Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Zeng, Jun; Fridman, M.; Maruta, H.; Treutlein, Herbert R.; Simonson, T., Protein-protein recognition: an experimental and computational study of the R89K mutation in Raf and its effect on Ras binding, Prot. Sci. 1999, 8, 50-64.
Pezo, V.; Metzgar, D.; Hendrickson, T.L.; Waas, W.F.; D öring, V.; Marli ère, P.; Schim-mel, P.; de Cr écy-Lagard, V., Artificially ambiguous genetic code confers growth yield advantage, Proc. Natl Acad. Sci. USA 2004, 101, 8593-8597.
Xie, J.; Schultz, P.G., Adding amino acids to the genetic repertoire, Curr. Opin. Chem. Biol. 2005, 9, 548-554.
Strømgaard, A.; Jensen, A. A.; Strømgaard, K., Site-specific incorporation of unnatural amino acids into proteins, ChemBioChem 2004, 5, 909-916.
Archontis, G.; Simonson, T.; Moras, D.; Karplus, M., Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations, J. Mol. Biol. 1998, 275, 823-846.
Archontis, G.; Simonson, T.; Karplus, M., Binding free energies and free energy com-ponents from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase, J. Mol. Biol. 2001, 306, 307-327.
Thompson, Damien; Plateau, Pierre; Simonson, Thomas, Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase., ChemBioChem Feb 2006, 7, 337-344.
Simonson, T.; Archontis, G.; Karplus, M., Continuum treatment of long-range interac-tions in free energy calculations. Application to protein-ligand binding, J. Phys. Chem. B 1997, 101, 8349-8362.
Simonson, T., Electrostatic free energy calculations for macromolecules: a hybrid mole-cular dynamics/continuum electrostatics approach, J. Phys. Chem. B 2000, 104, 6509-6513.
Archer-Lahlou, E.; Tikhonova, I.; Escrieut, C.; Dufresne, M.; Seva, C.; Clerc, P.; Pradayrol, L.; Moroder, L.; Maigret, B.; Fourmy, D., Modeled structure of a G-protein-coupled receptor: the cholecystokinin-1 receptor, J. Med. Chem. 2005, 48, 180-191.
H énin, J.; Maigret, B.; Tarek, M.; Escrieut, C.; Fourmy, D.; Chipot, C., Probing a model of a GPCR/ligand complex in an explicit membrane environment. The human cholecystokinin-1 receptor, Biophys. J. 2006, 90, 1232-1240.
Noskov, S.Y.; Bern èche, S.; Roux, B., Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands, Nature 2001, 431, 830-834.
Dolenc, J.; Oostenbrink, C.; Koller, J.; van Gunsteren, W.F., Molecular dynamics simu-lations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site, Nucl. Acids Res. 2005, 33, 725-733.
Talhout, R.; Villa, A.; Mark, A.E.; Engeberts, J.B.F.N., Understanding binding affinity: a combined isothermal tritration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin, J. Am. Chem. Soc. 2003, 125, 10570-10579.
Guo, Z.Y.; Durkin, J.; Fischmann, T.; Ingram, R.; Prongay, A.; Zhang, R.M.; Madison, V., Application of the lambda-dynamics method to evaluate the relative binding free energies of inhibitors to HCV protease, J. Med. Chem. 2003, 46, 5360-5364.
Archontis, G.; Watson, K.A.; Xie, Q.; Andreou, G.; Chrysina, E.D.; S.E. Zographos; Oikonomakos, N.G.; Karplus, M., Glycogen phosphorylase inhibitors: a free energy perturbation analysis of glucopyranose spirohydantoin analogues, Proteins 2005, 61, 984-998.
Villa, A.; Zangi, R.; Pieffet, G.; Mark, A.E., Sampling and convergence in free energy calculations of protein-ligand interactions: the binding of triphenoxypyridine derivatives to Factor Xa and Trypsin, J. Comp. Aided. Mol. Des. 2003, 17, 673-686.
Gouda, H.; Kuntz, I.D.; Case, D.A.; Kollman, P.A., Free energy calculations for theo-phylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods, Biopolymers 2003, 68, 16-34.
Jorgensen, W. L., The many roles of computation in drug discovery, Science 2004, 303, 1813-1818.
Wong, C.F.; McCammon, J.A. Drug design. in Encyclopedia of Supramolecular Chem-istry, Atwood, J.; Steed, J., Eds. Marcel Dekker: New York, 2004.
Woo, H. J.; Roux, B., Calculation of absolute protein-ligand binding free energy from computer simulations, Proc. Natl Acad. Sci. USA 2005, 102, 6825-6830.
