyme is a prominent member of small ribozymes since it
     does not require metal ions to achieve catalysis. Guanine 8 (G8) and
     adenine 38 (A38) have been identified as key participants in
     self-cleavage and -ligation. We have carried out hybrid
     quantum-mechanical/molecular mechanical (QM/MM) calculations to evaluate
     the energy along several putative reaction pathways. The error of our
     DFT description of the QM region was tested and shown to be similar to 1
     kcal/mol. We find that self-cleavage of the hairpin ribozyme may follow
     several competing microscopic reaction mechanisms, all with calculated
     activation barriers in good agreement with those from experiment (20-21
     kcal/mol). The initial nucleophilic attack of the A-1(2'-OH) group on
     the scissile phosphate is predicted to be rate-limiting in all these
     mechanisms. An unprotonated G8(-) (together with A38H(+)) yields a
     feasible activation barrier (20.4 kcal/mol). Proton transfer to a
     nonbridging phosphate oxygen also leads to feasible reaction pathways.
     Finally, our calculations consider thio-substitutions of one or both
     nonbridging oxygens of the scissile phosphate and predict that they have
     only a negligible effect on the reaction barrier, as observed
     experimentally.,
  DOI = 10.1021/jp206963g,
  ISSN = 1520-6106,
  Unique-ID = ISI:000297195400014,
  

• J. Granatier, P. Lazar, M. Otyepka, and P. Hobza, “The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and
  Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT
  Calculations,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 7, iss. 11, pp. 3743-3755, 2011.
  [Bibtex]

  @article ISI:000296597300030,
  Author = Granatier, Jaroslav and Lazar, Petr and Otyepka, Michal and Hobza, Pavel,
  Title = The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and
     Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT
     Calculations,
  Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
  Year = 2011,
  Volume = 7,
  Number = 11,
  Pages = 3743-3755,
  Month = NOV,
  Abstract = The adsorption of Ag, Au, and Pd atoms on benzene, coronene, and
     graphene has been studied using post Hartree-Fock wave function theory
     (CCSD(T), MP2) and density functional theory (M06-2X, DFT-D3, PBE,
     vdW-DF) methods. The CCSD(T) benchmark binding energies for benzene-M (M
     = Pd, Au, Ag) complexes are 19.7, 4.2, and 2.3 kcal/mol, respectively.
     We found that the nature of binding of the three metals is different:
     While silver binds predominantly through dispersion interactions, the
     binding of palladium has a covalent character, and the binding of gold
     involves a subtle combination of charge transfer and dispersion
     interactions as well as relativistic effects. We demonstrate that the
     CCSD(T) benchmark binding energies for benzene-M complexes can be
     reproduced in plane-wave density functional theory calculations by
     including a fraction of the exact exchange and a nonempirical van der
     Waals correction (EE+vdW). Applying the EE+vdW method, we obtained
     binding energies for the graphene-M (M = Pd, Au, Ag) complexes of 17.4,
     5.6, and 4.3 kcal/mol, respectively. The trends in binding energies
     found for the benzene M complexes correspond to those in coronene and
     graphene complexes. DFT methods that use empirical corrections to
     account for the effects of vdW interactions significantly overestimate
     binding energies in some of the studied systems.,
  DOI = 10.1021/ct200625h,
  ISSN = 1549-9618,
  Unique-ID = ISI:000296597300030,
  

• K. Berka, T. Hendrychova, P. Anzenbacher, and M. Otyepka, “Membrane Position of Ibuprofen Agrees with Suggested Access Path
  Entrance to Cytochrome P450 2C9 Active Site,” JOURNAL OF PHYSICAL CHEMISTRY A, vol. 115, iss. 41, pp. 11248-11255, 2011.
  [Bibtex]

  @article ISI:000295700600015,
  Author = Berka, Karel and Hendrychova, Tereza and Anzenbacher, Pavel and Otyepka,
     Michal,
  Title = Membrane Position of Ibuprofen Agrees with Suggested Access Path
     Entrance to Cytochrome P450 2C9 Active Site,
  Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
  Year = 2011,
  Volume = 115,
  Number = 41,
  Pages = 11248-11255,
  Month = OCT 20,
  Abstract = Cytochrome P450 2C9 (CYP2C9) is a membrane-anchored human microsomal
     protein involved in the drug metabolism in liver. CYP2C9 consists of an
     N-terminal transmembrane anchor and a catalytic cytoplasmic domain.
     While the structure of the catalytic domain is well-known from X-ray
     experiments, the complete structure and its incorporation into the
     membrane remains unsolved. We constructed an atomistic model of complete
     CYP2C9 in a dioleoylphosphatidylcholine membrane and evolved it by
     molecular dynamics simulations in explicit water on a 100+ ns
     time-scale. The model agrees well with known experimental data about
     membrane positioning of cytochromes P450. The entry to the substrate
     access channel is proposed to be facing the membrane interior while the
     exit of the product egress channel is situated above the interface
     pointing toward the water phase. The positions of openings of the
     substrate access and product egress channels correspond to free energy
     minima of CYP2C9 substrate ibuprofen and its metabolite in the membrane,
     respectively.,
  DOI = 10.1021/jp204488j,
  ISSN = 1089-5639,
  Unique-ID = ISI:000295700600015,
  

• M. Zgarbova, P. Jurecka, P. Banas, M. Otyepka, J. E. Sponer, N. B. Leontis, C. L. Zirbel, and J. Sponer, “Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of
  Key Base-Phosphate Interactions in Folded RNA Molecules Using
  Quantum-Chemical Calculations and Molecular Dynamics Simulations,” JOURNAL OF PHYSICAL CHEMISTRY A, vol. 115, iss. 41, pp. 11277-11292, 2011.
  [Bibtex]

  @article ISI:000295700600019,
  Author = Zgarbova, Marie and Jurecka, Petr and Banas, Pavel and Otyepka, Michal
     and Sponer, Judit E. and Leontis, Neocles B. and Zirbel, Craig L. and
     Sponer, Jiri,
  Title = Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of
     Key Base-Phosphate Interactions in Folded RNA Molecules Using
     Quantum-Chemical Calculations and Molecular Dynamics Simulations,
  Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
  Year = 2011,
  Volume = 115,
  Number = 41,
  Pages = 11277-11292,
  Month = OCT 20,
  Abstract = RNA molecules are stabilized by a wide range of non canonical
     interactions that are not present in DNA. Among them, the recently
     classified base phosphate (BPh) interactions belong to the most
     important ones. Twelve percent of nucleotides in the ribosomal crystal
     structures are involved in BPh interactions. BPh interactions are highly
     conserved and provide major constraints on RNA sequence evolution. Here
     we provide assessment of the energetics of BPh interactions using MP2
     computations extrapolated to the complete basis set of atomic orbitals
     and corrected for higher-order electron correlation effects. The
     reference computations are compared with DFT-D and DFT-D3 approaches,
     the SAPT method, and the molecular mechanics force field. The
     computations, besides providing the basic benchmark for the BPh
     interactions, allow some refinements of the original classification,
     including identification of some potential doubly bonded BPh patterns.
     The reference computations are followed by analysis of some larger RNA
     fragments that consider the context of the BPh interactions. The
     computations demonstrate the complexity of interaction patterns
     utilizing the BPh interactions in real RNA structures. The BPh
     interactions are often involved in intricate interaction networks. We
     studied BPh interactions of protonated adenine that can contribute to
     catalysis of hairpin ribozyme, the key BPh interaction in the S-turn
     motif of the sarcin ricin loop, which may predetermine the S-turn
     topology and complex BPh patterns-from the glmS riboswitch. Finally, the
     structural stability of BPh interactions in explicit solvent molecular
     dynamics simulations is assessed. The simulations well preserve key BPh
     interactions and allow dissection of structurally/functionally important
     water-meditated BPh bridges, which could not be considered in earlier
     bioinformatics classification of BPh interactions.,
  DOI = 10.1021/jp204820b,
  ISSN = 1089-5639,
  Unique-ID = ISI:000295700600019,
  

• F. Karlicky and M. Otyepka, “First Step in the Reaction of Zerovalent Iron with Water,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 7, iss. 9, pp. 2876-2885, 2011.
  [Bibtex]

  @article ISI:000294790400024,
  Author = Karlicky, Frantisek and Otyepka, Michal,
  Title = First Step in the Reaction of Zerovalent Iron with Water,
  Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
  Year = 2011,
  Volume = 7,
  Number = 9,
  Pages = 2876-2885,
  Month = SEP,
  Abstract = Here we present a comprehensive quantum chemical study. Of the simplest
     model system for the reactions of nanoscale zerovalent iron, i.e, the
     gas phase reaction of an iron atom with water, to identify a theoretical
     method that provides reasonably accurate geometries and thermochemical
     data for selected iron compounds along the reaction path (Fe, FeO,
     HFeOH, Fe(OH)(2)). The energies of selected stationary points on the
     ground electronic potential energy surface were systematically studied
     using HF and post-HF methods (MP2, MP3, MP4, CCSD, CCSD(T), CASSCF,
     MRCI) and selected DFT functionals (B3LYP, B97-I, BPW91, M06, M06-HF,
     M06-L, M06-2X and MPW1K) using various basis sets up to the complete
     basis set Scalar relativistic effects were modeled using the
     Douglas-Kroll-Hess Hamiltonian to the fourth Order, and the effects of
     valence plus outer core electronic correlation were also evaluated The
     calculations showed that (i) dynamic electron, correlation is crucial
     for accurate modeling of the reactions in question, (ii) the PES around
     the stationary points along the reaction path is rather flat, (iii) the
     single point energies calculated at the CCSD(T)/CBS level are in
     reasonably good agreemeny with experimental measurements, (iv) it is
     difficult to interpret DFT energies in the absence of benchmarking
     against data or results obtained at a level of theory that is known to
     accurately reproduce experimental results, (v) relativistic effects are
     relatively modest in this system but should be included if chemical
     accuracy is desired, and (vi) careful analysis of the multireference
     character of the system and potential spin contamination is important
     The CCSD(T)-3s3p-DKH2/CBS method can be considered the gold standard for
     this reaction because calculations at this level are in good agreement
     with experimental atomic excitation energies and thermochemical data.
     The gas-phase activation energy of the reaction between Fe and H(2)O is
     23.6 kcal/mol including the ZPVE correction (Delta G(298K)(double
     dagger) = 29.2 kcal/mol), and HFeOH is a stable intermediate lying -31.2
     kcal/mol below the reactants (Delta G(298K) = -25.4 kcal/mol).,
  DOI = 10.1021/ct200372y,
  ISSN = 1549-9618,
  Unique-ID = ISI:000294790400024,
  

• M. Zgarbova, M. Otyepka, J. Sponer, A. Mladek, P. Banas, T. E. Cheatham III, and P. Jurecka, “Refinement of the Cornell et al. Nucleic Acids Force Field Based on
  Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 7, iss. 9, pp. 2886-2902, 2011.
  [Bibtex]

  @article ISI:000294790400025,
  Author = Zgarbova, Marie and Otyepka, Michal and Sponer, Jiri and Mladek, Arnost
     and Banas, Pavel and Cheatham, III, Thomas E. and Jurecka, Petr,
  Title = Refinement of the Cornell et al. Nucleic Acids Force Field Based on
     Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles,
  Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
  Year = 2011,
  Volume = 7,
  Number = 9,
  Pages = 2886-2902,
  Month = SEP,
  Abstract = We report a reparameterization of the glycosidic torsion chi of the
     Cornell et al. AMBER force field for RNA, chi(OL) The parameters remove
     destabilization of the anti region found in the ff99 force field and
     thus prevent formation of spurious ladder-like structural distortions in
     RNA simulations. They also improve the description of the syn region and
     the syn anti balance as well as enhance MD simulations of various RNA
     structures. Although chi(OL) can be combined with both ff99 and
     ff99bsc0, we recommend the latter. We do not recommend using chi(OL) for
     B-DNA because it does not improve upon ff99bsc0 for canonical
     structures. However, it might be useful in simulations of DNA molecules
     containing syn nucleotides. Our parametrization is based on high-level
     QM calculations and differs from conventional parametrization approaches
     in that it incorporates some previously neglected solvation-related
     effects (which appear to be essential for obtaining correct
     anti/high-anti balance). Our chi(OL) force field is compared with
     several previous glycosidic torsion parametrizations.,
  DOI = 10.1021/ct200162x,
  ISSN = 1549-9618,
  Unique-ID = ISI:000294790400025,
  

• P. Sklenovsky, P. Florova, P. Banas, K. Reblova, F. Lankas, M. Otyepka, and J. Sponer, “Understanding RNA Flexibility Using Explicit Solvent Simulations: The
  Ribosomal and Group I Intron Reverse Kink-Turn Motifs,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 7, iss. 9, pp. 2963-2980, 2011.
  [Bibtex]

  @article ISI:000294790400032,
  Author = Sklenovsky, Petr and Florova, Petra and Banas, Pavel and Reblova, Kamila
     and Lankas, Filip and Otyepka, Michal and Sponer, Jiri,
  Title = Understanding RNA Flexibility Using Explicit Solvent Simulations: The
     Ribosomal and Group I Intron Reverse Kink-Turn Motifs,
  Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
  Year = 2011,
  Volume = 7,
  Number = 9,
  Pages = 2963-2980,
  Month = SEP,
  Abstract = Reverse kink-turn is a recurrent elbow-like RNA building block occurring
     in the ribosome and in the group I intron. Its sequence signature almost
     matches that of the conventional kink-turn. However, the reverse and
     conventional kink-turns have opposite directions of bending. The reverse
     kink-turn lacks basically any tertiary interaction between its stems. We
     report unrestrained, explicit solvent molecular dynamics simulations of
     ribosomal and intron reverse kink-turns (54 simulations with 7.4 mu s of
     data in total) with different variants (ff94,ff99,ff99bsc0, ff99
     chi(OL), and ff99bsc0 chi(OL)) of the Cornell et al. force field. We
     test several ion conditions and two water models. The simulations
     characterize the directional intrinsic flexibility of reverse kink turns
     pertinent to their folded functional geometries. The reverse kink-turns
     are the most flexible RNA motifs studied so far by explicit solvent
     simulations which are capable at the present simulation time scale to
     spontaneously and reversibly sample a wide range of geometries from
     tightly kinked ones through flexible intermediates up to extended,
     unkinked structures. A possible biochemical role of the flexibility is
     discussed. Among the tested force fields, the latest chi(OL) variant is
     essential to obtaining stable trajectories while all force field
     versions lacking the chi correction are prone to a swift degradation
     toward senseless ladder-like structures of stems, characterized by
     high-anti glycosidic torsions. The type of explicit water model affects
     the simulations considerably more than concentration and the type of
     ions.,
  DOI = 10.1021/ct200204t,
  ISSN = 1549-9618,
  Unique-ID = ISI:000294790400032,
  

• P. Dobes, J. Rezac, J. Fanfrlik, M. Otyepka, and P. Hobza, “Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry
  and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well,
  While the Empirical Potential Fails,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 115, iss. 26, pp. 8581-8589, 2011.
  [Bibtex]

