Karel Berka

2011

• M. Oncak, K. Berka, and P. Slavicek, “Novel Covalent Bond in Proteins: Calculations on Model Systems Question
  the Bond Stability,” CHEMPHYSCHEM, vol. 12, iss. 17, pp. 3449-3457, 2011.
  [Bibtex]

  @article ISI:000297693200041,
  Author = Oncak, Milan and Berka, Karel and Slavicek, Petr,
  Title = Novel Covalent Bond in Proteins: Calculations on Model Systems Question
     the Bond Stability,
  Journal = CHEMPHYSCHEM,
  Year = 2011,
  Volume = 12,
  Number = 17,
  Pages = 3449-3457,
  Month = DEC 9,
  Abstract = We have investigated the sulfilimine covalent link between methionine
     (Met) and lysine (Lys), recently identified in collagen IV (R. Vanacore,
     A.-J. L. Ham, M. Voehler, C. R. Sanders, T. P. Conrads, T. D. Veenstra,
     K. B. Sharpless, P. E. Dawson, B. G. Hudson, Science 2009, 325, 1230),
     and have explored its stability with respect to both the redox processes
     and UV radiation by means of advanced computational methods. We have
     concluded that the bond should be present in a protonated state,
     (?NH=S?)+. The bond is characterized by a relatively high standard
     reduction potential, that is, the bond should not be stable in a typical
     cell environment; if the sulfilimine bond exists (as suggested by the
     experiment) then the bond has to be supported by the protein
     environment. The sulfilimine bond then destabilizes the protein
     structure with respect to the alternative tertiary structure. We discuss
     conditions under which the bond could be formed as well as other
     possible structural arrangements consistent with the MetLys
     stoichiometry; some of the alternative bond motifs are more
     thermodynamically stable than the sulfilimine bond. We suggest that the
     character of the MetLys contact could be approached via NEXAFS
     spectroscopy. Finally, we show that the protonation brings
     photostability to the sulfilimine bond.,
  DOI = 10.1002/cphc.201100664,
  ISSN = 1439-4235,
  Unique-ID = ISI:000297693200041,
  

• 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,
  

• 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,
  

2010

• M. Kolar, K. Berka, P. Jurecka, and P. Hobza, “On the Reliability of the AMBER Force Field and its Empirical Dispersion
  Contribution for the Description of Noncovalent Complexes,” CHEMPHYSCHEM, vol. 11, iss. 11, pp. 2399-2408, 2010.
  [Bibtex]

  @article ISI:000281061500018,
  Author = Kolar, Michal and Berka, Karel and Jurecka, Petr and Hobza, Pavel,
  Title = On the Reliability of the AMBER Force Field and its Empirical Dispersion
     Contribution for the Description of Noncovalent Complexes,
  Journal = CHEMPHYSCHEM,
  Year = 2010,
  Volume = 11,
  Number = 11,
  Pages = 2399-2408,
  Month = AUG 2,
  Abstract = The reliability of the AMBER force field is tested by comparing the
     total interaction energy and dispersion energy with the reference data
     obtained at the density functional theory symmetry-adapted perturbation
     treatment (DFT-SAPT)/aug-cc-pVDZ level. The comparison is made for 194
     different geometries of noncovalent complexes (H-bonded, stacked, mixed,
     and dispersion-bound), at the equilibrium distances as well as at longer
     distances (up to a relative distance of two). The total interaction
     energies agree very well with the reference data and only the strength
     of H-bonded complexes is slightly underestimated. In the case of
     dispersion energy, the overall agreement is even better, with the
     exception of the stacked aromatic systems, where the empirical
     dispersion energy is overestimated. The use of AMBER interaction energy
     and AMBER dispersion energy for different types of noncovalent complexes
     at equilibrium as well as at longer distances is thus justified, except
     for, a few cases, such as the water molecule, where the dispersion
     energy is highly inaccurate.,
  DOI = 10.1002/cphc.201000109,
  ISSN = 1439-4235,
  Unique-ID = ISI:000281061500018,
  

• K. Berka, R. A. Laskowski, P. Hobza, and J. Vondrasek, “Energy Matrix of Structurally Important Side-Chain/Side-Chain
  Interactions in Proteins,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 6, iss. 7, pp. 2191-2203, 2010.
  [Bibtex]