Izrailev, S.; Stepaniants, S.; Isralewitz, B.; Kosztin, D.; Lu, H.; Molnar, F.; Wriggers, W.; Schulten, K. Steered molecular dynamics. in Computational Molecular Dynamics: Challenges, Methods, Ideas, Deuflhard, P.; Hermans, J.; Leimkuhler, B.; Mark, A. E.; Skeel, R.; Reich, S., Eds., vol. 4, Lecture Notes in Computational Science and Engineering. Springer Verlag: Berlin, 1998, pp. 39-65.
Grubm üller, H.; Heymann, B.; Tavan, P., Ligand binding: molecular mechanics calcula-tion of the streptavidin-biotin rupture force, Science 1996, 271, 997-999.
Izrailev, S.; Stepaniants, S.; Balsera, M.; Oono, Y.; Biophysical, K. Schulten., Molec-ular dynamics study of unbinding of the avidin-biotin complex, Biophys. J. 1997, 72, 1568-1581.
Jorgensen, W. L.; Buckner, J. K.; Boudon, S.; Tirado-Rives, J., Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water, J. Chem. Phys. 1988, 89, 3742-3746.
Hermans, J.; Wang, L., Inclusion of loss of translational and rotational freedom in the-oretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme, J. Am. Chem. Soc. 1997, 119, 2707-2714.
Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A., The statistical-thermodynamic basis for computation of binding affinities: a critical review, Biophys. J. 1997, 72, 1047-1069.
Boresch, S.; Tettinger, F.; Karplus, M., Absolute binding free energies: a quantitative approach to their calculation, J. Phys. Chem. B 2003, 107, 9535-9551.
Tembe, B. L.; McCammon, J. A., Ligand-receptor interactions, Comp. Chem. 1984, 8, 281-283.
Hermans, J.; Shankar, S., The free energy of xenon binding to myoglobin from molecular-dynamics simulation, Isr. J. Chem. 1986, 27, 225-227.
Merz Jr., K. M., Carbon dioxide binding to human carbonic anhydrase II, J. Am. Chem. Soc. 1991, 113, 406-411.
Lee, F. S.; Warshel, A., A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations, J. Chem. Phys. 1992, 97, 3100-3107.
Miyamoto, S.; Kollman, P. A., What determines the strength of noncovalent association of ligands to proteins in aqueous solution ?, Proc. Natl Acad. Sci. USA 1993, 90, 8402-8406.
Miyamoto, S.; Kollman, P. A., Proteins: Structure, Function and Genetics 1993, 16, 226-245.
Weber, P. C.; Ohlendorf, D. H.; Wendoloski, J. J.; Salemme, F. R., Structural origins of high-affinity biotin binding to Streptavidin, Science 1989, 243, 85-88.
Dixit, S. B.; Chipot, C., Can absolute free energies of association be estimated from molecular mechanical simulations ? The biotin-streptavidin system revisited, J. Phys. Chem. A 2001, 105, 9795-9799.
Roux, B.; Nina, M.; Pom ès, R.; Smith, J. C., Thermodynamic stability of water mole-cules in the Bacteriorhodopsin proton channel: a molecular dynamics and free energy perturbation study, Biophys. J. 1996, 71, 670-681.
Swanson, J. M. J.; Henchman, R. H.; McCammon, J. A., Revisiting free energy calcu-lations: A theoretical connection to MM/PBSA and direct calculation of the association free energy, Biophys. J. 2004, 86, 67-74.
Hamelberg, D.; McCammon, J. A., Standard free energy of releasing a localized water molecule from the binding pockets of proteins: Double-decoupling method, J. Am. Chem. Soc. 2004, 126, 7683-7689.
Woo, H. J.; Dinner, A. R.; Roux, B., Grand canonical Monte Carlo simulations of water in protein environments, J. Chem. Phys. 2004, 121, 6392-6400.
Fersht, A., Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, Freeman: New York, 1999.
Pons, J.; Rajpal, A.; Kirsch, J.F., Energetic analysis of an antibody/antigen interface: alanine scanning mutagenesis and double mutant cycles on the HyHEL-10/lysozyme interaction, Prot. Sci. 1999, 8, 958-968.
Horovitz, A., Double-mutant cycles: a powerful tool for analyzing protein structure and function, Fold. Des. 1996, 1, R121-126.
Liu, S. Y.; Mark, A. E.; van Gunsteren, W. F., Estimating the relative free energy of different molecular states with respect to a single reference state, J. Phys. Chem. 1996, 9485-9494, 1749.
Gao, J.; Kuczera, K.; Tidor, B.; Karplus, M., Hidden thermodynamics of mutant pro-teins: A molecular dynamics analysis, Science 1989, 244, 1069-1072.
Simonson, T.; Br ünger, A. T., Thermodynamics of protein-peptide binding in the ribonuclease S system studied by molecular dynamics and free energy calculations., Biochemistry 1992, 31, 8661-8674.