  @article ISI:000292281200025,
  Author = Dobes, Petr and Rezac, Jan and Fanfrlik, Jindrich and Otyepka, Michal
     and Hobza, Pavel,
  Title = Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry
     and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well,
     While the Empirical Potential Fails,
  Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
  Year = 2011,
  Volume = 115,
  Number = 26,
  Pages = 8581-8589,
  Month = JUL 7,
  Abstract = In the present study, we have investigated complexes of CK2 protein
     kinase with halogenated inhibitors by means of the advanced
     semiempirical quantum mechanical (SQM) PM6 method (called PM6-DH2X),
     which describes various types of noncovalent interactions including
     halogen bonding well. The PM6-DH2X method provides reliable geometries
     of those CK2 protein kinase-inhibitor complexes involving halogen bonds
     that agree well with the X-ray crystal structures. When the Amber
     empirical potential is applied, this agreement becomes considerably
     worse. Similarly, the binding free energies determined by the PM6-DH2X
     SQM method are much closer to the experimental inhibition constants than
     those based on the Amber empirical potential.,
  DOI = 10.1021/jp202149z,
  ISSN = 1520-6106,
  Unique-ID = ISI:000292281200025,
  

• P. Dobes, J. Fanfrlik, J. Rezac, M. Otyepka, and P. Hobza, “Transferable scoring function based on semiempirical quantum mechanical
  PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors,” JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, vol. 25, iss. 3, pp. 223-235, 2011.
  [Bibtex]

  @article ISI:000288179000005,
  Author = Dobes, Petr and Fanfrlik, Jindrich and Rezac, Jan and Otyepka, Michal
     and Hobza, Pavel,
  Title = Transferable scoring function based on semiempirical quantum mechanical
     PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors,
  Journal = JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN,
  Year = 2011,
  Volume = 25,
  Number = 3,
  Pages = 223-235,
  Month = MAR,
  Abstract = A semiempirical quantum mechanical PM6-DH2 method accurately covering
     the dispersion interaction and H-bonding was used to score fifteen
     structurally diverse CDK2 inhibitors. The geometries of all the
     complexes were taken from the X-ray structures and were reoptimised by
     the PM6-DH2 method in continuum water. The total scoring function was
     constructed as an estimate of the binding free energy, i.e., as a sum of
     the interaction enthalpy, interaction entropy and the corrections for
     the inhibitor desolvation and deformation energies. The applied scoring
     function contains a clear thermodynamical terms and does not involve any
     adjustable empirical parameter. The best correlations with the
     experimental inhibition constants (ln K (i)) were found for bare
     interaction enthalpy (r (2) = 0.87) and interaction enthalpy corrected
     for ligand desolvation and deformation energies (r (2) = 0.77); when the
     entropic term was considered, however, the correlation becomes worse but
     still acceptable (r (2) = 0.52). The resulting correlation based on the
     PM6-DH2 scoring function is better than previously published function
     based on various docking/scoring, SAR studies or advanced QM/MM
     approach, however, the robustness is limited by number of available
     experimental data used in the correlation. Since a very similar
     correlation between the experimental and theoretical results was found
     also for a different system of the HIV-1 protease, the suggested scoring
     function based on the PM6-DH2 method seems to be applicable in drug
     design, even if diverse protein-ligand complexes have to be ranked.,
  DOI = 10.1007/s10822-011-9413-5,
  ISSN = 0920-654X,
  Unique-ID = ISI:000288179000005,
  

• K. Berka and M. Otyepka, “Insenstivity to Close Contacts and Inability to Predict Protein
  Foldability,” JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol. 28, iss. 4, pp. 633-634, 2011.
  [Bibtex]

  @article ISI:000286482400027,
  Author = Berka, Karel and Otyepka, Michal,
  Title = Insenstivity to Close Contacts and Inability to Predict Protein
     Foldability,
  Journal = JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS,
  Year = 2011,
  Volume = 28,
  Number = 4,
  Pages = 633-634,
  Month = FEB,
  ISSN = 0739-1102,
  Unique-ID = ISI:000286482400027,
  

• T. Hendrychova, E. Anzenbacherova, J. Hudecek, J. Skopalik, R. Lange, P. Hildebrandt, M. Otyepka, and P. Anzenbacher, “Flexibility of human cytochrome P450 enzymes: Molecular dynamics and
  spectroscopy reveal important function-related variations,” BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, vol. 1814, iss. 1, SI, pp. 58-68, 2011.
  [Bibtex]

  @article ISI:000285277900009,
  Author = Hendrychova, Tereza and Anzenbacherova, Eva and Hudecek, Jiri and
     Skopalik, Josef and Lange, Reinhard and Hildebrandt, Peter and Otyepka,
     Michal and Anzenbacher, Pavel,
  Title = Flexibility of human cytochrome P450 enzymes: Molecular dynamics and
     spectroscopy reveal important function-related variations,
  Journal = BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS,
  Year = 2011,
  Volume = 1814,
  Number = 1, SI,
  Pages = 58-68,
  Month = JAN,
  Abstract = To gain more complete insight into flexibility and malleability of five
     forms of human liver cytochrome P450 enzymes, which play major roles in
     drug metabolism (CYPs 1A2, 2A6, 2C9, 2D6 and 3A4), we employed UV/VIS
     and resonance Raman spectroscopy in combination with all-atomic
     molecular dynamics simulations under normal and high pressure conditions
     (300 MPa). In general, the high pressure reduces the flexibility of
     CYPs, which become more dense and compact as their radii of gyration and
     temperature B-factors diminish. The flexibility of CYPs spans the
     regions, which are localized in solvent exposed loops. A considerable
     degree of flexibility is also observed at amino-acids making the pw2 and
     solvent channels, which are suggested to serve for substrate access
     and/or product release. The number of water molecules as well as the
     number of protein backbone atoms of the active site in close proximity
     of heme cofactor generally increases under high pressure. This finding
     provides new insights regarding the interpretation of pressure-related
     Soret band red shifts. Presented results also point towards considerable
     differences between the CYP forms studied: CYP2A6 and CYP1A2 have the
     least malleable active sites while those of CYP2D6, CYP2C9 and CYP3A4
     have considerably greater degrees of flexibility or malleability. In
     addition, the number of water molecules in the active site cavity of
     CYP3A4 anomalously decreases under high pressure due to opening of the
     active site. These results correlate with the known substrate
     promiscuity of the respective CYP forms, with CYP3A4 displaying the
     highest substrate promiscuity, corresponding to the most open and
     malleable active site, whereas CYP1A2 and CYP2A6 show a high
     substrate-specificity and have a small and rigid active sites. (C) 2010
     Elsevier B.V. All rights reserved.,
  DOI = 10.1016/j.bbapap.2010.07.017,
  ISSN = 1570-9639,
  Unique-ID = ISI:000285277900009,
  

2010

• R. Zboril, F. Karlicky, A. B. Bourlinos, T. A. Steriotis, A. K. Stubos, V. Georgakilas, K. Safarova, D. Jancik, C. Trapalis, and M. Otyepka, “Graphene Fluoride: A Stable Stoichiometric Graphene Derivative and its
  Chemical Conversion to Graphene,” SMALL, vol. 6, iss. 24, pp. 2885-2891, 2010.
  [Bibtex]

  @article ISI:000285793900015,
  Author = Zboril, Radek and Karlicky, Frantisek and Bourlinos, Athanasios B. and
     Steriotis, Theodore A. and Stubos, Athanasios K. and Georgakilas,
     Vasilios and Safarova, Klara and Jancik, Dalibor and Trapalis, Christos
     and Otyepka, Michal,
  Title = Graphene Fluoride: A Stable Stoichiometric Graphene Derivative and its
     Chemical Conversion to Graphene,
  Journal = SMALL,
  Year = 2010,
  Volume = 6,
  Number = 24,
  Pages = 2885-2891,
  Month = DEC 20,
  Abstract = Stoichoimetric graphene fluoride monolayers are obtained in a single
     step by the liquid-phase exfoliation of graphite fluoride with
     sulfolane. Comparative quantum-mechanical calculations reveal that
     graphene fluoride is the most thermodynamically stable of five studied
     hypothetical graphene derivatives; graphane, graphene fluoride, bromide,
     chloride, and iodide. The graphene fluoride is transformed into graphene
     via graphene iodide, a spontaneously decomposing intermediate. The
     calculated bandgaps of graphene halides vary from zero for graphene
     bromide to 3.1 eV for graphene fluoride. It is possible to design the
     electronic properties of such two-dimensional crystals.,
  DOI = 10.1002/smll.201001401,
  ISSN = 1613-6810,
  Unique-ID = ISI:000285793900015,
  

• A. Mladek, J. E. Sponer, P. Jurecka, P. Banas, M. Otyepka, D. Svozil, and J. Sponer, “Conformational Energies of DNA Sugar-Phosphate Backbone: Reference QM
  Calculations and a Comparison with Density Functional Theory and
  Molecular Mechanics,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 6, iss. 12, pp. 3817-3835, 2010.
  [Bibtex]

  @article ISI:000285217000018,
  Author = Mladek, Arnost and Sponer, Judit E. and Jurecka, Petr and Banas, Pavel
     and Otyepka, Michal and Svozil, Daniel and Sponer, Jiri,
  Title = Conformational Energies of DNA Sugar-Phosphate Backbone: Reference QM
     Calculations and a Comparison with Density Functional Theory and
     Molecular Mechanics,
  Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
  Year = 2010,
  Volume = 6,
  Number = 12,
  Pages = 3817-3835,
  Month = DEC,
  Abstract = The study investigates electronic structure and gas-phase energetics of
     the DNA sugar phosphate backbone via advanced quantum chemical (QM)
     methods. The analysis has been carried out on biologically relevant
     backbone conformations composed of 11 canonical BI-DNA structures, 8
     pathological structures with alpha/gamma torsion angles in the g+/t
     region, and 3 real noncanonical gamma-trans structures occurring in the
     loop region of guanine quadruplex DNA. The influence of backbone
     conformation on the intrinsic energetics was primarily studied using a
     model system consisting of two sugar moieties linked together via a
     phosphodiester bond (SPSOM model). To get the conformation of the
     studied system fully under control, for each calculation we have frozen
     majority of the dihedral angles to their target values. CCSD(T) energies
     extrapolated to the complete basis set were utilized as reference
     values. However, the calculations show that inclusion of higher-order
     electron correlation effects for this system is not crucial and complete
     basis set second-order perturbation calculations are sufficiently
     accurate. The reference QM data are used to assess performance of 10
     contemporary density functionals with the best performance delivered by
     the PBE-D/TZVPP combination along with the Grimme's dispersion
     correction, and by the TPSS-D/6-311++G(3df,3pd) augmented by Jurecka's
     dispersion term. In addition, the QM calculations are compared to
     molecular mechanics (MM) model based on the Cornell et al. force field.
     The destabilization of the pathological g+/t conformers with respect to
     the reference canonical structure and the network of intramolecular CH
     center dot center dot center dot O interactions were investigated by
     means of natural bond orbital analysis (NBO) and atoms-in-molecules
     (AIM) Bader analysis. Finally, four additional model systems of
     different sizes were assessed by comparing their energetics to that of
     the SPSOM system. Energetics of smaller MOSPM model consisting of a
     sugar moiety linked to a phosphate group and capped with methyl and
     methoxy group on the 5'- and 3'-ends, respectively, is fairly similar to
     that of SPSOM, while the role of undesired intramolecular interactions
     is diminished.,
  DOI = 10.1021/ct1004593,
  ISSN = 1549-9618,
  Unique-ID = ISI:000285217000018,
  

• P. Banas, D. Hollas, M. Zgarbova, P. Jurecka, M. Orozco, T. E. Cheatham III, J. Sponer, and M. Otyepka, “Performance of Molecular Mechanics Force Fields for RNA Simulations:
  Stability of UUCG and GNRA Hairpins,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 6, iss. 12, pp. 3836-3849, 2010.
  [Bibtex]

  @article ISI:000285217000019,
  Author = Banas, Pavel and Hollas, Daniel and Zgarbova, Marie and Jurecka, Petr
     and Orozco, Modesto and Cheatham, III, Thomas E. and Sponer, Jiri and
     Otyepka, Michal,
  Title = Performance of Molecular Mechanics Force Fields for RNA Simulations:
     Stability of UUCG and GNRA Hairpins,
  Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
  Year = 2010,
  Volume = 6,
  Number = 12,
  Pages = 3836-3849,
  Month = DEC,
  Abstract = The RNA hairpin loops represent important RNA topologies with
     indispensable biological functions in RNA folding and tertiary
     interactions. 5'-UNCG-3' and 5'-GNRA-3' RNA tetraloops are the most
     important classes of RNA hairpin loops. Both tetraloops are highly
     structured with characteristic signature three-dimensional features and
     are recurrently seen in functional RNAs and ribonucleoprotein particles.
     Explicit solvent molecular dynamics (MD) simulation is a computational
     technique which can efficiently complement the experimental data and
     provide unique structural dynamics information on the atomic scale.
     Nevertheless, the outcome of simulations is often compromised by
     imperfections in the parametrization of simplified pairwise additive
     empirical potentials referred to also as force fields. We have pointed
     out in several recent studies that a force field description of
     single-stranded hairpin segments of nucleic acids may be particularly
     challenging for the force fields. In this paper, we report a critical
     assessment of a broad set of MD simulations of UUCG, GAGA, and GAAA
     tetraloops using various force fields. First, we utilized the three
     widely used variants of Cornell et al. (AMBER) force fields known as
     694, 699, and ff99bsc0. Some simulations were also carried out with
     CHARMM27. The simulations reveal several problems which show that these
     force fields are not able to retain all characteristic structural
     features (structural signature) of the studied tetraloops. Then we
     tested four recent reparameterizations of glycosidic torsion of the
     Cornell et al. force field (two of them being currently parametrized in
     our laboratories). We show that at least some of the new versions show
     an improved description of the tetraloops, mainly in the syn glycosidic
     torsion region of the UNCG tetraloop. The best performance is achieved
     in combination with the bsc0 parametrization of the alpha/gamma angles.
     Another critically important region to properly describe RNA molecules
     is the anti/high-anti region of the glycosidic torsion, where there are
     significant differences among the tested force fields. The tetraloop
     simulations are complemented by simulations of short A-RNA stems, which
     are especially sensitive to an appropriate description of the
     anti/high-anti region. While excessive accessibility of the high-anti
     region converts the A-RNA into a senseless ``ladder-like'' geometry,
     excessive penalization of the high-anti region shifts the simulated
     structures away from typical A-RNA geometry to structures with a visibly
     underestimated inclination of base pairs with respect to the helical
     axis.,
  DOI = 10.1021/ct100481h,
  ISSN = 1549-9618,
  Unique-ID = ISI:000285217000019,
  

• P. Florova, P. Sklenovsky, P. Banas, and M. Otyepka, “Explicit Water Models Affect the Specific Solvation and Dynamics of
  Unfolded Peptides While the Conformational Behavior and Flexibility of
  Folded Peptides Remain Intact,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 6, iss. 11, 3285, pp. 3569-3579, 2010.
  [Bibtex]

