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