Hodel, A.; Simonson, T.; Fox, R. O.; Br ünger, A. T., Conformational substates and uncertainty in macromolecular free energy calculations., J. Phys. Chem. 1993, 97, 3409-3417.
van Gunsteren, W. F.; Beutler, T. C.; Fraternali, F.; King, P. M.; Mark, A. E.; Smith, P. E. Computation of free energy in practice: Choice of approximations and accuracy limiting factors. in Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Van Gunsteren, W. F.; Weiner, P. K.; Wilkinson, A. J., Eds., vol. 2. Escom: The Netherlands, 1993, pp. 315-348.
Mark, A.; van Gunsteren, W.F., Decomposition of the free energy of a system in terms of specific interactions: implications for theoretical and experimental studies, J. Mol. Biol. 1994,240,167-176.
Boresch, S.; Archontis, G.; Karplus, M., Free energy simulations: the meaning of the individual contributions from a component analysis, Proteins: Structure, Function and Genetics 1994, 20, 25-33.
Archontis, G.; Simonson, T. Dielectric relaxation in an enzyme active site: molecular dynamics simulations intepreted with a macroscopic continuum model, J. Am. Chem. Soc. 2001, 123, 11047-11056.
Boresch, S.; Karplus, M., The meaning of component analysis: decomposition of the free energy in terms of specific interactions, J. Mol. Biol. 1995, 254, 801-807.
Pitera, J.W.; van Gunsteren, W.F., The importance of solute-solvent van der Waals in-teractions with interior atoms of biopolymers, J. Am. Chem. Soc. 2001, 123, 3163-3164.
H énin, J.; Pohorille, A.; Chipot, C., Insights into the recognition and association of trans-membrane α-helices. The free energy of α-helix dimerization in glycophorin A, J. Am. Chem. Soc. 2005, 127, 8478-8484.
Carlsson, J.; Aqvist, J., Absolute and relative entropies from computer simulation with applications to ligand binding, J. Phys. Chem. B 2005, 109, 6448-6456.
van den Bosch, M.; Swart, M.; Snijders, J.G.; Berensen, H.J.C.; Mark, A.E.; Oostenbrink, C.; van Gunsteren, W.F.; Canters, G.W., Calculation of the redox poten-tial of the protein azurin and some mutants, ChemBioChem 2005, 6, 738-746.
Sagui, C.; Darden, T., Molecular dynamics simulations of biomolecules: long-range electrostatic effects, Ann. Rev. Biophys. Biomol. Struct. 1999, 28, 155-179.
Aqvist, J.; Luzhkov, V., Ion permeation mechanism of the potassium channel, Nature 2000,404,881-884.
Florian, J.; Goodman, M.F.; Warshel, A., Free energy perturbation calculations of DNA destabilization by base substitutions: the effect of neutral guanine-thymine, adenine-cytosine and adenine-difluorotoluene mismatches, J. Phys. Chem. B 2000, 104, 10092-10099.
Stote, R.; States, D.; Karplus, M., On the treatment of electrostatic interactions in bio-molecular simulation, J. Chim. Phys. 1991, 88, 2419-2433.
Warshel, A., Energetics of enzyme catalysis, Proc. Natl Acad. Sci. USA 1978, 75, 5250.
Resat, H.; McCammon, J.A., Free energy simulations: correcting for electrostatic cutoffs by use of the Poisson equation, J. Chem. Phys. 1996, 104, 7645-7651.
Warshel, A., Computer Modelling of Chemical Reactions in Enzymes and Solutions, John Wiley: New York, 1991.
Beglov, D.; Roux, B., Finite representation of an infinite bulk system: solvent boundary potential for computer simulations, J. Chem. Phys. 1994, 100, 9050-9063.
Im, W.; Bern èche, S.; Roux, B., Generalized solvent boundary potential for computer simulations, J. Chem. Phys. 2001, 114, 2924-2937.
Banavali, N.K.; Im, W.; Roux, B., Electrostatic free energy calculations using the generalized solvent boundary potential method, J. Chem. Phys. 2002, 117, 7381-7388.
Valleau, J. P.; Card, D. N., Monte Carlo estimation of the free energy by multistage sampling, J. Chem. Phys. 1972, 57, 5457-5462.
Torrie, G. M.; Valleau, J. P., Nonphysical sampling distributions in Monte Carlo free energy estimation: umbrella sampling, J. Comput. Phys. 1977, 23, 187-199.
Patey, G. N.; Valleau, J. P., A Monte Carlo method for obtaining the interionic potential of mean force in ionic solution, J. Chem. Phys. 1975, 63, 2334-2339.
Pangali, C.; Rao, M.; Berne, B. J., A Monte Carlo simulation of the hydrophobic interaction, J. Chem. Phys. 1979, 71, 2975-2981.