  @article ISI:000283884300026,
  Author = Florova, Petra and Sklenovsky, Petr and Banas, Pavel and Otyepka, Michal,
  Title = Explicit Water Models Affect the Specific Solvation and Dynamics of
     Unfolded Peptides While the Conformational Behavior and Flexibility of
     Folded Peptides Remain Intact,
  Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
  Year = 2010,
  Volume = 6,
  Number = 11, 3285,
  Pages = 3569-3579,
  Month = NOV,
  Abstract = Conventional molecular dynamics simulations on 50 ns to 1 mu s time
     scales were used to study the effects of explicit solvent models on the
     conformational behavior and solvation of two oligopeptide solutes:
     alpha-helical EK-peptide (14 amino acids) and a beta-hairpin chignolin
     (10 amino acids). The widely used AMBER force fields (ff99, ff99SB, and
     ff03) were combined with four of the most commonly used explicit solvent
     models (TIP3P, TIP4P, TIP5P, and SPC/E). Significant differences in the
     specific solvation of chignolin among the studied water models were
     identified. Chignolin was highly solvated in TIP5P, whereas reduced
     specific solvation was found in the TIP4P, SPC/E, and TIP3P models for
     kinetic, thermodynamic, and both kinetic and thermodynamic reasons,
     respectively. The differences in specific solvation did not influence
     the dynamics of structured parts of the folded peptide. However,
     substantial differences between TIP5P and the other models were observed
     in the dynamics of unfolded chignolin, stability of salt bridges, and
     specific solvation of the backbone carbonyls of EK-peptide. Thus, we
     conclude that the choice of water model may affect the dynamics of
     flexible parts of proteins that are solvent-exposed. On the other hand,
     all water models should perform similarly for well-structured folded
     protein regions. The merits of the TIP3P model include its high and
     overestimated mobility, which accelerates simulation processes and thus
     effectively increases sampling.,
  DOI = 10.1021/ct1003687,
  ISSN = 1549-9618,
  Unique-ID = ISI:000283884300026,
  

• P. Banas, N. G. Walter, J. Sponer, and M. Otyepka, “Protonation States of the Key Active Site Residues and Structural
  Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 114, iss. 26, pp. 8701-8712, 2010.
  [Bibtex]

  @article ISI:000279282600015,
  Author = Banas, Pavel and Walter, Nils G. and Sponer, Jiri and Otyepka, Michal,
  Title = Protonation States of the Key Active Site Residues and Structural
     Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics,
  Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
  Year = 2010,
  Volume = 114,
  Number = 26,
  Pages = 8701-8712,
  Month = JUL 8,
  Abstract = The glmS catalytic riboswitch is part of the 5'-untranslated region of
     mRNAs encoding glucosamine-6-phosphate (GlcN6P) synthetase (glmS) in
     numerous Gram-positive bacteria. Binding of the cofactor GlcN6P induces
     site-specific self-cleavage of the RNA. However, the detailed reaction
     mechanism as well as the protonation state of the glmS reactive form
     still remains elusive. To probe the dominant protonation states of key
     active site residues, we carried out explicit solvent molecular dynamic
     simulations involving various protonation states of three crucial active
     site moieties observed in the available crystal structures: (i) guanine
     G40 (following the Thermoanaerobacter tengcongensis numbering), (ii) the
     GlcN6P amino/ammonium group, and (iii) the GlcN6P phosphate moiety. We
     found that a deprotonated G40(-) seems incompatible with the observed
     glmS active site architecture. Our data suggest that the canonical form
     of G40 plays a structural role by stabilizing an in-line attack
     conformation of the cleavage site A-1(2'-OH) nucleophile, rather than a
     more direct chemical role. In addition, we observe weakened cofactor
     binding upon protonation of the GlcN6P phosphate moiety, which explains
     the experimentally observed increase in K(m) with decreasing pH.
     Finally, we discuss a possible role of cofactor binding and its
     interaction with the G65 and Gl purines in structural stabilization of
     the A-1(2'-01-I) in-line attack conformation. On the basis of the
     identified dominant protonation state of the reaction precursor, we
     propose a hypothesis of the self-cleavage mechanism in which A-1(2'-OH)
     is activated as a nucleophile by the Gl (pro-R(p)) nonbridging oxygen of
     the scissile phosphate, whereas the ammonium group of GlcN6P acts as the
     general acid protonating the Gl(O5') leaving group.,
  DOI = 10.1021/jp9109699,
  ISSN = 1520-6106,
  Unique-ID = ISI:000279282600015,
  

• E. S. Child, T. Hendrychova, K. McCague, A. Futreal, M. Otyepka, and D. J. Mann, “A cancer-derived mutation in the PSTAIRE helix of cyclin-dependent
  kinase 2 alters the stability of cyclin binding,” BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH, vol. 1803, iss. 7, pp. 858-864, 2010.
  [Bibtex]

  @article ISI:000279093300010,
  Author = Child, Emma S. and Hendrychova, Tereza and McCague, Karen and Futreal,
     Andy and Otyepka, Michal and Mann, David J.,
  Title = A cancer-derived mutation in the PSTAIRE helix of cyclin-dependent
     kinase 2 alters the stability of cyclin binding,
  Journal = BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH,
  Year = 2010,
  Volume = 1803,
  Number = 7,
  Pages = 858-864,
  Month = JUL,
  Abstract = Cyclin-dependent kinase 2 (cdk2) is a central regulator of the mammalian
     cell cycle. Here we describe the properties of a mutant form of cdk2
     identified during large-scale sequencing of protein kinases from
     cancerous tissue. The mutation substituted a leucine for a proline in
     the PSTAIRE helix, the central motif in the interaction of the cdk with
     its regulatory cyclin subunit. We demonstrate that whilst the mutant
     cdk2 is considerably impaired in stable cyclin association, it is still
     able to generate an active kinase that can functionally complement
     defective cdks in vivo. Molecular dynamic simulations and biophysical
     measurements indicate that the observed biochemical properties likely
     stem from increased flexibility within the cyclin-binding helix. (C)
     2010 Elsevier By. All rights reserved.,
  DOI = 10.1016/j.bbamcr.2010.04.004,
  ISSN = 0167-4889,
  Unique-ID = ISI:000279093300010,
  

• V. Mlynsky, P. Banas, D. Hollas, K. Reblova, N. G. Walter, J. Sponer, and M. Otyepka, “Extensive Molecular Dynamics Simulations Showing That Canonical G8 and
  Protonated A38H(+) Forms Are Most Consistent with Crystal Structures of
  Hairpin Ribozyme,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 114, iss. 19, pp. 6642-6652, 2010.
  [Bibtex]

  @article ISI:000277499700047,
  Author = Mlynsky, Vojtech and Banas, Pavel and Hollas, Daniel and Reblova, Kamila
     and Walter, Nils G. and Sponer, Jiri and Otyepka, Michal,
  Title = Extensive Molecular Dynamics Simulations Showing That Canonical G8 and
     Protonated A38H(+) Forms Are Most Consistent with Crystal Structures of
     Hairpin Ribozyme,
  Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
  Year = 2010,
  Volume = 114,
  Number = 19,
  Pages = 6642-6652,
  Month = MAY 20,
  Abstract = The hairpin ribozyme is a prominent member of the group of small
     catalytic RNAs (RNA enzymes or ribozymes) because it does not require
     metal ions to achieve catalysis. Biochemical and structural data have
     implicated guanine 8 (G8) and adenine 38 (A38) as catalytic participants
     in cleavage and ligation catalyzed by the hairpin ribozyme, yet their
     exact role in catalysis remains disputed. To gain insight into dynamics
     in the active site of a minimal self-cleaving hairpin ribozyme, we have
     performed extensive classical, explicit-solvent molecular dynamics (MD)
     simulations on time scales of 50-150 ns. Starting from the available
     X-ray crystal structures, we investigated the structural impact of the
     protonation states of G8 and A38, and the inactivating A-1(2'-methoxy)
     substitution employed in crystallography. Our simulations reveal that a
     canonical G8 agrees well with the crystal structures while a
     deprotonated G8 profoundly distorts the active site. Thus MD simulations
     do not support a straightforward participation of the deprotonated G8 in
     catalysis. By comparison, the G8 enol tautomer is structurally well
     tolerated, causing only local rearrangements in the active site.
     Furthermore, a protonated A38H(+) is more consistent with the
     crystallography data than a canonical A38. The simulations thus support
     the notion that A38H+ is the dominant form in the crystals, grown at pH
     6. In most simulations, the canonical A38 departs from the scissile
     phosphate and substantially perturbs the structures of the active site
     and S-turn. Yet, we occasionally also observe formation of a stable
     A-1(2'-OH)center dot center dot center dot A38(N1) hydrogen bond, which
     documents the ability of the ribozyme to form this hydrogen bond,
     consistent with a potential role of A38 as general base catalyst. The
     presence of this hydrogen bond is, however, incompatible with the
     expected in-line attack angle necessary for self-cleavage, requiring a
     rapid transition of the deprotonated 2'-oxyanion to a position more
     favorable for in-line attack after proton transfer from A-1(2'-OH) to
     A38(N1). The simulations revealed a potential force field artifact,
     occasional but irreversible formation of ``ladder-like'', underwound
     A-RNA structure in one of the external helices. Although it does not
     affect the catalytic center of the hairpin ribozyme, further studies are
     under way to better assess possible influence of such force field
     behavior on long RNA simulations.,
  DOI = 10.1021/jp1001258,
  ISSN = 1520-6106,
  Unique-ID = ISI:000277499700047,
  

• K. Dvorakova-Hola, A. Matuskova, M. Kubala, M. Otyepka, T. Kucera, J. Vecer, P. Herman, N. Parkhomenko, E. Kutejova, and J. Janata, “Glycine-Rich Loop of Mitochondrial Processing Peptidase alpha-Subunit Is
  Responsible for Substrate Recognition by a Mechanism Analogous to
  Mitochondrial Receptor Tom20,” JOURNAL OF MOLECULAR BIOLOGY, vol. 396, iss. 5, pp. 1197-1210, 2010.
  [Bibtex]

  @article ISI:000275691500002,
  Author = Dvorakova-Hola, Klara and Matuskova, Anna and Kubala, Martin and
     Otyepka, Michal and Kucera, Tomas and Vecer, Jaroslav and Herman, Petr
     and Parkhomenko, Natalya and Kutejova, Eva and Janata, Jiri,
  Title = Glycine-Rich Loop of Mitochondrial Processing Peptidase alpha-Subunit Is
     Responsible for Substrate Recognition by a Mechanism Analogous to
     Mitochondrial Receptor Tom20,
  Journal = JOURNAL OF MOLECULAR BIOLOGY,
  Year = 2010,
  Volume = 396,
  Number = 5,
  Pages = 1197-1210,
  Month = MAR 12,
  Abstract = Tryptophan fluorescence measurements were used to characterize the local
     dynamics of the highly conserved glycine-rich loop (GRL) of the
     mitochondrial processing peptidase (MPP) alpha-subunit in the presence
     of the substrate precursor. Reporter tryptophan residue was introduced
     into the GRL of the yeast alpha-MPP (Y299W) or at a proximal site
     (Y303W). Time-resolved and steady-state fluorescence spectroscopy
     demonstrated that for Trp299, the primary contact with the yeast malate
     dehydrogenase precursor evokes a change of the local GRL mobility.
     Moreover, time-resolved measurements showed that a functionless
     alpha-MPP with a single-residue deletion in the loop (Y303W/Delta G292)
     is defective particularly in the primary contact with substrate. Thus,
     the GRL was proved to be part of a contact site of the enzyme
     specifically recognizing the substrate. Regarding the surface exposure
     and presence of the hydrophobic patches within the GRL, we proposed a
     functional analogy between the presequence recognition by the
     hydrophobic binding groove of the Tom20 mitochondrial import receptor
     and the GRL of the alpha-MPP. A molecular dynamics (MD) simulation of
     the MPP-substrate peptide complex model was employed to test this
     hypothesis. The initial positioning and conformation of the substrate
     peptide in the model fitting were chosen based on the analogy of its
     interaction with the Tom20 binding groove. MD simulation confirmed the
     stability of the proposed interaction and showed also a decrease in GRL
     flexibility in the presence of substrate, in agreement with fluorescence
     measurements. Moreover, conserved substrate hydrophobic residues in
     positions +1 and -4 to the cleavage site remain in close contact with
     the side chains of the GRL during the entire production part of MD
     simulation as stabilizing points of the hydrophobic interaction. We
     conclude that the GRL of the MPP alpha-subunit is the crucial
     evolutional outcome of the presequence recognition by MPP and represents
     a functional parallel with Tom20 import receptor. (C) 2010 Elsevier Ltd.
     All rights reserved.,
  DOI = 10.1016/j.jmb.2009.12.054,
  ISSN = 0022-2836,
  Unique-ID = ISI:000275691500002,
  

• P. Sklenovsky and M. Otyepka, “In Silico Structural and Functional Analysis of Fragments of the Ankyrin
  Repeat Protein P18(INK4c),” JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol. 27, iss. 4, pp. 521-539, 2010.
  [Bibtex]

  @article ISI:000272599400011,
  Author = Sklenovsky, Petr and Otyepka, Michal,
  Title = In Silico Structural and Functional Analysis of Fragments of the Ankyrin
     Repeat Protein P18(INK4c),
  Journal = JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS,
  Year = 2010,
  Volume = 27,
  Number = 4,
  Pages = 521-539,
  Month = FEB,
  Abstract = Ankyrin repeat proteins (ARPs) are ubiquitous proteins that play
     critical regulatory roles in organisms and consist of repeating motifs
     (ankyrin repeats) stacked in non-globular, almost linear, ``quasi
     one-dimensional'' configurations. They also have highly unusual
     mechanical properties, notably ARPs can behave as nano-springs. Both
     their essential cellular functions and distinctive nano-mechanical
     properties have aroused interest in ARPs for potential applications in
     medicine and nanotechnology. Further, the modular architecture of ARPs,
     which lack the long-range contacts that typically stabilize globular
     proteins, provides a new paradigm for understanding protein stability
     and folding mechanisms of proteins. In the present study, the stability
     of ARP p18(INK4c) (p18) and fifty p18 fragments was investigated by
     all-atomic molecular dynamics (MD) simulations in explicit water on a
     similar to 3.3 microseconds timescale. The fragment simulations indicate
     that p18 alpha-helices are significantly stabilized by tertiary
     interactions, because in the absence of their native context they
     readily melt. All single p18 ARs and their structural elements are also
     unstable outside their native context. The minimal stable motifs are
     pairs of ARs, implying that inter-repeat contacts are essential for AR
     stability. Further, pairs of internal ARs are less stable than pairs
     that include a native capping AR. The MD simulations also provide
     indications of the functional roles of p18 turns and loops: the turns
     appear to be essential for the stability of the protein, while the loops
     both help to stabilize the p18 structure and are involved in recognition
     processes. Temperature-induced unfolding analysis shows that the p18
     melts from the N-terminus to the C-terminus.,
  ISSN = 0739-1102,
  Unique-ID = ISI:000272599400011,
  

• M. A. Ditzler, M. Otyepka, J. Sponer, and N. G. Walter, “Molecular Dynamics and Quantum Mechanics of RNA: Conformational and
  Chemical Change We Can Believe In,” ACCOUNTS OF CHEMICAL RESEARCH, vol. 43, iss. 1, pp. 40-47, 2010.
  [Bibtex]

