Prediction of Ph-dependent Properties of Proteins, Journal of Molecular Biology, vol.238, issue.3, pp.415-436, 1994. ,
DOI : 10.1006/jmbi.1994.1301
Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions, Journal of Computational Chemistry, vol.17, issue.14, pp.1587-1597, 1991. ,
DOI : 10.1002/(SICI)1096-987X(19961115)17:14<1587::AID-JCC1>3.0.CO;2-H
Ligand Binding Affinities from MD Simulations, Accounts of Chemical Research, vol.35, issue.6, pp.358-365, 2002. ,
DOI : 10.1021/ar010014p
Dielectric Relaxation in an Enzyme Active Site:?? Molecular Dynamics Simulations Interpreted with a Macroscopic Continuum Model, Journal of the American Chemical Society, vol.123, issue.44, pp.11047-11056, 2001. ,
DOI : 10.1021/ja010716+
Solvation energies and electronic spectra in polar, polarizable media: Simulation tests of dielectric continuum theory, The Journal of Chemical Physics, vol.104, issue.4, pp.1293-1308, 1995. ,
DOI : 10.1063/1.470787
Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration, Proteins: Structure, Function, and Genetics, vol.4, issue.4, pp.523-544, 1997. ,
DOI : 10.1002/(SICI)1097-0134(199704)27:4<523::AID-PROT6>3.0.CO;2-B
An object-oriented programming suite for electrostatic effects in biological molecules In Scientific Computing in Object- Oriented Parallel Environments, Lecture Notes in Computer Science, vol.1343, 1997. ,
pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model, Biochemistry, vol.29, issue.44, pp.10219-10225, 1990. ,
DOI : 10.1021/bi00496a010
Including Side Chain Flexibility in Continuum Electrostatic Calculations of Protein Titration, The Journal of Physical Chemistry, vol.100, issue.51, pp.20156-20163, 1996. ,
DOI : 10.1021/jp9623709
Dielectric studies of protein hydration and hydration-induced flexibility, Journal of Molecular Biology, vol.181, issue.2, pp.323-326, 1985. ,
DOI : 10.1016/0022-2836(85)90096-8
Bacterial Reaction Center:?? Structure and Interactions, The Journal of Physical Chemistry B, vol.107, issue.6, pp.1423-1431, 2003. ,
DOI : 10.1021/jp0270001
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules, Journal of the American Chemical Society, vol.117, issue.19, pp.5179-5197, 1995. ,
DOI : 10.1021/ja00124a002
Implicit Solvation Models:?? Equilibria, Structure, Spectra, and Dynamics, Chemical Reviews, vol.99, issue.8, pp.2161-2200, 1999. ,
DOI : 10.1021/cr960149m
Electrostatics in biomolecular structure and dynamics, Chemical Reviews, vol.90, issue.3, pp.509-521, 1990. ,
DOI : 10.1021/cr00101a005
Intrinsic pKas of ionizable residues in proteins: An explicit solvent calculation for lysozyme, Proteins: Structure, Function, and Genetics, vol.18, issue.1, pp.85-97, 1994. ,
DOI : 10.1002/prot.340200109
Constant-pH molecular dynamics simulations: a test case of succinic acid, Chemical Physics, vol.302, issue.1-3, pp.161-170, 2004. ,
DOI : 10.1016/j.chemphys.2004.03.031
Reorganization in apo- and holo-??-lactoglobulin upon protonation of Glu89: Molecular dynamics and pKa calculations, Proteins: Structure, Function, and Bioinformatics, vol.27, issue.4, pp.744-758, 2004. ,
DOI : 10.1002/prot.10643
Recent advances in the development and application of implicit solvent models in biomolecule simulations, Current Opinion in Structural Biology, vol.14, issue.2, pp.217-224, 2004. ,
DOI : 10.1016/j.sbi.2004.03.009
Theoretical Investigation of the Binding Free Energies and Key Substrate-Recognition Components of the Replication Fidelity of Human DNA Polymerase ??, The Journal of Physical Chemistry B, vol.106, issue.22, pp.5739-5753, 2002. ,