Pratt, L. R.; Chandler, D., Theory of hydrophobic effect, J. Chem. Phys. 1977, 67, 3683-3704.
New, M. H.; Berne, B. J., Molecular Dynamics Calculation of the Effect of Solvent Polarizability on the Hydrophobic Interaction, J. Am. Chem. Soc. 1995, 117, 7172-7179.
Chipot, C.; Kollman, P. A.; Pearlman, D. A., Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions, J. Comput. Chem. 1996, 17, 1112-1131.
Jorgensen, W. L.; Severance, D. L., Aromatic-aromatic interactions: free energy profiles for the benzene dimer in water, chloroform and liquid benzene, J. Am. Chem. Soc. 1990, 112,4768-4774.
Duffy, E. M.; Kowalczyk, P. J.; Jorgensen, W. L., Do denaturants interact with aromatic hydrocarbons in water ?, J. Am. Chem. Soc. 1993, 115, 9271-9275.
Tobias, D. J.; Brooks III, C. L., Calculation of free energy surfaces using the methods of thermodynamic perturbation theory, Chem. Phys. Lett. 1987, 142, 472-476.
Pratt, L. R., Molecular theory of hydrophobic effects: “She is too mean to have her name repeated”, Annu. Rev. Phys. Chem. 2002, 53, 409-436.
Pratt, L. R.; Pohorille, A., Hydrophobic effects and modeling of biophysical aqueous solution interfaces, Chem. Rev. 2002, 102, 2671-2692.
Chipot, C.; Jaffe, R.; Maigret, B.; Pearlman, D. A.; Kollman, P. A., Benzene dimer: a good model for π-π interactions in proteins? A comparison between the benzene and the toluene dimers in the gas phase and in an aqueous solution, J. Am. Chem. Soc. 1996, 118,11217-11224.
Chipot, C.; Maigret, B.; Pearlman, D. A.; Kollman, P. A., Molecular dynamics potential of mean force calculations: a study of the toluene-ammonium π-cation interactions, J. Am. Chem. Soc. 1996, 118, 2998-3005.
Berkowitz, M.; Karim, O. A.; McCammon, J. A.; Rossky, P. J., Sodium chloride ion pair interaction in water: computer simulation, Chem. Phys. Lett. 1984, 105, 577-580.
Belch, A. C.; Berkowitz, M.; McCammon, J. A., Solvation structure of a sodium chloride ion pair in water, J. Am. Chem. Soc. 1986, 108, 1755-1761.
Dang, L. X.; Pettitt, B. M., Solvated chloride ions at contact, J. Chem. Phys. 1987, 86, 6560-6561.
Jorgensen, W. L.; Buckner, J. K.; Huston, S. E.; Rossky, P. J., Hydration and energetics for tert-butyl chloride ion pairs in aqueous solution, J. Am. Chem. Soc. 1987, 109, 1891-1899.
Hummer, G.; Soumpasis, D. M.; Neumann, M., Computer simulations do not support Cl-Cl pairing in aqueous NaCl solution, Mol. Phys. 1993, 81, 1155-1163.
Rozanska, X.; Chipot, C., Modeling ion-ion interaction in proteins: a molecular dynam-ics free energy calculation of the guanidinium-acetate association, J. Chem. Phys. 2000, 112,9691-9694.
Straatsma, T. P.; Berendsen, H. J. C.; Postma, J. P. M., J. Chem. Phys. 1986, 85, 6720.
Kollman, P. A., Free energy calculations: applications to chemical and biochemical phenomena, Chem. Rev. 1993, 93, 2395-2417.
Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and compu-tational approaches to estimate solubility and permeability in drug discovery and devel-opment settings, Adv. Drug Deliv. Rev. 1997, 23, 3-25.
Hermans, J.; Pathiaseril, A.; Anderson, A., Excess free-energy of liquids from molecular-dynamics simulations — application to water models, J. Am. Chem. Soc. 1988,110,5982-5986.
Kaminski, G.; Duffy, E. M.; Matsui, T.; Jorgensen, W. L., Free-energies of hydration and pure liquid properties of hydrocarbons from the OPLS all-atom model, J. Phys. Chem. 1994,98,13077-13082.
Jorgensen, W. L.; Tirado-Rives, J., Free energies of hydration for organic molecules from Monte Carlo simulations, Perspectives in Drug Discovery and Design 1995, 3, 123-138.
Jorgensen, W. L.; Laird, E. R.; Nguyen, T. B.; Tirado-Rives, J., Monte Carlo simulations of pure liquid substituted Benzenes with OPLS potential functions, J. Comput. Chem. 1993,14,206-215.
