Structural interpretation of pH and salt-dependent processes in proteins with computational methods.

[1]  George I Makhatadze,et al.  Contribution of surface salt bridges to protein stability: guidelines for protein engineering. , 2003, Journal of molecular biology.

[2]  P. Harbury,et al.  Tanford-Kirkwood electrostatics for protein modeling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Homme W Hellinga,et al.  An empirical model for electrostatic interactions in proteins incorporating multiple geometry‐dependent dielectric constants , 2003, Proteins.

[4]  Arieh Warshel,et al.  Consistent Calculations of pKa's of Ionizable Residues in Proteins: Semi-microscopic and Microscopic Approaches , 1997 .

[5]  Steven T. Whitten and,et al.  pH dependence of stability of staphylococcal nuclease: evidence of substantial electrostatic interactions in the denatured state. , 2000 .

[6]  Kelly K. Lee,et al.  Electrostatic effects in highly charged proteins: salt sensitivity of pKa values of histidines in staphylococcal nuclease. , 2002, Biochemistry.

[7]  Huan‐Xiang Zhou,et al.  Modeling of protein conformational fluctuations in pKa predictions. , 1997, Journal of molecular biology.

[8]  A. Warshel,et al.  Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[9]  A. D. Robertson,et al.  Hydrogen bonds and the pH dependence of ovomucoid third domain stability. , 1995, Biochemistry.

[10]  F. Gurd,et al.  pH-dependent processes in proteins. , 1985, CRC critical reviews in biochemistry.

[11]  David A. Case,et al.  Including Side Chain Flexibility in Continuum Electrostatic Calculations of Protein Titration , 1996 .

[12]  F Guarnieri,et al.  A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins. , 1999, Biophysical journal.

[13]  M. Karplus,et al.  Electrostatic contributions to molecular free energies in solution. , 1998, Advances in protein chemistry.

[14]  I. Simon,et al.  The role of hydrophobic microenvironments in modulating pKa shifts in proteins , 2002, Proteins.

[15]  G. Makhatadze,et al.  Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface. , 1999, Biochemistry.

[16]  Barry Honig,et al.  Focusing of electric fields in the active site of Cu‐Zn superoxide dismutase: Effects of ionic strength and amino‐acid modification , 1986, Proteins.

[17]  Emil Alexov,et al.  Role of the protein side‐chain fluctuations on the strength of pair‐wise electrostatic interactions: Comparing experimental with computed pKas , 2002, Proteins.

[18]  A. Fersht,et al.  Histidine-aromatic interactions in barnase. Elevation of histidine pKa and contribution to protein stability. , 1992, Journal of molecular biology.

[19]  B. Tidor,et al.  Rational modification of protein stability by the mutation of charged surface residues. , 2000, Biochemistry.

[20]  Kevin L. Shaw,et al.  The effect of net charge on the solubility, activity, and stability of ribonuclease Sa , 2001, Protein science : a publication of the Protein Society.

[21]  M. Karplus,et al.  pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. , 1990, Biochemistry.

[22]  Kelly K. Lee,et al.  Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein , 2002, Protein science : a publication of the Protein Society.

[23]  E. Alexov,et al.  Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. , 1997, Biophysical journal.

[24]  A. Fersht,et al.  Surface electrostatic interactions contribute little of stability of barnase. , 1991, Journal of molecular biology.

[25]  M. Gilson,et al.  The determinants of pKas in proteins. , 1996, Biochemistry.

[26]  A. Warshel,et al.  Calculations of electrostatic interactions in biological systems and in solutions , 1984, Quarterly Reviews of Biophysics.

[27]  E. Lattman,et al.  High apparent dielectric constants in the interior of a protein reflect water penetration. , 2000, Biophysical journal.

[28]  J A Wozniak,et al.  Cumulative site-directed charge-change replacements in bacteriophage T4 lysozyme suggest that long-range electrostatic interactions contribute little to protein stability. , 1991, Journal of molecular biology.

[29]  Michael D. Daily,et al.  pK values of histidine residues in ribonuclease Sa: effect of salt and net charge. , 2003, Journal of molecular biology.

[30]  K. Sharp,et al.  Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models , 1994 .

[31]  M. Gilson,et al.  Prediction of pH-dependent properties of proteins. , 1994, Journal of molecular biology.

[32]  M K Gilson,et al.  Theoretical and experimental analysis of ionization equilibria in ovomucoid third domain. , 1998, Biochemistry.

[33]  Joanna Trylska,et al.  Thermodynamic linkage between the binding of protons and inhibitors to HIV‐1 protease , 2008, Protein science : a publication of the Protein Society.