  @article ISI:000274289400005,
  Author = Ditzler, Mark A. and Otyepka, Michal and Sponer, Jiri and Walter, Nils
     G.,
  Title = Molecular Dynamics and Quantum Mechanics of RNA: Conformational and
     Chemical Change We Can Believe In,
  Journal = ACCOUNTS OF CHEMICAL RESEARCH,
  Year = 2010,
  Volume = 43,
  Number = 1,
  Pages = 40-47,
  Month = JAN,
  Abstract = Structure and dynamics are both critical to RNA's vital functions in
     biology. Numerous techniques can elucidate the structural dynamics of
     RNA, but computational approaches based on experimental data arguably
     hold the promise of providing the most detail. In this Account, we
     highlight areas wherein molecular dynamics (MD) and quantum mechanical
     (QM) techniques are applied to RNA, particularly in relation to
     complementary experimental studies.
     We have expanded on atomic-resolution crystal structures of RNAs in
     functionally relevant states by applying explicit Solvent MD simulations
     to explore their dynamics and conformational changes on the
     submicrosecond time scale. MD relies simplified atomistic, pairwise
     additive interaction potentials (force fields). Because of limited
     sampling, due to the finite accessible simulation time scale and the
     approximated force field, high-quality starting structures are required.
     Despite their imperfection, we find that currently available force
     fields empower MD to provide meaningful and predictive information on
     RNA dynamics around a crystallographically defined energy minimum. The
     performance of force fields can be estimated by precise QM calculations
     on small model systems. Such calculations agree reasonably well with the
     Cornell et al. AMBER force field, particularly for stacking and
     hydrogen-bonding interactions. A final verification of any force field
     is accomplished by simulations of complex nucleic acid structures.
     The performance of the Cornell et al. AMBER force field generally
     corresponds well with and augments experimental data, but one notable
     exception could be the capping loops of double-helical stems. In
     addition, the performance of pairwise additive force fields is obviously
     unsatisfactory for inclusion of divalent cations, because their
     interactions lead to major polarization and charge-transfer effects
     neglected by the force field. Neglect of polarization also limits,
     albeit to a lesser extent, the description accuracy of other
     contributions, such as interactions with monovalent ions, conformational
     flexibility of the anionic sugar-phosphate backbone, hydrogen bonding,
     and solute polarization by solvent. Still, despite limitations, MD
     simulations are a valid tool for analyzing the structural dynamics of
     existing experimental structures. Careful analysis of MD simulations can
     identify problematic aspects of an experimental RNA structure, unveil
     structural characteristics masked by experimental constraints, reveal
     functionally significant stochastic fluctuations, evaluate the
     structural role of base ionization, and predict structurally and
     potentially functionally important details of the solvent behavior,
     including the presence of tightly bound water molecules. Moreover,
     combining classical MD simulations with QM calculations in hybrid QM/MM
     approaches helps in the assessment of the plausibility of chemical
     mechanisms of catalytic RNAs (ribozymes).
     In contrast, the reliable prediction of structure from sequence
     information is beyond the applicability of MD tools. The ultimate
     utility of computational studies in understanding RNA function thus
     requires that the results are neither blindly accepted nor flatly
     rejected, but rather considered in the context of all available
     experimental data, with great care given to assessing limitations
     through the available starting structures, force field approximations,
     and sampling limitations. The examples given in this Account showcase
     how the judicious use of basic MD simulations has already served as a
     powerful tool to help evaluate the role of structural dynamics in
     biological function of RNA.,
  DOI = 10.1021/ar900093g,
  ISSN = 0001-4842,
  Unique-ID = ISI:000274289400005,
  

• J. E. Sponer, A. Vazquez-Mayagoitia, B. G. Sumpter, J. Leszczynski, J. Sponer, M. Otyepka, P. Banas, and M. Fuentes-Cabrera, “Theoretical Studies on the Intermolecular Interactions of Potentially
  Primordial Base-Pair Analogues,” CHEMISTRY-A EUROPEAN JOURNAL, vol. 16, iss. 10, pp. 3057-3065, 2010.
  [Bibtex]

  @article ISI:000275943400013,
  Author = Sponer, Judit E. and Vazquez-Mayagoitia, Alvaro and Sumpter, Bobby G.
     and Leszczynski, Jerzy and Sponer, Jiri and Otyepka, Michal and Banas,
     Pavel and Fuentes-Cabrera, Miguel,
  Title = Theoretical Studies on the Intermolecular Interactions of Potentially
     Primordial Base-Pair Analogues,
  Journal = CHEMISTRY-A EUROPEAN JOURNAL,
  Year = 2010,
  Volume = 16,
  Number = 10,
  Pages = 3057-3065,
  Abstract = Recent experimental studies on the Watson-Crick type base pairing of
     triazine and aminopyrimidine derivatives suggest that acid/base
     properties of the constituent bases might be related to the duplex
     stabilities measured in solution. Herein we use high-level quantum
     chemical calculations and molecular dynamics simulations to evaluate the
     base pairing and stacking interactions of seven selected base pairs,
     which are common in that they are stabilized by two N-H center dot
     center dot center dot O hydrogen bonds separated by one N-H center dot
     center dot center dot N hydrogen bond. We show that neither the base
     pairing nor the base stacking interaction energies correlate with the
     reported pK(a) data of the bases and the melting points of the duplexes.
     This suggests that the experimentally observed correlation between the
     melting point data of the duplexes and the pKa values of the constituent
     bases is not rooted in the intrinsic base pairing and stacking
     properties. The physical chemistry origin of the observed experimental
     correlation thus remains unexplained and requires further
     investigations. In addition, since out-calculations are carried out with
     extrapolation to the complete basis set of atomic orbitals and with
     inclusion of higher electron correlation effects, they provide reference
     data for stacking and base pairing energies of non-natural bases.,
  DOI = 10.1002/chem.200902068,
  ISSN = 0947-6539,
  Unique-ID = ISI:000275943400013,
  

• M. Zgarbova, M. Otyepka, J. Sponer, P. Hobza, and P. Jurecka, “Large-scale compensation of errors in pairwise-additive empirical force
  fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT
  calculations,” PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 12, iss. 35, pp. 10476-10493, 2010.
  [Bibtex]

  @article ISI:000281352300043,
  Author = Zgarbova, Marie and Otyepka, Michal and Sponer, Jiri and Hobza, Pavel
     and Jurecka, Petr,
  Title = Large-scale compensation of errors in pairwise-additive empirical force
     fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT
     calculations,
  Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
  Year = 2010,
  Volume = 12,
  Number = 35,
  Pages = 10476-10493,
  Abstract = The intermolecular interaction energy components for several molecular
     complexes were calculated using force fields available in the AMBER
     suite of programs and compared with Density Functional Theory-Symmetry
     Adapted Perturbation Theory (DFT-SAPT) values. The extent to which such
     comparison is meaningful is discussed. The comparability is shown to
     depend strongly on the intermolecular distance, which means that
     comparisons made at one distance only are of limited value. At large
     distances the coulombic and van der Waals 1/r(6) empirical terms
     correspond fairly well with the DFT-SAPT electrostatics and dispersion
     terms, respectively. At the onset of electronic overlap the empirical
     values deviate from the reference values considerably. However, the
     errors in the force fields tend to cancel out in a systematic manner at
     equilibrium distances. Thus, the overall performance of the force fields
     displays errors an order of magnitude smaller than those of the
     individual interaction energy components. The repulsive 1/r(12)
     component of the van der Waals expression seems to be responsible for a
     significant part of the deviation of the force field results from the
     reference values. We suggest that further improvement of the force
     fields for intermolecular interactions would require replacement of the
     nonphysical 1/r(12) term by an exponential function. Dispersion
     anisotropy and its effects are discussed. Our analysis is intended to
     show that although comparing the empirical and non-empirical interaction
     energy components is in general problematic, it might bring insights
     useful for the construction of new force fields. Our results are
     relevant to often performed force-field-based interaction energy
     decompositions.,
  DOI = 10.1039/c002656e,
  ISSN = 1463-9076,
  Unique-ID = ISI:000281352300043,
  

2009

• M. Pavlova, M. Klvana, Z. Prokop, R. Chaloupkova, P. Banas, M. Otyepka, R. C. Wade, M. Tsuda, Y. Nagata, and J. Damborsky, “Redesigning dehalogenase access tunnels as a strategy for degrading an
  anthropogenic substrate,” NATURE CHEMICAL BIOLOGY, vol. 5, iss. 10, pp. 727-733, 2009.
  [Bibtex]

  @article ISI:000270039900010,
  Author = Pavlova, Martina and Klvana, Martin and Prokop, Zbynek and Chaloupkova,
     Radka and Banas, Pavel and Otyepka, Michal and Wade, Rebecca C. and
     Tsuda, Masataka and Nagata, Yuji and Damborsky, Jiri,
  Title = Redesigning dehalogenase access tunnels as a strategy for degrading an
     anthropogenic substrate,
  Journal = NATURE CHEMICAL BIOLOGY,
  Year = 2009,
  Volume = 5,
  Number = 10,
  Pages = 727-733,
  Month = OCT,
  Abstract = Engineering enzymes to degrade anthropogenic compounds efficiently is
     challenging. We obtained Rhodococcus rhodochrous haloalkane dehalogenase
     mutants with up to 32-fold higher activity than wild type toward the
     toxic, recalcitrant anthropogenic compound 1,2,3-trichloropropane (TCP)
     using a new strategy. We identified key residues in access tunnels
     connecting the buried active site with bulk solvent by rational design
     and randomized them by directed evolution. The most active mutant has
     large aromatic residues at two out of three randomized positions and two
     positions modified by site-directed mutagenesis. These changes
     apparently enhance activity with TCP by decreasing accessibility of the
     active site for water molecules, thereby promoting activated complex
     formation. Kinetic analyses confirmed that the mutations improved
     carbon-halogen bond cleavage and shifted the rate-limiting step to the
     release of products. Engineering access tunnels by combining
     computer-assisted protein design with directed evolution may be a
     valuable strategy for refining catalytic properties of enzymes with
     buried active sites.,
  DOI = 10.1038/nchembio.205,
  ISSN = 1552-4450,
  Unique-ID = ISI:000270039900010,
  

• P. Banas, P. Jurecka, N. G. Walter, J. Sponer, and M. Otyepka, “Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their
  comparison with MD and QM,” METHODS, vol. 49, iss. 2, pp. 202-216, 2009.
  [Bibtex]

  @article ISI:000270443600015,
  Author = Banas, Pavel and Jurecka, Petr and Walter, Nils G. and Sponer, Jiri and
     Otyepka, Michal,
  Title = Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their
     comparison with MD and QM,
  Journal = METHODS,
  Year = 2009,
  Volume = 49,
  Number = 2,
  Pages = 202-216,
  Month = OCT,
  Abstract = Hybrid QM/MM methods combine the rigor of quantum mechanical (QM)
     calculations with the low computational cost of empirical molecular
     mechanical (MM) treatment allowing to capture dynamic properties to
     probe critical atomistic details of enzyme reactions. Catalysis by RNA
     enzymes (ribozymes) has only recently begun to be addressed with QM/MM
     approaches and is thus still a field under development. This review
     surveys methodology as well as recent advances in QM/MM applications to
     RNA mechanisms, including those of the HDV, hairpin, and hammerhead
     ribozymes, as well as the ribosome. We compare and correlate QM/MM
     results with those from QM and/or molecular dynamics (MD) simulations,
     and discuss scope and limitations with a critical eye on current
     shortcomings in available methodologies and computer resources. We thus
     hope to foster mutual appreciation and facilitate collaboration between
     experimentalists and theorists to jointly advance our understanding of
     RNA catalysis at an atomistic level. (c) 2009 Elsevier Inc. All rights
     reserved.,
  DOI = 10.1016/j.ymeth.2009.04.007,
  ISSN = 1046-2023,
  Unique-ID = ISI:000270443600015,
  

• M. Kubala, L. Grycova, Z. Lansky, P. Sklenovsky, M. Janovska, M. Otyepka, and J. Teisinger, “Changes in Electrostatic Surface Potential of Na(+)/K(+)-ATPase
  Cytoplasmic Headpiece Induced by Cytoplasmic Ligand(s) Binding,” BIOPHYSICAL JOURNAL, vol. 97, iss. 6, pp. 1756-1764, 2009.
  [Bibtex]

  @article ISI:000270380800027,
  Author = Kubala, Martin and Grycova, Lenka and Lansky, Zdenek and Sklenovsky,
     Petr and Janovska, Marika and Otyepka, Michal and Teisinger, Jan,
  Title = Changes in Electrostatic Surface Potential of Na(+)/K(+)-ATPase
     Cytoplasmic Headpiece Induced by Cytoplasmic Ligand(s) Binding,
  Journal = BIOPHYSICAL JOURNAL,
  Year = 2009,
  Volume = 97,
  Number = 6,
  Pages = 1756-1764,
  Month = SEP 16,
  Abstract = A set of single-tryptophan mutants of the Na(+)/K(+)-ATPase isolated,
     large cytoplasmic loop connecting transmembrane helices M4 and M5 (C45)
     was prepared to monitor effects of the natural cytoplasmic ligands
     (i.e., Mg(2+) and/or ATP) binding. We introduced a novel method for the
     monitoring of the changes in the electrostatic surface potential (ESP)
     induced by ligand binding, using the quenching of the intrinsic
     tryptophan fluorescence by acrylamide or iodide. This approach opens a
     new way to understanding the interactions within the proteins. Our
     experiments revealed that the C45 conformation in the presence of the
     ATP (without magnesium) substantially differed from the conformation in
     the presence of Mg(2+) or MgATP or in the absence of any ligand not only
     in the sense of geometry but also in the sense of the ESP. Notably, the
     set of ESP-sensitive residues was different from the set of
     geometry-sensitive residues. Moreover, our data indicate that the effect
     of the ligand binding is not restricted only to the close environment of
     the binding site and that the information is in fact transmitted also to
     the distal parts of the molecule. This property could be important for
     the communication between the cytoplasmic headpiece and the cation
     binding sites located within the transmembrane domain.,
  DOI = 10.1016/j.bpj.2009.07.002,
  ISSN = 0006-3495,
  Unique-ID = ISI:000270380800027,
  

• P. Anzenbacher, E. Anzenbacherova, T. Hendrychova, M. Otyepka, J. Hudecek, P. Hildebrandt, and R. Lange, “Flexibility and plasticity of the structures of cytochromes P450 as a
  property determining their function,” FEBS JOURNAL, vol. 276, pp. 26, 2009.
  [Bibtex]

  @article ISI:000267069900070,
  Author = Anzenbacher, P. and Anzenbacherova, E. and Hendrychova, T. and Otyepka,
     M. and Hudecek, J. and Hildebrandt, P. and Lange, R.,
  Title = Flexibility and plasticity of the structures of cytochromes P450 as a
     property determining their function,
  Journal = FEBS JOURNAL,
  Year = 2009,
  Volume = 276,
  Pages = 26,
  Month = JUL,
  Note = 34th Congress of the Federation-of-European-Biochemical-Societies,
     Prague, CZECH REPUBLIC, JUL 04-09, 2009,
  Organization = Federat European Biochem Soc,
  ISSN = 1742-464X,
  Unique-ID = ISI:000267069900070,
  

• P. Banas, N. G. Walter, J. Sponer, and M. Otyepka, “Structural Insight into RNA Catalysis Revealed by Molecular Dynamics
  Simulations and QM/MM Calculation,” JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol. 26, iss. 6, pp. 50, 2009.
  [Bibtex]

  @article ISI:000266300700062,
  Author = Banas, Pavel and Walter, Nils G. and Sponer, Jiri and Otyepka, Michal,
  Title = Structural Insight into RNA Catalysis Revealed by Molecular Dynamics
     Simulations and QM/MM Calculation,
  Journal = JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS,
  Year = 2009,
  Volume = 26,
  Number = 6,
  Pages = 50,
  Month = JUN,
  ISSN = 0739-1102,
  Unique-ID = ISI:000266300700062,
  

• L. Grycova, P. Sklenovsk, Z. Lansky, M. Janovska, M. Otyepka, E. Amler, J. Teisinger, and M. Kubala, “ATP and magnesium drive conformational changes of the Na(+)/K(+)-ATPase
  cytoplasmic headpiece,” BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, vol. 1788, iss. 5, pp. 1081-1091, 2009.
  [Bibtex]