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P. A., Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of sol-vation, J. Am. Chem. Soc. 1993, 115, 9620-9631.
Chipot, C., Rational determination of charge distributions for free energy calculations, J. Comput. Chem. 2003, 24, 409-415.
Udier-Blagovic, M.; De Tirado, P. M.; Pearlman, S. A.; Jorgensen, W. L., Accuracy of free energies of hydration using CM1 and CM3 atomic charges, J. Comput. Chem. 2004, 25,1322-1332.
Daura, X.; Mark, A. E.; van Gunsteren, W. F., Parametrization of aliphatic CHn united atoms of GROMOS96 force field, J. Comput. Chem. 1998, 19, 535-547.
Daura, X.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E., Reversible peptide folding in solution by molecular dynamics simulation, J. Mol. Biol. 1998, 280, 925-932.
Villa, A.; Mark, A. E., Calculation of the free energy of solvation for neutral analogs of amino acid side chains, J. Comput. Chem. 2002, 23, 548-553.
Maccallum, J. L.; Tieleman, D. P., Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field, J. Comput. Chem. 2003, 24, 1930-1935.
Shirts, M.; Pitera, J.; Swope, W.; Pande, V., Extremely precise free energy calculations of amino acid chain analogs: comparison of common molecular mechanical force fields for proteins, J. Chem. Phys. 2003, 119, 5740-5761.
MacKerell Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prod-hom, B.; Reiher III, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wi órkiewicz-Kuczera, J.; Yin, D.; Karplus, M., All-atom empirical potential for molecular modeling and dynamics studies of proteins, J. Phys. Chem. B 1998,102,3586-3616.
Oostenbrink, C.; Villa, A.; Mark, A. E; van Gunsteren, W. F., A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6., J. Comput. Chem. Oct 2004, 25, 1656-1676.
Shirts, M. R.; Pande, V. S., Solvation free energies of amino acid side chain analogs for common molecular mechanics water models, J. Chem. Phys. 2005, 122, 134508.
Rao, B. G.; Singh, U. C., Hydrophobic hydration: a free energy perturbation study J. Am. Chem. Soc. 1989, 111, 3125-3133.
Morgantini, P. Y.; Kollman, P. A., Solvation free-energies of amides and amines — Disagreement between free-energy calculations and experiment, J. Am. Chem. Soc. 1995, 117,6057-6063.
Ding, Y. B.; Bernardo, D. N.; Kroghjespersen, K.; Levy, R. M., Solvation free-energies of small amides and amines from molecular-dynamics free-energy perturbation simulations using pairwise additive and many-body polarizable potentials, J. Phys. Chem. 1995,99,11575-11583.
Meng, E. C.; Caldwell, J. W.; Kollman, P. A., Investigating the anomalous solvation free energies of amines with a polarizable potential, J. Phys. Chem. 1996, 100, 2367-2371.
Rizzo, R. C.; Jorgensen, W. L., OPLS all-atom model for amines: resolution of the amine hydration problem, J. Am. Chem. Soc. 1999, 121, 4827-4836.
Oostenbrink, C.; van Gunsteren, W. F., Free energies of ligand binding for structurally diverse compounds, Proc. Natl Acad. Sci. USA 2005, 102, 6750-6754.
Jorgensen, W. L.; Briggs, J. M.; Contreras, M. L., Relative partition coefficients for organic solutes from fluid simulations, J. Phys. Chem. 1990, 94, 1683-1686.
Essex, J. W.; Reynolds, C. A.; Richards, W. G., Theoretical determination of partition coefficients, J. Am. Chem. Soc. 1992, 114, 3634-3639.
Orozco, M.; Colominas, C.; Luque, F. J., Theoretical determination of the solvation free energy in water and chloroform of the nucleic acid bases, Chem. Phys. 1996, 9, 209-678.
Best, S. A.; Merz Jr., K. M.; Reynolds, C. H., Free energy perturbation study of octanol/water partition coefficients: Comparison with continuum GB/SA calculations, J. Phys. Chem. B 1999, 103, 714-726.
Bas, D.; Dorison-Duval, D.; Moreau, S.; Bruneau, P.; Chipot, C., Rational determination of transfer free energies of small drugs across the water-oil interface, J. Med. Chem. 2002,45,151-159.
Hicks, J. M.; Kemnitz, K.; Eisenthal, K. B.; Heinz, T. F., Studies of liquid surfaces by second harmonic generation, J. Phys. Chem. 1986, 90, 560-562.
Eisenthal, K. B., Liquid interfaces, Acc. Chem. Res. 1993, 26, 636-643.
Pohorille, A.; Benjamin, I., Molecular dynamics of phenol at the liquid-vapor interface of water, J. Chem. Phys. 1991, 94, 5599-5605.