DOI : 10.1021/jp020790u
Computer simulation studies of the fidelity of DNA polymerases, Biopolymers, vol.36, issue.3, pp.286-299, 2003. ,
DOI : 10.1002/bip.10244
Error estimates on averages of correlated data, The Journal of Chemical Physics, vol.91, issue.1, pp.461-466, 1989. ,
DOI : 10.1063/1.457480
Empirical relationships between protein structure and carboxyl pKa values in proteins, Proteins: Structure, Function, and Genetics, vol.30, issue.2, pp.388-403, 2002. ,
DOI : 10.1002/prot.10174
Combining Conformational Flexibility and Continuum Electrostatics for Calculating pKas in Proteins, Biophysical Journal, vol.83, issue.4, pp.1731-1748, 2002. ,
DOI : 10.1016/S0006-3495(02)73940-4
Multiple-site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins, Proteins: Structure, Function, and Genetics, vol.31, issue.3, pp.266-282, 1993. ,
DOI : 10.1002/prot.340150305
Dielectric relaxation in proteins: a continuum electrostatics model incorporating dielectric heterogeneity of the protein and time-dependent charges, Journal of Computational Chemistry, vol.105, issue.3, pp.290-305, 2001. ,
DOI : 10.1002/1096-987X(200102)22:3<290::AID-JCC1002>3.0.CO;2-V
Classical electrostatics in biology and chemistry, Science, vol.268, issue.5214, pp.1144-1149, 1995. ,
DOI : 10.1126/science.7761829
The Many Roles of Computation in Drug Discovery, Science, vol.303, issue.5665, pp.1813-1818, 2004. ,
DOI : 10.1126/science.1096361
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin, Journal of the American Chemical Society, vol.110, issue.6, pp.1657-1666, 1988. ,
DOI : 10.1021/ja00214a001
Microscopic simulations of macroscopic dielectric constants of solvated proteins, The Journal of Chemical Physics, vol.95, issue.6, pp.4366-4377, 1991. ,
DOI : 10.1063/1.461760
Electrostatics of proteins: Description in terms of two dielectric constants simultaneously, Proteins: Structure, Function, and Genetics, vol.98, issue.2, pp.174-182, 1997. ,
DOI : 10.1002/(SICI)1097-0134(199706)28:2<174::AID-PROT6>3.0.CO;2-F
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, Biochemistry, vol.30, issue.30, pp.7603-7609, 1991. ,
DOI : 10.1021/bi00244a032
Linkage of thioredoxin stability to titration of ionizable groups with perturbed pKa, Biochemistry, vol.30, issue.30, pp.7609-7614, 1991. ,
DOI : 10.1021/bi00244a033
Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603, "Protein Engineering, Design and Selection", vol.5, issue.3, pp.215-228, 1992. ,
DOI : 10.1093/protein/5.3.215
Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs, Journal of Computational Chemistry, vol.95, issue.2, pp.161-185, 1993. ,
DOI : 10.1002/jcc.540140205
Constant-pH molecular dynamics using continuous titration coordinates, Proteins: Structure, Function, and Bioinformatics, vol.17, issue.4, pp.731-752, 2003. ,
DOI : 10.1002/prot.20128
pH dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: application to 29GMP/39GMP binding to ribonuclease T 1 and implications for catalysis, J. Mol. Biol, vol.247, pp.774-807, 1995. ,
Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program, Computer Physics Communications, vol.91, issue.1-3, pp.57-95, 1995. ,
DOI : 10.1016/0010-4655(95)00043-F
Electrostatic Free Energy and Other Properties of States Having Nonequilibrium Polarization. I, The Journal of Chemical Physics, vol.24, issue.5, pp.979-989, 1956. ,
DOI : 10.1063/1.1742724
Chemical and Electrochemical Electron-Transfer Theory, Annual Review of Physical Chemistry, vol.15, issue.1, pp.155-196, 1964. ,