  @article ISI:000266190600019,
  Author = Grycova, Lenka and Sklenovsk, Petr and Lansky, Zdenek and Janovska,
     Marika and Otyepka, Michal and Amler, Evzen and Teisinger, Jan and
     Kubala, Martin,
  Title = ATP and magnesium drive conformational changes of the Na(+)/K(+)-ATPase
     cytoplasmic headpiece,
  Journal = BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES,
  Year = 2009,
  Volume = 1788,
  Number = 5,
  Pages = 1081-1091,
  Month = MAY,
  Abstract = Conformational changes of the Na(+)/K(+)-ATPase isolated large
     cytoplasmic segment connecting transmembrane helices M4 and M5 (C45)
     induced by the interaction with enzyme ligands (i.e. Mg(2+) and/or ATP)
     were investigated by means of the intrinsic tryptophan fluorescence
     measurement and molecular dynamic simulations. Our data revealed that
     this model system consisting of only two domains retained the ability to
     adopt open or closed conformation, i.e. behavior, which is expected from
     the crystal structures of relative Ca(2+)-ATPase from sarco(endo)plasmic
     reticulum for the corresponding part of the entire enzyme. Our data
     revealed that the C45 is found in the closed conformation in the absence
     of any ligand, in the presence of Mg(2+) only, or in the simultaneous
     presence of Mg(2+) and ATP. Binding of the ATP alone (i.e. in the
     absence of Mg(2+)) induced open conformation of the C45. The fact that
     the transmembrane part of the enzyme was absent in our experiments
     suggested that the observed conformational changes are consequences only
     of the interaction with ATP or Mg(2+) and may not be related to the
     transported cations binding/ release, as generally believed. Our data
     are consistent with the model, where ATP binding to the low-affinity
     site induces conformational change of the cytoplasmic part of the
     enzyme, traditionally attributed to E2 -> E1 transition, and subsequent
     Mg(2+) binding to the enzyme-ATP complex induces in turn conformational
     change traditionally attributed to E1 -> E2 transition. (C) 2009
     Elsevier B.V. All rights reserved.,
  DOI = 10.1016/j.bbamem.2009.02.004,
  ISSN = 0005-2736,
  Unique-ID = ISI:000266190600019,
  

• I. Besseova, M. Otyepka, K. Reblova, and J. Sponer, “Dependence of A-RNA simulations on the choice of the force field and
  salt strength,” PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 11, iss. 45, pp. 10701-10711, 2009.
  [Bibtex]

  @article ISI:000271907200016,
  Author = Besseova, Ivana and Otyepka, Michal and Reblova, Kamila and Sponer, Jiri,
  Title = Dependence of A-RNA simulations on the choice of the force field and
     salt strength,
  Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
  Year = 2009,
  Volume = 11,
  Number = 45,
  Pages = 10701-10711,
  Abstract = We present an extensive molecular dynamics study (0.6 mu s in total) on
     three A-RNA duplexes. The dependence of the A-RNA geometry on force
     fields (Parm99 and Parmbsc0) and salt strength conditions (similar to
     0.18 M net-neutralizing Na(+) and similar to 0.3 M KCl) was
     investigated. The Parmbsc0 force field makes the A-RNA duplex more
     compact in comparison to the Parm99 by preventing temporary alpha/beta
     t/t flips common in Parm99 simulations. Nevertheless, since the
     alpha/gamma t/t sub-state occurs to certain extent in experimental A-RNA
     structures, we consider both force fields as viable. The stabilization
     of the A-RNA helices caused by the Parmbsc0 force field includes visible
     reduction of the major groove width, increase of the base pair roll,
     larger helical inclination and small increases of twist. Therefore, the
     Parmbsc0 shifts the simulated duplexes more deeply into the A-form.
     Further narrowing of the deep major groove is observed in excess salt
     simulations, again accompanied by larger roll, inclination and twist.
     The cumulative difference between Parm99/lower-salt and
     Parmbsc0/higher-salt simulations is similar to 4-8 angstrom for the
     average P center dot center dot center dot P distances, and -0.7 to -2.5
     degrees, -2.0 to -5.4 degrees, -2.6 to -8.6 degrees and 1.7 to 7.0
     degrees for the twist, roll, inclination and propeller, respectively.
     The effects of the force field and salt condition are
     sequence-dependent. Thus, the compactness of A-RNA is sensitive to the
     sequence and the salt strength which may, for example, modulate the
     end-to-end distance of the A-RNA helix. The simulations neatly reproduce
     the known base pair roll re-distribution in alternating
     purine-pyrimidine A-RNA helices.,
  DOI = 10.1039/b911169g,
  ISSN = 1463-9076,
  Unique-ID = ISI:000271907200016,
  

2008

• P. Banas, L. Rulisek, V. Hanosova, D. Svozil, N. G. Walter, J. Sponer, and M. Otyepka, “General base catalysis for cleavage by the active-site cytosine of the
  hepatitis delta virus ribozyme: QM/MM calculations establish chemical
  feasibility,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 112, iss. 35, pp. 11177-11187, 2008.
  [Bibtex]

  @article ISI:000258800300054,
  Author = Banas, Pavel and Rulisek, Lubomir and Hanosova, Veronika and Svozil,
     Daniel and Walter, Nils G. and Sponer, Jiri and Otyepka, Michal,
  Title = General base catalysis for cleavage by the active-site cytosine of the
     hepatitis delta virus ribozyme: QM/MM calculations establish chemical
     feasibility,
  Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
  Year = 2008,
  Volume = 112,
  Number = 35,
  Pages = 11177-11187,
  Month = SEP 4,
  Abstract = The hepatitis delta virus (HDV) ribozyme is an RNA motif embedded in
     human pathogenic HDV RNA. Previous experimental studies have established
     that the active-site nucleotide C75 is essential for self-cleavage of
     the ribozyme, although its exact catalytic role in the process remains
     debated. Structural data from X-ray crystallography generally indicate
     that C75 acts as the general base that initiates catalysis by
     deprotonating the 2'-OH nucleophile at the cleavage site, while a
     hydrated magnesium ion likely protonates the 5'-oxygen leaving group. In
     contrast, some mechanistic studies support the role of C75 acting as
     general acid and thus being protonated before the reaction. We report
     combined quantum chemical/molecular mechanical calculations for the C75
     general base pathway, utilizing the available structural data for the
     wild type HDV genomic ribozyme as a starting point. Several starting
     configurations differing in magnesium ion placement were considered and
     both one-dimensional and two-dimensional potential energy surface scans
     were used to explore plausible reaction paths. Our calculations show
     that C75 is readily capable of acting as the general base, in concert
     with the hydrated magnesium ion as the general acid. We identify a most
     likely position for the magnesium ion, which also suggests it acts as a
     Lewis acid. The calculated energy barrier of the proposed mechanism,
     similar to 20 kcal/mol, would lower the reaction barrier by similar to
     15 kcal/mol compared with the uncatalyzed reaction and is in good
     agreement with experimental data.,
  DOI = 10.1021/jp802592z,
  ISSN = 1520-6106,
  Unique-ID = ISI:000258800300054,
  

• P. Sklenovsky, P. Banas, and M. Otyepka, “Two C-terminal ankyrin repeats form the minimal stable unit of the
  ankyrin repeat protein p18(INK4c),” JOURNAL OF MOLECULAR MODELING, vol. 14, iss. 8, pp. 747-759, 2008.
  [Bibtex]

  @article ISI:000257330700012,
  Author = Sklenovsky, Petr and Banas, Pavel and Otyepka, Michal,
  Title = Two C-terminal ankyrin repeats form the minimal stable unit of the
     ankyrin repeat protein p18(INK4c),
  Journal = JOURNAL OF MOLECULAR MODELING,
  Year = 2008,
  Volume = 14,
  Number = 8,
  Pages = 747-759,
  Month = AUG,
  Abstract = Ankyrin repeat proteins (ARPs) appear to be abundant in organisms from
     all phyla, and play critical regulatory roles, mediating specific
     interactions with target biomolecules and thus ordering the sequence of
     events in diverse cellular processes. ARPs possess a non-globular
     scaffold consisting of repeating motifs named ankyrin (ANK) repeats,
     which stack on each other. The modular architecture of ARPs provides a
     new paradigm for understanding protein stability and folding mechanisms.
     In the present study, the stability of various C-terminal fragments of
     the ARP p18(INK4c) was investigated by all-atomic 450 ns molecular
     dynamics (MD) simulations in explicit water solvent. Only motifs with at
     least two ANK repeats made stable systems in the available timescale.
     All smaller fragments were unstable, readily losing their native fold
     and alpha-helical content. Since each non-terminal ANK repeat has two
     hydrophobic sides, we may hypothesize that at least one hydrophobic side
     must be fully covered and shielded from the water as a necessary, but
     not sufficient, condition to maintain ANK repeat stability.
     Consequently, at least two ANK repeats are required to make a stable
     ARP.,
  DOI = 10.1007/s00894-008-0300-5,
  ISSN = 1610-2940,
  Unique-ID = ISI:000257330700012,
  

• I. Bartova, J. Koca, and M. Otyepka, “Regulatory phosphorylation of cyclin-dependent kinase 2: insights from
  molecular dynamics simulations,” JOURNAL OF MOLECULAR MODELING, vol. 14, iss. 8, pp. 761-768, 2008.
  [Bibtex]

  @article ISI:000257330700013,
  Author = Bartova, Iveta and Koca, Jaroslav and Otyepka, Michal,
  Title = Regulatory phosphorylation of cyclin-dependent kinase 2: insights from
     molecular dynamics simulations,
  Journal = JOURNAL OF MOLECULAR MODELING,
  Year = 2008,
  Volume = 14,
  Number = 8,
  Pages = 761-768,
  Month = AUG,
  Abstract = The structures of fully active cyclin-dependent kinase-2 (CDK2)
     complexed with ATP and peptide substrate, CDK2 after the catalytic
     reaction, and CDK2 inhibited by phosphorylation at Thr14/Tyr15 were
     studied using molecular dynamics (MD) simulations. The structural
     details of the CDK2 catalytic site and CDK2 substrate binding box were
     described. Comparison of MD simulations of inhibited complexes of CDK2
     was used to help understand the role of inhibitory phosphorylation at
     Thr14/Tyr15. Phosphorylation at Thr14/Tyr15 causes ATP misalignment for
     the phosphate-group transfer, changes in the Mg(2+)coordination sphere,
     and changes in the H-bond network formed by CDK2 catalytic residues
     (Asp127, Lys129, Asn132). The inhibitory phosphorylation causes the
     G-loop to shift from the ATP binding site, which leads to opening of the
     CDK2 substrate binding box, thus probably weakening substrate binding.
     All these effects explain the decrease in kinase activity observed after
     inhibitory phosphorylation at Thr14/Tyr15 in the G-loop. Interaction of
     the peptide substrate, and the phosphorylated peptide product, with CDK2
     was also studied and compared. These results broaden hypotheses drawn
     from our previous MD studies as to why a basic residue (Arg/Lys) is
     preferred at the P(+2) substrate position.,
  DOI = 10.1007/s00894-008-0312-1,
  ISSN = 1610-2940,
  Unique-ID = ISI:000257330700013,
  

• J. Skopalik, P. Anzenbacher, and M. Otyepka, “Flexibility of human cytochromes P450: Molecular dynamics reveals
  differences between CYPs 3A4, 2C9, and 2A6, which correlate with their
  substrate preferences,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 112, iss. 27, pp. 8165-8173, 2008.
  [Bibtex]

  @article ISI:000257335200028,
  Author = Skopalik, Josef and Anzenbacher, Pavel and Otyepka, Michal,
  Title = Flexibility of human cytochromes P450: Molecular dynamics reveals
     differences between CYPs 3A4, 2C9, and 2A6, which correlate with their
     substrate preferences,
  Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
  Year = 2008,
  Volume = 112,
  Number = 27,
  Pages = 8165-8173,
  Month = JUL 10,
  Abstract = Molecular dynamics (MD) simulations at normal and high temperature were
     used to study the flexibility and malleability of three microsomal
     cytochromes P450 (CYPs): CYP3A4, CYP2C9, and CYP2A6. Comparison of
     B-factors (describing the atomic fluctuations) between X-ray and MD data
     shows that the X-ray B-factors are significantly lower in the regions
     where the crystal contacts occur than for other regions. Consequently,
     the conclusions about CYP flexibility based solely on the X-ray data
     might be misleading. Comparison of flexibility patterns of the three
     CYPs enabled common features and variations in flexibility and
     malleability of the studied CYPs to be identified. The previously
     described pattern of flexibility in topological elements of microsomal
     CYPs (a rigid heme binding core, a malleable distal side and
     intermediately flexible proximal side) was confirmed. These topological
     features provide an important combination of high stereo- and
     regio-specificity (mediated by the relative rigidity in the neighborhood
     of the heme), together with high substrate promiscuity due to the more
     flexible active site and the malleability of the distal side. The data
     acquired here show that the malleability of the three studied CYPs
     correlates with their substrate specificity: CYP2A6 has a narrow
     substrate range and is the most rigid, CYP3A4 is the most promiscuous
     CYP known and is the most malleable, and CYP2C9 is intermediate in terms
     of both its substrate specificity and malleability. Thus, the
     malleability of CYPs is probably a major determinant of their substrate
     specificity.,
  DOI = 10.1021/jp800311c,
  ISSN = 1520-6106,
  Unique-ID = ISI:000257335200028,
  

• P. Dzubak, J. Sarek, P. Anzenbacher, V. Masek, P. Novak, V. Havlicek, M. Otyepka, D. Vydra, and M. Hajduch, “Betulinine JS8 induces apoptosis in tumor cells by mitochondrial
  disruption via specific non-covalent interactions with cytochrome c,” FEBS JOURNAL, vol. 275, iss. 1, pp. 447, 2008.
  [Bibtex]

  @article ISI:000256633301588,
  Author = Dzubak, P. and Sarek, J. and Anzenbacher, P. and Masek, V. and Novak, P.
     and Havlicek, V. and Otyepka, M. and Vydra, D. and Hajduch, M.,
  Title = Betulinine JS8 induces apoptosis in tumor cells by mitochondrial
     disruption via specific non-covalent interactions with cytochrome c,
  Journal = FEBS JOURNAL,
  Year = 2008,
  Volume = 275,
  Number = 1,
  Pages = 447,
  Month = JUN,
  Note = Joint Conference of the 33rd FEBS Congress/11th IUBMB Conference,
     Athens, GREECE, JUN 28-JUL 03, 2008,
  ISSN = 1742-464X,
  Unique-ID = ISI:000256633301588,
  

• M. Otyepka, P. Banas, A. Magistrato, P. Carloni, and J. Damborsky, “Second step of hydrolytic dehalogenation in haloalkane dehalogenase
  investigated by QM/MM methods,” PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, vol. 70, iss. 3, pp. 707-717, 2008.
  [Bibtex]

