Email: pavel.banas@upol.cz
Location: 17. listopadu 12, Olomouc
Phone: (+420) 58 563 4769
Fax: (+420) 585 634 761
Oblast výzkumu:
Classical and quantum molecular dynamics of biomolecules, quantum chemical and hybrid QM/MM calculations and their application. RNA catalysis, structure and function of non-coding RNAs. Software development (e.g., CAVER).
Kvalifikace:
Mgr.: Applied physics, Palacký University, Olomouc
Mgr.: Analytical chemistry, Palacký University, Olomouc
Ph.D.: Physical chemistry, Palacký University, Olomouc
Publications
2011
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![[DOI]](http://www.rcptm.com/wp-content/plugins/papercite/img/external.png)
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, - 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, - 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,
2010
- 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, - 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, - 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,
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, - 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,
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, - 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,
2006
- P. Banas, J. Rehacek, and Z. Hradil, “Perturbative quantum-state estimation,” PHYSICAL REVIEW A, vol. 74, iss. 1, 2006.
[Bibtex]@article ISI:000239425900129, Author = Banas, P. and Rehacek, J. and Hradil, Z., Title = Perturbative quantum-state estimation, Journal = PHYSICAL REVIEW A, Year = 2006, Volume = 74, Number = 1, Month = JUL, Abstract = A perturbative approach to quantum-state estimation is formulated. Each perturbation simultaneously affects the eigenvalues and eigenvectors of the density matrix. Fast convergence of the proposed algorithm is illustrated on a simple three-dimensional system observed via the process of stimulated Raman adiabatic passage., DOI = 10.1103/PhysRevA.74.014101, Article-Number = 014101, ISSN = 1050-2947, Unique-ID = ISI:000239425900129, - 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,