  @article ISI:000279751500026,
  Author = Berka, Karel and Laskowski, Roman A. and Hobza, Pavel and Vondrasek,
     Jiri,
  Title = Energy Matrix of Structurally Important Side-Chain/Side-Chain
     Interactions in Proteins,
  Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
  Year = 2010,
  Volume = 6,
  Number = 7,
  Pages = 2191-2203,
  Month = JUL,
  Abstract = The interactions between amino acid side chains in proteins are
     generally considered to be the most important stabilizing factor
     controlling the precise arrangement of the polypeptide chain into a
     well-defined spatial structure. We used the RI-DFT-D method to calculate
     the full 20 x 20 matrix of interaction energies between all pairs of
     amino acid side chains. For each pair, we used a representative 3D
     conformation extracted from an analysis of known protein structures from
     Protein Data Bank (PDB). The representative comes from the largest
     cluster of relative orientations of the two side chains. We find that
     all of the calculated interaction energies between selected pairs of
     amino acids are attractive in the gas phase with the exception of side
     chain pairs having the same total charge. We compared these data with
     those calculated by the parm03 and OPLS-AA/L force fields to investigate
     the reliability of simple methods in modeling biomolecules and their
     behavior. The force fields yield good overall interaction energies for
     our set but have problems in evaluation of some particular interactions
     which could be of principal importance for protein stability. We then
     looked in detail at the 20 side chain interactions involving tryptophan.
     The histograms of interaction energies showed that the distributions of
     the interaction energies are neither normal nor Boltzmann-like and that
     our representative geometries correspond mostly to the minimum energy
     geometry which is rather poorly populated in the whole pairwise energy
     distribution. We concluded that cluster representatives obtained by the
     clusterization algorithm based on geometry criteria cannot be considered
     as a typical interaction for the whole side chain/side chain interaction
     distribution. They seem to epitomize the strongest interactions in a
     protein and are often functionally or structurally important.,
  DOI = 10.1021/ct100007y,
  ISSN = 1549-9618,
  Unique-ID = ISI:000279751500026,
  

2009

• K. Berka, P. Hobza, and J. Vondrasek, “Analysis of Energy Stabilization inside the Hydrophobic Core of
  Rubredoxin,” CHEMPHYSCHEM, vol. 10, iss. 3, pp. 543-548, 2009.
  [Bibtex]

  @article ISI:000264229900014,
  Author = Berka, Karel and Hobza, Pavel and Vondrasek, Jiri,
  Title = Analysis of Energy Stabilization inside the Hydrophobic Core of
     Rubredoxin,
  Journal = CHEMPHYSCHEM,
  Year = 2009,
  Volume = 10,
  Number = 3,
  Pages = 543-548,
  Month = FEB 23,
  Abstract = The hydrophobic core of globular proteins is responsible for major
     stabilization of the protein tertiary structure. The prevailing amino
     acid residues in the core are of aliphatic or aromatic character and
     therefore the core in a folded protein structure is mostly stabilized by
     noncovalent interactions of van der Waals origin between the amino acid
     side chains. Herein, we present a theoretical analysis of the
     interaction energy between the amino acids of the hydrophobic core of
     the small globular protein rubredoxin (Rd) based on the symmetry-adapted
     perturbation theory (SAPT) method. The results show uniform proportions
     between the second-order dispersion and first-order electrostatic energy
     terms in favor of dispersion interaction which plays a major role in the
     stabilization of this important structural element. To demonstrate the
     contrast between systems stabilized by different mechanisms, we perform
     a SAPT analysis of the typical hydrogen bonds involved in the formation
     of protein secondary structure elements in Rd, where dispersion still
     plays a non-negligible role but electrostatic energy is the major
     stabilizing factor.,
  DOI = 10.1002/cphc.200800401,
  ISSN = 1439-4235,
  Unique-ID = ISI:000264229900014,
  

2008

• J. Rezac, P. Jurecka, K. E. Riley, J. Cerny, H. Valdes, K. Pluhackova, K. Berka, T. Rezac, M. Pitonak, J. Vondrasek, and P. Hobza, “QUANTUM CHEMICAL BENCHMARK ENERGY AND GEOMETRY DATABASE FOR MOLECULAR
  CLUSTERS AND COMPLEX MOLECULAR SYSTEMS (www.begdb.com): A USERS MANUAL
  AND EXAMPLES,” COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, vol. 73, iss. 10, pp. 1261-1270, 2008.
  [Bibtex]

  @article ISI:000263121400003,
  Author = Rezac, Jan and Jurecka, Petr and Riley, Kevin E. and Cerny, Jiri and
     Valdes, Haydee and Pluhackova, Kristyna and Berka, Karel and Rezac,
     Tomas and Pitonak, Michal and Vondrasek, Jiri and Hobza, Pavel,
  Title = QUANTUM CHEMICAL BENCHMARK ENERGY AND GEOMETRY DATABASE FOR MOLECULAR
     CLUSTERS AND COMPLEX MOLECULAR SYSTEMS (www.begdb.com): A USERS MANUAL
     AND EXAMPLES,
  Journal = COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS,
  Year = 2008,
  Volume = 73,
  Number = 10,
  Pages = 1261-1270,
  Abstract = Our previous benchmark CCSD(T)/ complete basis set limit calculations
     were collected into a database named begdb - Benchmark Energy and
     Geometry DataBase. Web-based interface to this database was prepared and
     is available at www.begdb.com. Users can browse, search and plot the
     data online or download structures and energy tables.,
  DOI = 10.1135/cccc20081261,
  ISSN = 0010-0765,
  Unique-ID = ISI:000263121400003,