  @article ISI:000252836300009,
  Author = Otyepka, Michal and Banas, Pavel and Magistrato, Alessandra and Carloni,
     Paolo and Damborsky, Jiri,
  Title = Second step of hydrolytic dehalogenation in haloalkane dehalogenase
     investigated by QM/MM methods,
  Journal = PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,
  Year = 2008,
  Volume = 70,
  Number = 3,
  Pages = 707-717,
  Month = FEB 15,
  Abstract = Mechanistic studies on the hydrolytic dehalogenation catalyzed by
     haloalkane dehalogenases are of importance for environmental and
     industrial applications. Here, Car-Parrinello (CP) and ONIOM hybrid
     quantum-mechanical/molecular mechanics (QM/MM) are used investigate the
     second reaction step of the catalytic cycle, which comprises a general
     base-catalyzed hydrolysis of an ester intermediate (EI) to alcohol and
     free enzyme. We focus on the enzyme LinB from Sphingo-monas paucimobilis
     UT26, for which the X-ray structure at atomic resolution is available.
     In agreement with previous proposals, our calculations suggest that a
     histidine residue (His272), polarized by glutamate (Glu132), acts as a
     base, accepting a proton from the catalytic water molecule and
     transferring it to an alcoholate ion. The reaction proceeds through a
     metastable tetrahedral intermediate, which shows an easily reversed
     reaction to the EI In the formation of the products, the protonated
     aspartic acid (Asp 108) can easily adopt conformation of the relaxed
     state found in the free enzyme. The overall free energy barrier of the
     reaction calculated by potential of the mean force integration using
     CP-QM/MM calculations is equal to 19.5 +/- 2 kcal . mol(-1). The
     lowering of the energy barrier of catalyzed reaction with respect to the
     water reaction is caused by strong stabilization of the reaction
     intermediate and transition state and their preorganization by
     electrostatic field of the enzyme.,
  DOI = 10.1002/prot.21523,
  ISSN = 0887-3585,
  Unique-ID = ISI:000252836300009,
  

• P. Anzenbacher, E. Anzenbacherova, R. Lange, J. Skopalik, and M. Otyepka, “Active sites of cytochromes P450: What are they like?,” ACTA CHIMICA SLOVENICA, vol. 55, iss. 1, pp. 63-66, 2008.
  [Bibtex]

  @article ISI:000254379100008,
  Author = Anzenbacher, Pavel and Anzenbacherova, Eva and Lange, Reinhard and
     Skopalik, Josef and Otyepka, Michal,
  Title = Active sites of cytochromes P450: What are they like?,
  Journal = ACTA CHIMICA SLOVENICA,
  Year = 2008,
  Volume = 55,
  Number = 1,
  Pages = 63-66,
  Abstract = Although the x-ray crystallography is giving a relatively precise
     picture of spatial arrangement of the majority of protein structure, it
     is not able to give detailed information on the flexibility of the
     protein active site. The properties of active sites of cytochromes P450
     (CYP) were supposed earlier to be relatively similar, reflecting the
     substrate specificities of the individual enzymes mainly by the amino
     acid residues present in the respective active site. On the other hand,
     the most recent experimental as well as theoretical results document
     that it is the flexibility of this part of protein which gives the
     active site the property to bind substrates correctly and to accommodate
     them. It is also the flexibility or plasticity of the structure which
     determines or limits the property of the protein to keep the
     conformation which guarantees the function of the enzyme.,
  ISSN = 1318-0207,
  Unique-ID = ISI:000254379100008,
  

• I. Bartova, J. Koca, and M. Otyepka, “Functional flexibility of human cyclin-dependent kinase-2 and its
  evolutionary conservation,” PROTEIN SCIENCE, vol. 17, iss. 1, pp. 22-33, 2008.
  [Bibtex]

  @article ISI:000251834500004,
  Author = Bartova, Iveta and Koca, Jaroslav and Otyepka, Michal,
  Title = Functional flexibility of human cyclin-dependent kinase-2 and its
     evolutionary conservation,
  Journal = PROTEIN SCIENCE,
  Year = 2008,
  Volume = 17,
  Number = 1,
  Pages = 22-33,
  Month = JAN,
  Abstract = Cyclin-dependent kinase 2 (CDK2) is the most thoroughly studied of the
     cyclin-dependent kinases that regulate essential cellular processes,
     including the cell cycle, and it has become a model for studies of
     regulatory mechanisms at the molecular level. This contribution
     identifies flexible and rigid regions of CDK2 based on temperature
     B-factors acquired from both X-ray data and molecular dynamics
     simulations. In addition, the biological relevance of the identified
     flexible regions and their motions is explored using information from
     the essential dynamics analysis related to conformational changes of
     CDK2 and knowledge of its biological function(s). The conserved regions
     of CMGC protein kinases' primary sequences are located in the most rigid
     regions identified in our analyses, with the sole exception of the
     absolutely conserved G13 in the tip of the glycine-rich loop. The
     conserved rigid regions are important for nucleotide binding, catalysis,
     and substrate recognition. In contrast, the most flexible regions
     correlate with those where large conformational changes occur during
     CDK2 regulation processes. The rigid regions flank and form a rigid
     skeleton for the flexible regions, which appear to provide the
     plasticity required for CDK2 regulation. Unlike the rigid regions (which
     as mentioned are highly conserved) no evidence of evolutionary
     conservation was found for the flexible regions.,
  DOI = 10.1110/ps.072951208,
  ISSN = 0961-8368,
  Unique-ID = ISI:000251834500004,
  

2007

• M. Petrek, P. Kosinova, J. Koca, and M. Otyepka, “MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and
  tunnels,” STRUCTURE, vol. 15, iss. 11, pp. 1357-1363, 2007.
  [Bibtex]

  @article ISI:000251023400007,
  Author = Petrek, Martin and Kosinova, Pavlina and Koca, Jaroslav and Otyepka,
     Michal,
  Title = MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and
     tunnels,
  Journal = STRUCTURE,
  Year = 2007,
  Volume = 15,
  Number = 11,
  Pages = 1357-1363,
  Month = NOV,
  Abstract = We have developed an algorithm, ``MOLE,'' for the rapid, fully
     automated location and characterization of molecular channels, tunnels,
     and pores. This algorithm has been made freely available on the Internet
     (http://mole.chemi. muni.cz/) and overcomes many of the shortcomings and
     limitations of the recently developed CAVER software. The core of our
     MOLE algorithm is a Dijkstra's path search algorithm, which is applied
     to a Voronoi mesh. Tests on a wide variety of biomolecular systems
     including gramicidine, acetylcholinesterase, cytochromes P450, potassium
     channels, DNA quadruplexes, ribozymes, and the large ribosomal subunit
     have demonstrated that the MOLE algorithm performs well. MOLE is thus a
     powerful tool for exploring large molecular channels, complex networks
     of channels, and molecular dynamics trajectories in which analysis of a
     large number of snapshots is required.,
  DOI = 10.1016/j.str.2007.10.007,
  ISSN = 0969-2126,
  Unique-ID = ISI:000251023400007,
  

• M. Kubala, L. Grycova, Z. Lansky, M. Otyepka, P. Sklenovsky, and J. Teisinger, “Conformational changes of the cytoplasmic part of Na+/K+-ATPase induced
  by the ligand binding,” FEBS JOURNAL, vol. 274, iss. 1, pp. 127, 2007.
  [Bibtex]

  @article ISI:000253283800335,
  Author = Kubala, M. and Grycova, L. and Lansky, Z. and Otyepka, M. and
     Sklenovsky, P. and Teisinger, J.,
  Title = Conformational changes of the cytoplasmic part of Na+/K+-ATPase induced
     by the ligand binding,
  Journal = FEBS JOURNAL,
  Year = 2007,
  Volume = 274,
  Number = 1,
  Pages = 127,
  Month = JUL,
  Note = 32nd Congress of the Federation-of-European-Biochemical-Societies
     (FEBS), Vienna, AUSTRIA, JUL 07-12, 2007,
  Organization = Federat European Biochem Soc,
  ISSN = 1742-464X,
  Unique-ID = ISI:000253283800335,
  

• J. Filip, R. Zboril, O. Schneeweiss, J. Zeman, M. Cernik, P. Kvapil, and M. Otyepka, “Environmental applications of chemically pure natural ferrihydrite,” ENVIRONMENTAL SCIENCE & TECHNOLOGY, vol. 41, iss. 12, pp. 4367-4374, 2007.
  [Bibtex]

  @article ISI:000247187600026,
  Author = Filip, Jan and Zboril, Radek and Schneeweiss, Oldrich and Zeman, Josef
     and Cernik, Miroslav and Kvapil, Petr and Otyepka, Michal,
  Title = Environmental applications of chemically pure natural ferrihydrite,
  Journal = ENVIRONMENTAL SCIENCE \& TECHNOLOGY,
  Year = 2007,
  Volume = 41,
  Number = 12,
  Pages = 4367-4374,
  Month = JUN 15,
  Abstract = Fresh precipitates, deposited from seepage waters of complex-ore
     mine-tailing impoundment at Zlate Hory, Czech Republic, were
     characterized by means of X-ray diffraction, transmission electron
     microscopy, low temperature and in-field Mossbauer spectroscopy, and
     Brunauer-Emmett-Teller surface area measurements. The prevailing phases
     (similar to 96 wt \%) found in precipitates are poorly crystalline, 2-6
     nm sized two-line ferrihydrite, forming globular aggregates of about 150
     nm in diameter, rimmed by acicular irregular nanocrystals of goethite.
     These nanocrystalline ferrihydrite-goethite precipitates are of a
     relatively high chemical purity (similar to 3\% SiO2, Zn similar to 1300
     ppm, trace and rare earth elements < 100 ppm) and thus applicable in
     various nanotechnologies. With a surface area of 270 m(2) g(-1),
     precipitate possesses a high catalytic activity in the decomposition of
     hydrogen peroxide, which is comparable with that found for commercially
     accessible FeO(OH) catalyst. Another superior aspect of such natural
     nanoparticles presents a cheap and suitable precursor for a thermally
     induced solid-state synthesis of the stable core-shell alpha-Fe-FeO
     nanoparticles that are well applicable in reductive technologies of
     groundwater treatment. Just the possibility of using the undesirable
     waste contaminating the environment in further environmental
     technologies is the key practical benefit discussed in this paper.,
  DOI = 10.1021/es062312t,
  ISSN = 0013-936X,
  Unique-ID = ISI:000247187600026,
  

• M. Otyepka, J. Skopalik, E. Anzenbacherova, and P. Anzenbacher, "What common structural features and variations of mammalian P450s are
  known to date?," BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, vol. 1770, iss. 3, pp. 376-389, 2007.
  [Bibtex]

  @article ISI:000244384800006,
  Author = Otyepka, Michal and Skopalik, Josef and Anzenbacherova, Eva and
     Anzenbacher, Pavel,
  Title = What common structural features and variations of mammalian P450s are
     known to date?,
  Journal = BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS,
  Year = 2007,
  Volume = 1770,
  Number = 3,
  Pages = 376-389,
  Month = MAR,
  Abstract = Sufficient structural information on mammalian cytochromes P450 has now
     been published (including seventeen X-ray structures of these enzymes by
     June 2006) to allow characteristic features of these enzymes to be
     identified, including: (i) the presence of a common fold, typical of all
     P450s, (ii) similarities in the positioning of the heme cofactor, (iii)
     the spatial arrangement of certain structural elements, and (iv) the
     access/egress paths for substrates and products, (v) probably common
     orientation in the membrane, (vi) characteristic properties of the
     active sites with networks of water molecules, (vii) mode of interaction
     with redox partners and (viii) a certain degree of flexibility of the
     structure and active site determining the ease with which the enzyme may
     bind the substrates. As well as facilitating the identification of
     common features, comparison of the available structures allows
     differences among the structures to be identified, including variations
     in: (i) preferred access/egress paths to/from the active site, (ii) the
     active site volume and (iii) flexible regions. The availability of
     crystal structures provides opportunities for molecular dynamic
     simulations, providing data that are apparently complementary to
     experimental findings but also allow the dynamic behavior of
     access/egress paths and other dynamic features of the enzymes to be
     explored. (c) 2006 Elsevier B.V. All rights reserved.,
  DOI = 10.1016/j.bbagen.2006.09.013,
  ISSN = 0304-4165,
  Unique-ID = ISI:000244384800006,
  

2006

• M. Petrek, M. Otyepka, P. Banas, P. Kosinova, J. Koca, and J. Damborsky, "CAVER: a new tool to explore routes from protein clefts, pockets and
  cavities," BMC BIOINFORMATICS, vol. 7, 2006.
  [Bibtex]

  @article ISI:000239737800001,
  Author = Petrek, Martin and Otyepka, Michal and Banas, Pavel and Kosinova,
     Pavlina and Koca, Jaroslav and Damborsky, Jiri,
  Title = CAVER: a new tool to explore routes from protein clefts, pockets and
     cavities,
  Journal = BMC BIOINFORMATICS,
  Year = 2006,
  Volume = 7,
  Month = JUN 22,
  Abstract = Background: The main aim of this study was to develop and implement an
     algorithm for the rapid, accurate and automated identification of paths
     leading from buried protein clefts, pockets and cavities in dynamic and
     static protein structures to the outside solvent.
     Results: The algorithm to perform a skeleton search was based on a
     reciprocal distance function grid that was developed and implemented for
     the CAVER program. The program identifies and visualizes routes from the
     interior of the protein to the bulk solvent. CAVER was primarily
     developed for proteins, but the algorithm is sufficiently robust to
     allow the analysis of any molecular system, including nucleic acids or
     inorganic material. Calculations can be performed using discrete
     structures from crystallographic analysis and NMR experiments as well as
     with trajectories from molecular dynamics simulations. The fully
     functional program is available as a stand-alone version and as plug-in
     for the molecular modeling program PyMol. Additionally, selected
     functions are accessible in an online version.
     Conclusion: The algorithm developed automatically finds the path from a
     starting point located within the interior of a protein. The algorithm
     is sufficiently rapid and robust to enable routine analysis of molecular
     dynamics trajectories containing thousands of snapshots. The algorithm
     is based on reciprocal metrics and provides an easy method to find a
     centerline, i.e. the spine, of complicated objects such as a protein
     tunnel. It can also be applied to many other molecules. CAVER is freely
     available from the web site http://loschmidt.chemi.muni.cz/caver/.,
  DOI = 10.1186/1471-2105-7-316,
  Article-Number = 316,
  ISSN = 1471-2105,
  Unique-ID = ISI:000239737800001,
  

• P. Banas, M. Otyepka, P. Jerabek, M. Petrek, and J. Damborsky, "Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant
  haloalkane dehalogenase revealed by molecular modeling," JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, vol. 20, iss. 6, pp. 375-383, 2006.
  [Bibtex]

  @article ISI:000241900000003,
  Author = Banas, Pavel and Otyepka, Michal and Jerabek, Petr and Petrek, Martin
     and Damborsky, Jiri,
  Title = Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant
     haloalkane dehalogenase revealed by molecular modeling,
  Journal = JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN,
  Year = 2006,
  Volume = 20,
  Number = 6,
  Pages = 375-383,
  Month = JUN,
  Abstract = 1,2,3-Trichloropropane (TCP) is a highly toxic, recalcitrant byproduct
     of epichlorohydrin manufacture. Haloalkane dehalogenase (DhaA) from
     Rhodococcus sp. hydrolyses the carbon-halogen bond in various
     halogenated compounds including TCP, but with low efficiency (k(cat)/K-m
     = 36 s(-1)M(-1)). A Cys176Tyr-DhaA mutant with a threefold higher
     catalytic efficiency for TCP dehalogenation has been previously obtained
     by error-prone PCR. We have used molecular simulations and quantum
     mechanical calculations to elucidate the molecular mechanisms involved
     in the improved catalysis of the mutant, and enantioselectivity of DhaA
     toward TCP. The Cys176Tyr mutation modifies the protein access and
     export routes. Substitution of the Cys residue by the bulkier Tyr
     narrows the upper tunnel, making the second tunnel ``slot'' the
     preferred route. TCP can adopt two major orientations in the DhaA
     enzyme, in one of which the halide-stabilizing residue Asn41 forms a
     hydrogen bond with the terminal halogen atom of the TCP molecule, while
     in the other it bonds with the central halogen atom. The differences in
     these binding patterns explain the preferential formation of the (R)-
     over the (S)-enantiomer of 2,3-dichloropropane-1-ol in the reaction
     catalyzed by the enzyme.,
  DOI = 10.1007/s10822-006-9071-1,
  ISSN = 0920-654X,
  Unique-ID = ISI:000241900000003,
  