Alper, H. E.; Stouch, T. R., Orientation and diffusion of a drug analogue in biomem-branes: molecular dynamics simulations, J. Phys. Chem. 1995, 99, 5724-5731.
Bassolino-Klimas, D.; Alper, H. E.; Stouch, T. R., Drug-membrane interactions studied by molecular dynamics simulation: size dependence of diffusion, Drug Des. Discov. 1996,13,135-141.
Tu, K.; Klein, M.; Tobias, D. J., Constant-pressure molecular dynamics investigations of cholesterol effects in a dipalmitoylphosphatidylcholine bilayer, Biophys. J. 1998, 75, 2147-2156.
Koubi, L.; Tarek, M.; Klein, M. L.; Scharf, D., Distribution of halothane in a dipalmitoylphosphatidylcholine bilayer from molecular dynamics calculations, Biophys. J. 2000, 78, 800-811.
Pohorille, A.; Chipot, C.; New, M.; Wilson, M. A. Molecular modeling of protocellular functions, in Pacific Symposium on Biocomputing ’96, Hunter, L.; Klein, T. E., Eds. World Scientific: Singapore, 1996, pp. 550-569.
Overton, E., Studien über die Narkose zugleich ein Betrag zur allgemeinen Pharmakologie, Verlag von Gustav Fischer: Jena, 1901.
Pohorille, A.; Wilson, M.A.; New, M.H.; Chipot, C., Concentrations of anesthetics across the water-membrane interface; the Meyer-Overton hypothesis revisited, Toxicology Lett. 1998, 100, 421-430.
Wilson, M. A.; Pohorille, A., Mechanism of unassisted ion transport across membrane bilayers, J. Am. Chem. Soc. 1996, 118, 6580-6587.
. Pohorille, A. Private communication, 1999.
Tieleman, D. P.; Berendsen, H. J. C.; Samson, M. S. P., Voltage-dependent insertion of alamethicin at phospholipid/water and octane/water, Biophys. J. 2001, 80, 331-346.
Roux, B., Theoretical and computational models of ion channels, Curr. Opin. Struct. Biol. 2002, 12, 182-189.
Chakrabarti, N.; Tajkhorshid, E.; Roux, B.; Pom ès, R., Molecular basis of proton block-age in aquaporins, Structure 2004, 12, 65-74.
Wang, Y.; Schulten, K.; Tajkhorshid, E., What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF, Structure 2005, 13, 1107-1118.
Bern èche, S.; Roux, B., Energetics of ion conduction through the K+ channel, Nature 2001,414,73-77.
Allen, T.W.; Andersen, O.S.; Roux, B., Energetics of ion conduction through the gramicidin channel, Proc. Natl Acad. Sci. USA 2004, 101, 117-122.
Burykin, A.; Kato, M.; Warshel, A., Exploring the origin of the ion selectivity of the KcsA potassium channel, Proteins 2003, 52, 412-426.
Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex, Science 1987, 235,574-576.
Dang, L. X.; Merz, K. M.; Kollman, P. A., Free-energy calculations on protein stability - Thr157 -Val157 Mutation of T4 lysozyme, J. Am. Chem. Soc. 1989, 111, 8505-8508.
Shi, Y. Y.; Mark, A. E.; Wang, C. X.; Huang, F. H.; Berendsen, H. J. C.; van Gunsteren, W. F., Can the stability of protein mutants be predicted by free-energy calculations, Prot. Eng. 1993, 6, 289-295.
Pan, Y. P.; Daggett, V., Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor. 2: Free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding, Biochemistry 2001, 40, 2723-2731.
Hodel, A.; Rice, L. M.; Simonson, T.; Fox, R. O.; Br ünger, A. T., Proline cis -trans isomerization in staphylococcal nuclease — multi-substate free-energy perturbation calculations, Prot. Sci. 1995, 4, 636-654.
Tidor, B., Helix-capping interaction in λ-Cro protein — a free-energy simulation analysis, Proteins: Struct. Func. Genet. 1994, 19, 310-323.
Simonson, T.; Archontis, G.; Karplus, M., Free energy simulations come of age: protein-ligand recognition, Acc. Chem. Res. 2002, 35, 430-437.
Prevost, M.; Wodak, S. J.; Tidor, B.; Karplus, M., Contribution of the hydrophobic effect to protein stability — analysis based on simulations of the Ile-96- Ala mutation in barnase, Proc. Natl Acad. Sci. USA 1991, 88, 10880-10884.
Sun, Y. C.; Veenstra, D. L.; Kollman, P. A., Free energy calculations of the mutation of Ile96 → Ala in barnase: contributions to the difference in stability, Prot. Eng. 1996, 9, 273-281.
Warshel, A.; Sussman, F.; King, G., Free energy changes in solvated proteins: micro-scopic calculations using a reversible charging process, Biochemistry 1986, 25, 8368-8372.