DOI : 10.1146/annurev.pc.15.100164.001103
On the Theory of Shifts and Broadening of Electronic Spectra of Polar Solutes in Polar Media, The Journal of Chemical Physics, vol.43, issue.4, pp.1261-1274, 1965. ,
DOI : 10.1063/1.1696913
A Self-Consistent, Microenvironment Modulated Screened Coulomb Potential Approximation to Calculate pH-Dependent Electrostatic Effects in Proteins, Biophysical Journal, vol.77, issue.1, pp.3-22, 1999. ,
DOI : 10.1016/S0006-3495(99)76868-2
Low dielectric response in enzyme active site, Proc. Natl. Acad. Sci. USA, pp.2081-2086, 2000. ,
DOI : 10.1073/pnas.050316997
Continuum model calculations of solvation free energies: accurate evaluation of electrostatic contributions, The Journal of Physical Chemistry, vol.96, issue.15, pp.6428-6431, 1992. ,
DOI : 10.1021/j100194a060
Native-state conformational dynamics of GART: A regulatory pH-dependent coil-helix transition examined by electrostatic calculations, Protein Science, vol.31, issue.11, pp.2363-2378, 2001. ,
DOI : 10.1110/ps.17201
Revisited, The Journal of Physical Chemistry B, vol.101, issue.5, pp.825-836, 1997. ,
DOI : 10.1021/jp962478o
Roles of electrostatic interaction in proteins, Quarterly Reviews of Biophysics, vol.87, issue.01, pp.1-90, 1996. ,
DOI : 10.1002/bip.360210111
Calculating pKa values in enzyme active sites, Protein Science, vol.15, issue.9, pp.1894-1901, 2003. ,
DOI : 10.1110/ps.03114903
Dielectric Properties of Proteins from Simulation: The Effects of Solvent, Ligands, pH, and Temperature, Biophysical Journal, vol.80, issue.6, pp.2546-2555, 2001. ,
DOI : 10.1016/S0006-3495(01)76226-1
pKa calculations for class A beta-lactamases: methodological and mechanistic implications, Biophysical Journal, vol.73, issue.5, pp.2416-2426, 1997. ,
DOI : 10.1016/S0006-3495(97)78270-5
Implicit solvent models, Biophysical Chemistry, vol.78, issue.1-2, pp.1-20, 1999. ,
DOI : 10.1016/S0301-4622(98)00226-9
Electrostatic Contributions to Molecular Free Energies in Solution, Adv. Protein Chem, vol.51, pp.1-57, 1998. ,
DOI : 10.1016/S0065-3233(08)60650-6
What are the dielectric ?constants? of proteins and how to validate electrostatic models?, Proteins: Structure, Function, and Genetics, vol.89, issue.4, pp.400-417, 2001. ,
DOI : 10.1002/prot.1106
's of Ionizable Residues in Proteins:?? Semi-microscopic and Microscopic Approaches, The Journal of Physical Chemistry B, vol.101, issue.22, pp.4458-4472, 1997. ,
DOI : 10.1021/jp963412w
The Effect of Protein Relaxation on Charge-Charge Interactions and Dielectric Constants of Proteins, Biophysical Journal, vol.74, issue.4, pp.1744-1753, 1998. ,
DOI : 10.1016/S0006-3495(98)77885-3
Calculation of Electron Transfer Reorganization Energies Using the Finite Difference Poisson-Boltzmann Model, Biophysical Journal, vol.74, issue.3, pp.1241-1250, 1998. ,
DOI : 10.1016/S0006-3495(98)77838-5
Gaussian fluctuations and linear response in an electron transfer protein, Proc. Natl. Acad. Sci. USA, pp.6544-6549, 2002. ,
DOI : 10.1073/pnas.082657099
Electrostatics and dynamics of proteins, Reports on Progress in Physics, vol.66, issue.5, pp.737-787, 2003. ,
DOI : 10.1088/0034-4885/66/5/202
URL : https://hal.archives-ouvertes.fr/hal-00770715
A Poisson???Boltzmann Study of Charge Insertion in an Enzyme Active Site:?? The Effect of Dielectric Relaxation, The Journal of Physical Chemistry B, vol.103, issue.29, pp.6142-6156, 1999. ,
DOI : 10.1021/jp991354j