• P. Dobes, M. Otyepka, M. Strnad, and P. Hobza, "Interaction energies for the purine inhibitor roscovitine with
  cyclin-dependent kinase 2: Correlated ab initio quantum-chemical, DFT
  and empirical calculations," CHEMISTRY-A EUROPEAN JOURNAL, vol. 12, iss. 16, pp. 4297-4304, 2006.
  [Bibtex]

  @article ISI:000238032400009,
  Author = Dobes, P and Otyepka, M and Strnad, M and Hobza, P,
  Title = Interaction energies for the purine inhibitor roscovitine with
     cyclin-dependent kinase 2: Correlated ab initio quantum-chemical, DFT
     and empirical calculations,
  Journal = CHEMISTRY-A EUROPEAN JOURNAL,
  Year = 2006,
  Volume = 12,
  Number = 16,
  Pages = 4297-4304,
  Month = MAY 24,
  Abstract = The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2)
     was investigated by performing correlated ab initio quantum-chemical
     calculations. The whole protein was fragmented into smaller systems
     consisting of one or a few amino acids, and the interaction energies of
     these fragments with roscovitine were determined by using the MP2 method
     with the extended aug-cc-pVDZ basis set. For selected complexes, the
     complete basis set limit MP2 interaction energies, as well as the
     coupled-cluster corrections with inclusion of single, double and
     noninteractive triples contributions [CCSD(T)], were also evaluated.
     The energies of interaction between roscovitine and small fragments and
     between roscovitine and substantial sections of protein (722 atoms) were
     also computed by using density-functional tight-binding methods covering
     dispersion energy (DFTB-D) and the Cornell empirical potential. Total
     stabilisation energy originates predominantly from dispersion energy and
     methods that do not account for the dispersion energy cannot, therefore,
     be recommended for the study of protein-inhibitor interactions. The
     Cornell empirical potential describes reasonably well the interaction
     between roscovitine and protein; therefore, this method can be applied
     in future thermodynamic calculations. A limited number of amino acid
     residues contribute significantly to the binding of roscovitine and
     cdk2, whereas a rather large number of amino acids make a negligible
     contribution.,
  DOI = 10.1002/chem.200501269,
  ISSN = 0947-6539,
  Unique-ID = ISI:000238032400009,
  

• M. Otyepka, I. Bartova, Z. Kriz, and J. Koca, "Different mechanisms of CDK5 and CDK2 activation as revealed by CDK5/p25
  and CDK2/cyclin A dynamics," JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 281, iss. 11, pp. 7271-7281, 2006.
  [Bibtex]

  @article ISI:000236030900045,
  Author = Otyepka, M and Bartova, I and Kriz, Z and Koca, J,
  Title = Different mechanisms of CDK5 and CDK2 activation as revealed by CDK5/p25
     and CDK2/cyclin A dynamics,
  Journal = JOURNAL OF BIOLOGICAL CHEMISTRY,
  Year = 2006,
  Volume = 281,
  Number = 11,
  Pages = 7271-7281,
  Month = MAR 17,
  Abstract = A detailed analysis is presented of the dynamics of human CDK5 in
     complexes with the protein activator p25 and the purine-like inhibitor
     roscovitine. These and other findings related to the activation of CDK5
     are critically reviewed from a molecular perspective. In addition, the
     results obtained on the behavior of CDK5 are compared with data on CDK2
     to assess the differences and similarities between the two kinases in
     terms of (i) roscovitine binding, (ii) regulatory subunit association,
     (iii) conformational changes in the T-loop following CDK/regulatory
     subunit complex formation, and (iv) specificity in CDK/regulatory
     subunit recognition. An energy decomposition analysis, used for these
     purposes, revealed why the binding of p25 alone is sufficient to
     stabilize the extended active T-loop conformation of CDK5, whereas the
     equivalent conformational change in CDK2 requires both the binding of
     cyclin A and phosphorylation of the Thr(160) residue. The interaction
     energy of the CDK5 T-loop with p25 is about 26 kcal . mol(-1) greater
     than that of the CDK2T-loop with cyclin A. The binding pattern between
     CDK5 and p25 was compared with that of CDK2/cyclin A to find specific
     regions involved in CDK/regulatory subunit recognition. The analyses
     performed revealed that the alpha NT-helix of cyclin A interacts with
     the alpha 6-alpha 7 loop and the alpha 7 helix of CDK2, but these
     regions do not interact in the CDK5/p25 complex. Further differences
     between the CDK5/p25 and CDK2/cyclin A systems studied are discussed
     with respect to their specific functionality.,
  DOI = 10.1074/jbc.M509699200,
  ISSN = 0021-9258,
  Unique-ID = ISI:000236030900045,
  

• M. Otyepka, P. Sklenovsky, D. Horinek, T. Kubar, and P. Hobza, "How the stabilization of INK4 tumor suppressor 3D structure evaluated by
  quantum chemical and molecular mechanics calculations corresponds well
  with experimental results: Interplay of association enthalpy, entropy,
  and solvation effects," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 110, iss. 9, pp. 4423-4429, 2006.
  [Bibtex]

  @article ISI:000235944500084,
  Author = Otyepka, M and Sklenovsky, P and Horinek, D and Kubar, T and Hobza, P,
  Title = How the stabilization of INK4 tumor suppressor 3D structure evaluated by
     quantum chemical and molecular mechanics calculations corresponds well
     with experimental results: Interplay of association enthalpy, entropy,
     and solvation effects,
  Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
  Year = 2006,
  Volume = 110,
  Number = 9,
  Pages = 4423-4429,
  Month = MAR 9,
  Abstract = The folding free energy of the INK4c tumor suppressor core, consisting
     of 10 helices, was determined as the sum of gas-phase interaction
     enthalpy, gas-phase interaction entropy, and dehydration and hydration
     free energy. The interaction energy and the hydration free energy were
     determined using the nonempirical density functional theory (DFT)
     method, augmented by a dispersion-energy correction term, the
     semiempirical density-functional tight-binding method covering the
     dispersion energy, and the density functional theory/conductor-like
     screening model (DFT/COSMO) procedure, whereas the interaction entropy
     was calculated with the empirical Cornell et al. force field.
     Alternatively, all contributions were evaluated consistently using
     empirical methods. All the values of the interaction energy of helix
     pairs are stabilizing, and the dominant stabilizing terms stem from the
     London dispersion energy and, in the case of charged systems, the
     electrostatic energy. The stabilization energy of the core, determined
     as the difference of the energy of the core and 10 separate helices,
     amounts to similar to 450 kcal/mol. Systematically, the difference in
     the hydration free energy of a helix pair and its separate components is
     smaller in magnitude than the interaction energy, and it is negative for
     some pairs while positive for others. The average total free energy of a
     core formation amounts to -29.6 kcal/mol (yielded by scaled
     quantum-chemical methods) and + 13.9 kcal/mol (resulting from empirical
     methods). These values are considerably smaller than their single
     components, which are dominated by the interaction energy. The
     computationally predicted interval encloses the experimental value of
     the folding free energy (-2.8 kcal/mol).,
  DOI = 10.1021/jp056890s,
  ISSN = 1520-6106,
  Unique-ID = ISI:000235944500084,
  

2005

• I. Bartova, M. Otyepka, Z. Kriz, and J. Koca, "The mechanism of inhibition of the cyclin-dependent kinase-2 as revealed
  by the molecular dynamics study on the complex CDK2 with the peptide
  substrate HHASPRK," PROTEIN SCIENCE, vol. 14, iss. 2, pp. 445-451, 2005.
  [Bibtex]

  @article ISI:000226626000019,
  Author = Bartova, I and Otyepka, M and Kriz, Z and Koca, J,
  Title = The mechanism of inhibition of the cyclin-dependent kinase-2 as revealed
     by the molecular dynamics study on the complex CDK2 with the peptide
     substrate HHASPRK,
  Journal = PROTEIN SCIENCE,
  Year = 2005,
  Volume = 14,
  Number = 2,
  Pages = 445-451,
  Month = FEB,
  Abstract = Molecular dynamics (MD) simulations were used to explain structural
     details of cyclin-dependent kinaSe-2 (CDK2) inhibition by
     phosphorylation at T14 and/or Y15 located in the glycine-rich loop
     (G-loop). Ten-nanosecond-long simulations of fully active CDK2 in a
     complex with a short peptide (HHASPRK) Substrate and of CDK2 inhibited
     by phosphorylation of T14 and/or Y15 were produced. The inhibitory
     phosphorylations at T14 and/or Y15 show namely an ATP misalignment and a
     G-loop shift (similar to5 Angstrom) causing the opening of the substrate
     binding box. The biological functions of the G-loop and GxGxxG inotif
     evolutionary conservation in protein kinases are discussed. The position
     of the ATP gamma-phosphate relative to the phosphorylation site (S/T) of
     the peptide substrate in the active CDK2 is described and compared with
     inhibited forms of CDK2. The MID results clearly provide an explanation
     previously not known as to why a basic residue (R/K) is preferred at the
     P, position in phosphorylated S/T peptide substrates.,
  DOI = 10.1110/ps.04959705,
  ISSN = 0961-8368,
  Unique-ID = ISI:000226626000019,
  

2004

• I. Bartova, M. Otyepka, Z. Kriz, and J. Koca, "Activation and inhibition of cyclin-dependent kinase-2 by
  phosphorylation; a molecular dynamics study reveals the functional
  importance of the glycine-rich loop," PROTEIN SCIENCE, vol. 13, iss. 6, pp. 1449-1457, 2004.
  [Bibtex]

  @article ISI:000221630900002,
  Author = Bartova, I and Otyepka, M and Kriz, Z and Koca, J,
  Title = Activation and inhibition of cyclin-dependent kinase-2 by
     phosphorylation; a molecular dynamics study reveals the functional
     importance of the glycine-rich loop,
  Journal = PROTEIN SCIENCE,
  Year = 2004,
  Volume = 13,
  Number = 6,
  Pages = 1449-1457,
  Month = JUN,
  Abstract = Nanoseconds long molecular dynamics (MD) trajectories of differently
     active complexes of human cyclin-dependent kinase 2 (inactive CDK2/ATP,
     semiactive CDK2/Cyclin A/ATP, fully active pT160-CDK2/Cyclin A/ATP,
     inhibited pT14-; pY15-; and pT14,pY15,pT160-CDK2/Cyclin A/ATP) were
     compared. The MD simulations results of CDK2 inhibition by
     phosphorylation at T14 and/or Y15 sites provide insight into the
     structural aspects of CDK2 deactivation. The inhibitory sites are
     localized in the glycine-rich loop (G-loop) positioned opposite the
     activation T-loop. Phosphorylation of T14 and both inhibitory sites T14
     and Y15 together causes ATP misalignment for phosphorylation and G-loop
     conformational change. This conformational change leads to the opening
     of the CDK2 Substrate binding box. The phosphorylated Y15 residue
     negatively affects Substrate binding or its correct alignment for ATP
     terminal phospho-group transfer to the CDK2 substrate. The MD
     simulations of the CDK2 activation process provide results in agreement
     with previous X-ray data.,
  DOI = 10.1110/ps.03578504,
  ISSN = 0961-8368,
  Unique-ID = ISI:000221630900002,
  

• Z. Kriz, M. Otyepka, I. Bartova, and J. Koca, "Analysis of CDK2 active-site hydration: A method to design new
  inhibitors," PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, vol. 55, iss. 2, pp. 258-274, 2004.
  [Bibtex]

  @article ISI:000220980600007,
  Author = Kriz, Z and Otyepka, M and Bartova, I and Koca, J,
  Title = Analysis of CDK2 active-site hydration: A method to design new
     inhibitors,
  Journal = PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,
  Year = 2004,
  Volume = 55,
  Number = 2,
  Pages = 258-274,
  Month = MAY 1,
  Abstract = The interactions between the protein and the solvent were analyzed, and
     protein regions with a high density of water molecules, as well as
     structural water molecules, were determined by using molecular dynamics
     (MD) simulations. A number of water molecules that were in contact with
     the protein for the whole trajectory were determined. Their interaction
     energies and hydrogen bonds with protein residues were analyzed.
     Altogether, 39, 27, 49, and 32 water molecules bound to the protein were
     found for trajectories of the free CDK2, CDK2/ATP, CDK2/roscovitine, and
     CDK2/isopentenyladenine complexes, respectively. Positions of observed
     water molecules were compared with X-ray crystallography data. Special
     attention was paid to water molecules in the active site of the enzyme,
     and especially to the deep pocket, where the N9 roscovitine side-chain
     is buried. Exchange of active-site water molecules with bulk water
     through the tunnel from the pocket was observed. In the
     CDK2/isopentenyladenine complex simulation, two water molecules that
     arrange interaction between the inhibitor and the enzyme via an H-bond
     were observed. Two stable water molecules in the trajectory of the free
     CDK2 were found that occupy the same position as the nitrogens N3 and N9
     of the isopentenyladenine or N1 and N6 nitrogens of the adenosine
     triphosphate (ATP). The positions of structural water molecules were
     compared with the positions of substrate polar groups and
     crystallographic water molecules found in the Brookhaven Protein Data
     Bank for various CDK2 complexes. It was concluded that tracing tightly
     bound water molecules may substantially help in designing new
     inhibitors. (C) 2004 Wiley-Liss, Inc.,
  DOI = 10.1002/prot.20026,
  ISSN = 0887-3585,
  Unique-ID = ISI:000220980600007,
  

• A. Oakley, M. Klvana, M. Otyepka, Y. Nagata, M. Wilce, and J. Damborsky, "Crystal structure of haloalkane dehalogenase LinB from Sphingomonas
  paucimobilis UT26 at 0.95 angstrom resolution: Dynamics of catalytic
  residues," BIOCHEMISTRY, vol. 43, iss. 4, pp. 870-878, 2004.
  [Bibtex]