[34]  M Karplus,et al.  Improving the accuracy of protein pKa calculations: Conformational averaging versus the average structure , 1998, Proteins.

[35]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[36]  B. Kuhlman,et al.  pKa values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions. , 1999, Biochemistry.

[37]  R. Levy,et al.  Intrinsic pKas of ionizable residues in proteins: An explicit solvent calculation for lysozyme , 1994, Proteins.

[38]  Arieh Warshel,et al.  Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs , 1993, J. Comput. Chem..

[39]  A. Warshel Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes. , 1981, Biochemistry.

[40]  Eaton E Lattman,et al.  Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration. , 2002, Biophysical journal.

[41]  D. Bashford,et al.  Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin , 1992 .

[42]  W E Stites,et al.  In a staphylococcal nuclease mutant the side-chain of a lysine replacing valine 66 is fully buried in the hydrophobic core. , 1991, Journal of molecular biology.

[43]  B. Rabenstein,et al.  Calculated pH-dependent population and protonation of carbon-monoxy-myoglobin conformers. , 2001, Biophysical journal.

[44]  J. Antosiewicz,et al.  Empirical relationships between protein structure and carboxyl pKa values in proteins , 2002, Proteins.

[45]  V L Arcus,et al.  pKA values of carboxyl groups in the native and denatured states of barnase: the pKA values of the denatured state are on average 0.4 units lower than those of model compounds. , 1995, Biochemistry.

[46]  R. Dimitrov,et al.  Self‐consistent field approach to protein structure and stability. i: pH dependenceof electrostatic contribution , 1997, Proteins.

[47]  U. Sauer,et al.  Contributions of engineered surface salt bridges to the stability of T4 lysozyme determined by directed mutagenesis. , 1991, Biochemistry.

[48]  A. Warshel,et al.  What are the dielectric “constants” of proteins and how to validate electrostatic models? , 2001, Proteins.

[49]  E. Lattman,et al.  Experimental measurement of the effective dielectric in the hydrophobic core of a protein. , 1997, Biophysical chemistry.

[50]  K. P. Murphy,et al.  Variability in the pKa of histidine side‐chains correlates with burial within proteins , 2002, Proteins.

[51]  B. García-Moreno E.,et al.  Salt effects on ionization equilibria of histidines in myoglobin. , 2000, Biophysical journal.

[52]  Bo Svensson,et al.  An efficient simulation technique for electrostatic free energies with applications to azurin , 1995, J. Comput. Chem..

[53]  L. Kay,et al.  Site-specific contributions to the pH dependence of protein stability , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[54]  C Woodward,et al.  The conserved, buried aspartic acid in oxidized Escherichia coli thioredoxin has a pKa of 7.5. Its titration produces a related shift in global stability. , 1991, Biochemistry.

[55]  Rebecca C. Wade,et al.  Improving the Continuum Dielectric Approach to Calculating pKas of Ionizable Groups in Proteins , 1996 .

[56]  C. Tanford,et al.  Extension of the theory of linked functions to incorporate the effects of protein hydration. , 1969, Journal of molecular biology.

[57]  A. Karshikoff,et al.  A model of a local dielectric constant in proteins , 1998 .

[58]  E. Alexov,et al.  Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins. , 2002, Biophysical journal.

[59]  A. D. Robertson,et al.  Insensitivity of perturbed carboxyl pK(a) values in the ovomucoid third domain to charge replacement at a neighboring residue. , 2000, Biochemistry.

[60]  R. Wade,et al.  pKa calculations for class A beta-lactamases: methodological and mechanistic implications. , 1997, Biophysical journal.

[61]  B. Matthews,et al.  Structural and thermodynamic consequences of burying a charged residue within the hydrophobic core of T4 lysozyme. , 1991, Biochemistry.

[62]  E. BertrandGarcía-Moreno [28] Estimating binding constants for site-specific interactions between monovalent ions and proteins , 1994 .

[63]  K. Sharp,et al.  On the calculation of pKas in proteins , 1993, Proteins.

[64]  David Schell,et al.  Charge-charge interactions are key determinants of the pK values of ionizable groups in ribonuclease Sa (pI=3.5) and a basic variant (pI=10.2). , 2003, Journal of molecular biology.

[65]  P E Wright,et al.  Electrostatic calculations of side-chain pK(a) values in myoglobin and comparison with NMR data for histidines. , 1993, Biochemistry.

[66]  M K Gilson,et al.  The dielectric constant of a folded protein , 1986, Biopolymers.

[67]  Tony J. You,et al.  Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility. , 1995, Biophysical journal.