Solvation Free Energies Estimated from Macroscopic Continuum Theory: An Accuracy Assessment, The Journal of Physical Chemistry, vol.98, issue.17, pp.4683-4694, 1994. ,
DOI : 10.1021/j100068a033
Calculations with Explicit and Implicit Solvent Models, Journal of the American Chemical Society, vol.126, issue.13, pp.4167-4180, 2004. ,
DOI : 10.1021/ja039788m
URL : https://hal.archives-ouvertes.fr/hal-00770711
Internal and interfacial dielectric properties of cytochrome c from molecular dynamics simulations in aqueous solution, Proc. Natl. Acad. Sci. USA, pp.1082-1086, 1995. ,
Microscopic Dielectric Properties of Cytochrome c from Molecular Dynamics Simulations in Aqueous Solution, Journal of the American Chemical Society, vol.117, issue.30, 1995. ,
DOI : 10.1021/ja00135a018
Microscopic theory of the dielectric properties of proteins, Biophysical Journal, vol.59, issue.3, pp.670-690, 1991. ,
DOI : 10.1016/S0006-3495(91)82282-2
Dielectric properties of trypsin inhibitor and lysozyme calculated from molecular dynamics simulations, The Journal of Physical Chemistry, vol.97, issue.9, pp.2009-2014, 1993. ,
DOI : 10.1021/j100111a046
Dielectric asymmetry in the photosynthetic reaction center, Science, vol.264, pp.810-816, 1994. ,
Calculation of the dielectric permittivity profile for a nonuniform system: Application to a lipid bilayer simulation, The Journal of Chemical Physics, vol.118, issue.7, 2003. ,
DOI : 10.1063/1.1537244
Prediction of electrostatic effects of engineering of protein charges, Nature, vol.330, issue.6143, pp.86-88, 1987. ,
DOI : 10.1038/330086a0
pH-dependent Stability and Conformation of the Recombinant Human Prion Protein PrP(90-231), Journal of Biological Chemistry, vol.272, issue.44, pp.27517-27520, 1997. ,
DOI : 10.1074/jbc.272.44.27517
Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH, Journal of Molecular Biology, vol.275, issue.2, pp.295-308, 1998. ,
DOI : 10.1006/jmbi.1997.1418
Effects of buried ionizable amino acids on the reduction potential of recombinant myoglobin, Science, vol.243, issue.4887, pp.69-72, 1989. ,
DOI : 10.1126/science.2563171
Calculations of enzymic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes, Biochemistry, vol.20, issue.11, pp.3167-3177, 1981. ,
DOI : 10.1021/bi00514a028
What about protein polarity?, Nature, vol.330, issue.6143, pp.15-17, 1987. ,
DOI : 10.1038/330015a0
Calculations of electrostatic interactions in biological systems and in solutions, Quarterly Reviews of Biophysics, vol.8, issue.03, pp.283-422, 1985. ,
DOI : 10.1021/ja01051a002
Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability., Proc. Natl. Acad. Sci. USA, pp.4785-4789, 1984. ,
DOI : 10.1073/pnas.81.15.4785
Simplified methods for pKa and acid pH-dependent stability estimation in proteins: Removing dielectric and counterion boundaries, Protein Science, vol.267, issue.2, pp.418-425, 1999. ,
DOI : 10.1110/ps.8.2.418
Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme, Protein Science, vol.267, issue.10, pp.2793-2805, 2004. ,
DOI : 10.1110/ps.04785604
Calculation of the electric potential in the active site cleft due to ??-helix dipoles, Journal of Molecular Biology, vol.157, issue.4, pp.671-679, 1982. ,
DOI : 10.1016/0022-2836(82)90505-8
On the pH Dependence of Protein Stability, Journal of Molecular Biology, vol.231, issue.2, pp.459-474, 1993. ,
DOI : 10.1006/jmbi.1993.1294
Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility, Biophysical Journal, vol.69, issue.5, pp.1721-1733, 1995. ,
DOI : 10.1016/S0006-3495(95)80042-1