B örjesson, Ulf; H ünenberger, Philippe H., Explicit-solvent molecular dynamics simulation at constant pH: methodology and application to small amines, J. Chem. Phys. 2001, 114,9706-9719.
Mongan, J.; Case, D.A.; McCammon, J.A., Constant pH molecular dynamics in generalized Born implicit solvent, J. Comp. Chem. 2004, 25, 2038-2048.
Lee, M.S.; Salsbury Jr., F.R.; Brooks III, C.L., Constant pH molecular dynamics using continuous titration coordinates, Proteins 2004, 56, 738-752.
Simonson, T., Electrostatics and dynamics of proteins, Rep. Prog. Phys. 2003, 66, 737-787.
Ichiye, T. Simulating redox proteins. in Computational Biochemistry & Biophysics, Becker, O.; Mackerell Jr., A.; Roux, B.; Watanabe, M., Eds. Marcel Dekker: New York, 2001.
Simonson, T., Gaussian fluctuations and linear response in an electron transfer protein, Proc. Natl Acad. Sci. USA 2002, 99, 6544-6549.
Sterpone, F.; Ceccarelli, M.; Marchi, M., Linear response and electron transfer in complex biomolecular systems and a reaction center protein, J. Phys. Chem. B 2003, 107, 11208-11215.
Tan, M.L.; Dolan, E.A.; Ichiye, T., Understanding intramolecular electron transfer in ferredoxin: a molecular dynamics study, J. Phys. Chem. B 2004, 108, 20435-20441.
Warshel, A.; Chu, Z.T.; Parson, W.W., Dispersed polaron simulations of electron transfer in photosynthetic reaction centers, Science 1989, 246, 112-116.
Li, G.H.; Zhang, X.D.; Cui, Q., Free energy perturbation calculations with combined QM/MM. Potential complications, simplifications, and applications to redox potential calculations, J. Phys. Chem. B 2003, 107, 8643-8653.
Hummer, G.; Pratt, L.; Garcia, A. E., Free energy of ionic hydration, J. Phys. Chem. 1996,100,1206-1215.
Simonson, T.; Carlsson, J.; Case, D. A., Proton binding to proteins: pKa calculations with explicit and implicit solvent models, J. Am. Chem. Soc. 2004, 126, 4167-4180.
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz Jr., K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. C.; Kollman, P. A., A second generation force field for the simulation of proteins, nucleic acids, and organic molecules, J. Am. Chem. Soc. 1995, 117, 5179-5197.
Garcia-Viloca, M.; Gao, J.; Karplus, M.; Truhlar, D.G., How enzymes work: analysis by modern reaction rate theory and computer simulations, Science 2004, 303, 186-195.
Mulholland, A., Modelling enzyme reaction mechanisms, specificity and catalysis, Drug Disc. Today 2005, 10, 1393-13402.
Maupin, C. M.; Wong, K. F.; Soudackov, A. V.; Kim, S.; Voth, G. A., A multistate empirical valence bond description of protonatable amino acids, J. Phys. Chem. A 2006, 110,631-639.
Xu, J.; Voth, G. A., Computer simulation of explicit proton translocation in cytochrome c oxidase: the D-pathway, Proc. Natl Acad. Sci. U S A 2005, 102, 6795-6800.
Xu, J.; Voth, G. A., Free energy profiles for H+ conduction in the D-pathway of Cytochrome c oxidase: a study of the wild type and N98D mutant enzymes, Biochim. Biophys. Acta 2006, 1757, 852-859.
Voth, G. A., Computer simulation of proton solvation and transport in aqueous and biomolecular systems, Acc. Chem. Res. 2006, 39, 143-150.
Lyne, P. Mixed quantum/classical methods. in Computational Biochemistry & Biophysics, Becker, O.; Mackerell Jr., A.; Roux, B.; Watanabe, M., Eds. , N.Y., New York, 2001.
Ridder, L.; Rietjens, I.M.; Vervoort, J.A.; Mulholland, A., Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9,10-oxide, J. Am. Chem. Soc. 2002, 123, 9926-9936.
Cummins, P.L.; Gready, J.E., Computational methods for the study of enzymic reac-tion mechanisms III: a perturbation plus QM/MM approach for calculating relative free energies of protonation, J. Comp. Chem. 2005, 26, 561-568.
Gumbart, J.; Wang, Y.; Aksimentiev, A.; Tajkhorshid, E.; Schulten, K., Molecular dynamics simulations of proteins in lipid bilayers, Curr. Opin. Struct. Biol. Aug 2005, 15, 423-431.