  @article ISI:000188504800005,
  Author = Oakley, AJ and Klvana, M and Otyepka, M and Nagata, Y and Wilce, MCJ and
     Damborsky, J,
  Title = Crystal structure of haloalkane dehalogenase LinB from Sphingomonas
     paucimobilis UT26 at 0.95 angstrom resolution: Dynamics of catalytic
     residues,
  Journal = BIOCHEMISTRY,
  Year = 2004,
  Volume = 43,
  Number = 4,
  Pages = 870-878,
  Month = FEB 3,
  Abstract = We present the structure of LinB, a 33-kDa haloalkane dehalogenase from
     Sphingomonas paucimobilis UT26, at 0.95 Angstrom resolution. The data
     have allowed us to directly observe the anisotropic motions of the
     catalytic residues. In particular, the side-chain of the catalytic
     nucleophile, Asp 108, displays a high degree of disorder. It has been
     modeled in two conformations, one similar to that observed previously
     (conformation A) and one strained (conformation 13) that approached the
     catalytic base (His272). The strain in conformation B was mainly in the
     C-alpha-C-beta-C-gamma angle (126degrees) that deviated by 13.4degrees
     from the ``ideal'' bond angle of 112.6degrees. On the basis of these
     observations, we propose a role for the charge state of the catalytic
     histidine in determining the geometry of the catalytic residues. We
     hypothesized that double-protonation of the catalytic base (His272)
     reduces the distance between the side-chain of this residue and that of
     the Asp108. The results of molecular dynamics simulations were
     consistent with the structural data showing that protonation of the
     His272 side-chain nitrogen atoms does indeed reduce the distance between
     the side-chains of the residues in question, although the simulations
     failed to demonstrate the same degree of strain in the Asp 108
     C-alpha-C-beta-C-gamma angle. Instead, the changes in the molecular
     dynamics structures were distributed over several bond and dihedral
     angles. Quantum mechanics calculations on Linl3 with
     1-chloro-2,2-dimethylpropane as a substrate were performed to determine
     which active site conformations and protonation states were most likely
     to result in catalysis. It was shown that His272 singly protonated at
     N-delta1 and Asp108 in conformation A gave the most exothermic reaction
     (DeltaH = -22 kcal/mol). With His272 doubly protonated at N-delta1 and
     N-epsilon2, the reactions were only slightly exothermic or were
     endothermic. In all calculations starting with Asp108 in conformation B,
     the Asp108 C-alpha-C-beta-C-gamma angle changed during the reaction and
     the Asp108 moved to conformation A. The results presented here indicate
     that the positions of the catalytic residues and charge state of the
     catalytic base are important for determining reaction energetics in
     LinB.,
  DOI = 10.1021/bi034748g,
  ISSN = 0006-2960,
  Unique-ID = ISI:000188504800005,
  

2003

• O. Pytela, M. Otyepka, J. Kulhanek, E. Otyepkova, and T. Nevecna, "Correlation of dissociation constants of 2-and 2,6-substituted anilines
  in water by methods based on the similarity principle and
  quantum-chemistry calculations," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 107, iss. 51, pp. 11489-11496, 2003.
  [Bibtex]

  @article ISI:000187446900028,
  Author = Pytela, O and Otyepka, M and Kulhanek, J and Otyepkova, E and Nevecna, T,
  Title = Correlation of dissociation constants of 2-and 2,6-substituted anilines
     in water by methods based on the similarity principle and
     quantum-chemistry calculations,
  Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
  Year = 2003,
  Volume = 107,
  Number = 51,
  Pages = 11489-11496,
  Month = DEC 25,
  Abstract = In the context of studies of the ortho effect, two series of
     2-monosubstituted (H, CH3, CF3, OH, CH3O, F, Cl, NH2, CN, NO2) and
     2,6-disubstituted anilines (containing all combinations of CH3, CH3O,
     Cl, and NO2 substituents) were chosen for this work. Commercially
     unavailable derivatives were synthesized, and dissociation constants in
     water were determined for those substances for which the proper
     measurements had not yet been carried out. A critical compilation of
     pK(a) literature data has been summarized and compared with the authors'
     own data. The analysis and interpretation of the ortho substitution
     effect and its manifestation in the dissociation constants of the
     studied anilines (as log K,,) was based on two different
     approaches-correlation analysis (similarity principle) and
     quantum-chemistry calculations. The classical correlation equation with
     substituent constants sigma(1) and sigmaR was extended by the parameter
     v describing the steric effects, but the correlation was not close
     enough (s = 0.514, R = 0.986). The AISE theory (alternative
     interpretation of substituent effects), extended by parameter v for the
     steric effects description, significantly improved the correlation (s =
     0.139, R = 0.9991). The B3LYP/6-311G(d,p) method was used for the
     calculation of physical-chemical properties of protonated and
     nonprotonated forms of aniline derivatives. Quantum chemically
     calculated properties were correlated with experimental data. The data
     mining regression method showed that the statistically most suitable
     interpreting variables are the Gibbs energy of the dissociation
     equilibrium (DeltaG(eq)) and the sum of the natural charges of the
     nonprotonated amino group hydrogen atoms (Q(n)(SigmaH)) and the dipole
     moment of the aniline protonated form (mu(+)). This correlation is
     closer (s = 0.316, R = 0.995) than that based on the similarity
     principle. The correlation with quantum-chemical characteristics
     indicates a close interrelation of the dissociation constant with the
     energy of the equilibrium participants and the delocalization energy of
     the nonprotonated form of aniline. The meaning of the SigmaH quantity in
     the correlation relation is related to the presence of a nitro
     substituent (intramolecular hydrogen bond with the reaction center). The
     dipole moment of the aniline protonated form mu(+) is in relation with
     nonspecific solvation in an aqueous medium.,
  DOI = 10.1021/jp022664w,
  ISSN = 1089-5639,
  Unique-ID = ISI:000187446900028,
  

• J. Moravec, V. Krystof, J. Hanus, L. Havlicek, D. Moravcova, K. Fuksova, M. Kuzma, R. Lenobel, M. Otyepka, and M. Strnad, "2,6,8,9-tetrasubstituted purines as new CDK1 inhibitors," BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, vol. 13, iss. 18, pp. 2993-2996, 2003.
  [Bibtex]

  @article ISI:000185221400010,
  Author = Moravec, J and Krystof, V and Hanus, J and Havlicek, L and Moravcova, D
     and Fuksova, K and Kuzma, M and Lenobel, R and Otyepka, M and Strnad, M,
  Title = 2,6,8,9-tetrasubstituted purines as new CDK1 inhibitors,
  Journal = BIOORGANIC \& MEDICINAL CHEMISTRY LETTERS,
  Year = 2003,
  Volume = 13,
  Number = 18,
  Pages = 2993-2996,
  Month = SEP 15,
  Abstract = Purine inhibitors of cyclin-dependent kinases attract attention as
     potential anticancer drugs because their first representative
     roscovitine recently entered clinical trials. Although well described in
     terms of structure-activity relationships, we still present here a novel
     modification of the purine scaffold influencing their inhibitory
     properties. The introduced C-8 substituents, however, lowered the CDK
     inhibitory activity of roscovitine, whereas the antiproliferative
     potential of several derivatives remained high. (C) 2003 Elsevier Ltd.
     All rights reserved.,
  DOI = 10.1016/S0960-894X(03)00632-2,
  ISSN = 0960-894X,
  Unique-ID = ISI:000185221400010,
  

• I. Wiedermannova, M. Otyepka, J. Styskala, and J. Slouka, "The synthesis of some polycyclic N-H acids with quinoxaline and
  [1,2,4]triazines," ARKIVOC, iss. Part 15, pp. 65-74, 2003.
  [Bibtex]

  @article ISI:000220561700008,
  Author = Wiedermannova, I and Otyepka, M and Styskala, J and Slouka, J,
  Title = The synthesis of some polycyclic N-H acids with quinoxaline and
     [1,2,4]triazines,
  Journal = ARKIVOC,
  Year = 2003,
  Number = Part 15,
  Pages = 65-74,
  Abstract = 3-(4-Aminophenyl)-1,2-dihydro-quinoxaline-2-one (2b),
     3-(2-aminophenyl)-6,7-dimethyl-1,2-dihydro-quinoxaline-2-one (1b), its
     3-(4-aminophenyl)-isomer (3b),
     3-(2-aminobenzyl)-1,2-dihydro-quinoxaline-2-one (4b), its
     3-(4-aminobenzyl)-isomer (6b),
     3-(2-aminobenzyl)-6,7-dimethyl-1,2-dihydro-quinoxaline-2-one (5b) and
     its 3-(4-aminobenzyl)-isomer (7b) were diazotised and the resulting
     diazonium salts were coupled with ethyl cyanoacetylcarbamate,
     3-methyl-1,2-dihydro-quinoxaline-2-one,
     3,6,7-trimethyl-1,2-dihydro-quinoxaline-2-one and
     3-methyl-6,7-dichloro-1,2-dihydro-quinoxaline-2-one. In this manner the
     corresponding hydrazones with one 1,2-dihydro-quinoxaline-2-one ring
     (1d, 3d, 5d, 7d) and hydrazones with two 1,2-dihydro-quinoxaline-2-one
     rings (3e-3g, 4e-4g, 5e-5g, 6e-6g, 7e-7g) were obtained. Cyclization of
     hydrazones (1d, 3d, 5d, 7d) afforded compounds (1h, 3h, 5h, 7h)
     containing 6-azauracil and also 1,2-dihydroquinoxaline-2-one rings. The
     starting amino derivative (1b) was prepared by the reaction of
     N-acetylisatine with 4,5-dimethyl-o-phenylenediamine followed by
     hydrolysis of the N-acetyl derivative. The amino derivative (5b) was
     prepared by the condensation of 2-nitrophenylpyruvic acid with
     4,5-dimethyl-o-phenylenediamine and by reduction of the formed nitro
     derivative (5a). The amino derivative (3b) was prepared by the
     condensation of 4-acetylaminophenylglyoxylic acid with
     4,5-dimethyl-o-phenylenediamine and hydrolysis of the N-acetyl
     derivative. The amino derivative (7b) resulted from the condensation of
     4,5-dimethyl-o-phenylenediamine with 4-aminophenylpyruvic acid.,
  Unique-ID = ISI:000220561700008,
  

2002

• M. Otyepka, Z. Kriz, and J. Koca, "Dynamics and binding modes of free cdk2 and its two complexes with
  inhibitors studied by computer simulations," JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol. 20, iss. 2, pp. 141-154, 2002.
  [Bibtex]

  @article ISI:000179043800001,
  Author = Otyepka, M and Kriz, Z and Koca, J,
  Title = Dynamics and binding modes of free cdk2 and its two complexes with
     inhibitors studied by computer simulations,
  Journal = JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS,
  Year = 2002,
  Volume = 20,
  Number = 2,
  Pages = 141-154,
  Month = OCT,
  Abstract = This article presents a molecular dynamics (MD) study of the cdk2 enzyme
     and its two complexes with the inhibitors isopentenyladenine and
     roscovitine using the Cornell et at. force field from the AMBER software
     package. The results show that inserting an inhibitor into the enzyme
     active site does not considerably change enzyme structure but it
     seemingly changes the distribution of internal motions. The inhibitor
     causes differences in the domain motions in free cdk2 and in its
     complexes. It was found out that repulsion of roscovitine N9 substituent
     causes conformational change on Lys 33 side chain. Isopentenyladenine
     forms with Lys 33 side chain terminal amino group a hydrogen bond. It
     implies that the cavity, where N9 substituent of roscovitine is buried,
     can adopt larger substituent due to Lys 33 side chain flexibility. The
     composition of electrostatic and van der Waals interactions between the
     inhibitor and the enzyme were also calculated along both cdk2/inhibitor
     MD trajectories together with MM-PB/GBSA analysis. These results show
     that isopentenyladenine-like inhibitors could be more effective after
     modifications leading to an increase in their van der Waals contact with
     the enzyme. We suggest that a way leading to better inhibitors occupying
     isopentenyladenine binding mode could be: to keep N9 and N7 purine
     positions free, to keep 3,3-dimethylallylamino group at C6 position, and
     to add, e.g., benzylamino group at C2 position. The results support the
     idea that the isopentenyl adenine binding mode can be used for cdk2
     inhibitors design and that all possibilities to improve this binding
     mode were not uncovered yet.,
  ISSN = 0739-1102,
  Unique-ID = ISI:000179043800001,
  

• M. Otyepka and J. Damborsky, "Functionally relevant motions of haloalkane dehalogenases occur in the
  specificity-modulating cap domains," PROTEIN SCIENCE, vol. 11, iss. 5, pp. 1206-1217, 2002.
  [Bibtex]

  @article ISI:000175141900021,
  Author = Otyepka, M and Damborsky, J,
  Title = Functionally relevant motions of haloalkane dehalogenases occur in the
     specificity-modulating cap domains,
  Journal = PROTEIN SCIENCE,
  Year = 2002,
  Volume = 11,
  Number = 5,
  Pages = 1206-1217,
  Month = MAY,
  Abstract = One-nanosecond molecular dynamics trajectories of three haloalkane
     dehalogenases (Dh1A. LinB. and DhaA) are compared. The main domain was
     rigid in all three dehalogenases, whereas the substrate
     specificity-modulating cap domains showed considerably higher mobility.
     The functionally relevant motions were spread over the entire cap domain
     in Dh1A, whereas they were more localized in LinB and DhaA. The highest
     amplitude of essential motions of Dh1A was noted in the
     alpha4'-helix-loop-alpha4-helix region, formerly proposed to participate
     in the large conformation change needed for product release. The highest
     amplitude of essential motions of LinB and DhaA was observed in the
     random coil before helix 4, linking two domains of these proteins. This
     flexibility is the consequence of the modular composition of haloalkane
     dehalogenases. Two members of the catalytic triad. that is, the
     nucleophile and the base, showed a very high level of rigidity in all
     three dehalogenases. This rigidity is essential for their function. One
     of the halide-stabilizing residues, important for the catalysis, shows
     significantly higher flexibility in Dh1A compared with LinB and DhaA.
     Enhanced flexibility may be required for destabilization of the
     electrostatic interactions during the release of the halide ion from the
     deeply buried active site of Dh1A. The exchange of water molecules
     between the enzyme active site and bulk solvent was very different among
     the three dehalogenases. The differences could be related to the
     flexibility of the cap domains and to the number of entrance tunnels.,
  DOI = 10.1110/ps3830102,
  ISSN = 0961-8368,
  Unique-ID = ISI:000175141900021,
  

2000

• M. Otyepka, V. Krystof, L. Havlicek, V. Siglerova, M. Strnad, and J. Koca, "Docking-based development of purine-like inhibitors of cyclin-dependent
  kinase-2," JOURNAL OF MEDICINAL CHEMISTRY, vol. 43, iss. 13, pp. 2506-2513, 2000.
  [Bibtex]

  @article ISI:000087924900003,
  Author = Otyepka, M and Krystof, V and Havlicek, L and Siglerova, V and Strnad, M
     and Koca, J,
  Title = Docking-based development of purine-like inhibitors of cyclin-dependent
     kinase-2,
  Journal = JOURNAL OF MEDICINAL CHEMISTRY,
  Year = 2000,
  Volume = 43,
  Number = 13,
  Pages = 2506-2513,
  Month = JUN 29,
  Abstract = The cell division cycle is controlled by cyclin-dependent kinases (cdk),
     which consist of a catalytic subunit (cdk1-cdk8) and a regulatory
     subunit (cyclin A-H). Purine-like inhibitors of cyclin-dependent kinases
     have recently been found to be of potential use as anticancer drugs.
     Rigid and flexible docking techniques were used for analysis of binding
     mode and design of new inhibitors. X-ray structures of three (ATP,
     olomoucine, roscovitine) cdk2 complexes were available at the beginning
     of the study and were used to optimize the docking parameters. The new
     potential inhibitors were then docked into the cdk2 enzyme, and the
     enzyme/inhibitor interaction energies were calculated and tested against
     the assayed activities of cdk1 (37 compounds) and cdk2 (9 compounds). A
     significant rank correlation between the activity and the rigid docking
     interaction energy has been found. This implies that (i) the rigid
     docking can be used as a tool for qualitative prediction of activity and
     (ii) values obtained by the rigid docking technique into the cdk2 active
     site can also be used for the prediction of cdk1 activity. While the
     resulting geometries obtained by the rigid docking are in good agreement
     with the X-ray data, the flexible docking did not always produce the
     same inhibitor conformation as that found in the crystal.,
  DOI = 10.1021/jm990506w,
  ISSN = 0022-2623,
  Unique-ID = ISI:000087924900003,