Tajkhorshid, E.; Nollert, P.; Jensen, M. Ø.; Miercke, L. J. W.; O’Connell, J.; Stroud, R. M.; Schulten, K., Control of the selectivity of the aquaporin water channel family by global orientational tuning, Science 2002, 296, 525-530.
Roux, B., The art of dissecting the function of a potassium channel, Neuron Sep 2005, 47,777-778.
Roux, B., Ion conduction and selectivity in K+ channels, Annu. Rev. Biophys. Biomol. Struct. 2005, 34, 153-171.
Bohannon, John, Distributed computing. Grassroots supercomputing., Science May 2005,308,810-813.
Shirts, M.; Pande, V., Screen savers of the world unite!, Science 2000, 290, 1903-1904.
Shirts, M. R.; Pande, V. S., Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration, J. Chem. Phys. Apr 2005, 122, 144107.
Shea, J. E.; Brooks III, C. L., From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding, Annu. Rev. Phys. Chem. 2001, 52, 499-535.
Ferrenberg, A. M.; Swendsen, R. H., Optimized Monte Carlo data analysis, Phys. Rev. Lett. 1989, 63, 1195-1198.
Boczko, E.M.; Brooks III, C.L., First-principles calculation of the folding free energy of a three-helix bundle protein, Science 1995, 269, 393-396.
Sheinerman, F. B.; Brooks, C. L., Calculations on folding of segment B1 of streptococcal protein G., J. Mol. Biol. May 1998, 278, 439-456.
Sheinerman, F. B.; Brooks, C. L., Molecular picture of folding of a small alpha/beta protein., Proc. Natl Acad. Sci. USA Feb 1998, 95, 1562-1567.
Shea, J. E.; Onuchic, J. N.; III, C. L. Brooks, Probing the folding free energy landscape of the Src-SH3 protein domain, Proc. Natl Acad. Sci. USA Dec 2002, 99, 16064-16068.
Mitsutake, A.; Sugita, Y.; Okamoto, Y., Generalized-ensemble algorithms for molecular simulations of biopolymers, Biopolymers 2001, 60, 96-123.
Sugita, Y.; Okamoto, Y., Replica-exchange molecular dynamics method for protein folding, Chem. Phys. Lett. 1999, 314, 141-151.
Sanbonmatsu, K. Y.; García, A. E., Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics, Prot. Struct. Function Genetics Feb 2002,46,225-234.
Zhou, F. X.; Berne, B. J.; Germain, R., The free energy landscape of β hairpin folding in explicit water, Proc. Natl Acad. Sci. USA 2001, 98, 14931-14936.
Rhee, Y. M.; Pande, V. S., Multiplexed-replica exchange molecular dynamics method for protein folding simulation, Biophys. J. 2003, 84, 775-786.
Nymeyer, H.; García, A. E., Simulation of the folding equilibrium of α-helical peptides: a comparison of the generalized Born approximation with explicit solvent, Proc. Natl Acad. Sci. USA. Nov 2003, 100, 13934-13939.
García, A. E.; Sanbonmatsu, K. Y., Exploring the energy landscape of a beta hairpin in explicit solvent., Proteins 2001, 42, 345-354.
Lifson, S.; Roig, A., Theory of helix-coil transition in polypeptides, J. Chem. Phys. 1961,34,1963-1974.
Qian, H.; Schellman, J.A., Helix-coil theories: a comparative study for finite length polypeptides, J. Phys. Chem. 1992, 96, 3987-3994.
Vila, J. A.; Ripoll, D. R.; Scheraga, H. A., Physical reasons for the unusual α-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides, Proc. Natl Acad. Sci. USA 2000, 97, 13075-13079.
Wu, X.; Wang, S., Helix folding of an alanine-based peptide in explicit water, J. Phys. Chem. B 2001, 105, 2227-2235.
Sugita, A. Kitao; Okamoto, Y., Multidimensional replica-exchange method for free-energy calculations, J. Chem. Phys. 2000, 113, 6042-6051.
Fukunishi, O. Watanabe; Takada, S., On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction, J. Chem. Phys. 2002, 116, 9058-9067.
Jang, S. Shin; Pak, Y., Replica-exchange method using the generalized effective potentia, Phys. Rev. Lett. 2003, 91, 058305-4.
Singhal, N.; Snow, C. D.; Pande, V. S., Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin, J. Chem. Phys. Jul 2004, 121, 415-425.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Chipot, C., Mark, A.E., Pande, V.S., Simonson, T. (2007). Applications of Free Energy Calculations to Chemistry and Biology. In: Chipot, C., Pohorille, A. (eds) Free Energy Calculations. Springer Series in CHEMICAL PHYSICS, vol 86. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-38448-9_13
Download citation
DOI: https://doi.org/10.1007/978-3-540-38448-9_13
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-38447-2
Online ISBN: 978-3-540-38448-9
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)