Skip to main content

Applications of Free Energy Calculations to Chemistry and Biology

  • Chapter
Free Energy Calculations

Part of the book series: Springer Series in CHEMICAL PHYSICS ((CHEMICAL,volume 86))

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 299.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 379.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 379.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 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.

    CAS  Google Scholar 

  2. 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.

    CAS  Google Scholar 

  3. Xie, J.; Schultz, P.G., Adding amino acids to the genetic repertoire, Curr. Opin. Chem. Biol. 2005, 9, 548-554.

    CAS  Google Scholar 

  4. Strømgaard, A.; Jensen, A. A.; Strømgaard, K., Site-specific incorporation of unnatural amino acids into proteins, ChemBioChem 2004, 5, 909-916.

    Google Scholar 

  5. 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.

    CAS  Google Scholar 

  6. 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.

    CAS  Google Scholar 

  7. 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.

    CAS  Google Scholar 

  8. 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.

    Google Scholar 

  9. Simonson, T., Electrostatic free energy calculations for macromolecules: a hybrid mole-cular dynamics/continuum electrostatics approach, J. Phys. Chem. B 2000, 104, 6509-6513.

    CAS  Google Scholar 

  10. 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.

    CAS  Google Scholar 

  11. 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.

    Google Scholar 

  12. 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.

    Google Scholar 

  13. 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.

    CAS  Google Scholar 

  14. 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.

    CAS  Google Scholar 

  15. 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.

    CAS  Google Scholar 

  16. 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.

    CAS  Google Scholar 

  17. 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.

    CAS  Google Scholar 

  18. 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.

    CAS  Google Scholar 

  19. Jorgensen, W. L., The many roles of computation in drug discovery, Science 2004, 303, 1813-1818.

    CAS  Google Scholar 

  20. Wong, C.F.; McCammon, J.A. Drug design. in Encyclopedia of Supramolecular Chem-istry, Atwood, J.; Steed, J., Eds. Marcel Dekker: New York, 2004.

    Google Scholar 

  21. 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.

    CAS  Google Scholar 

  22. 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.

    Google Scholar 

  23. Grubm üller, H.; Heymann, B.; Tavan, P., Ligand binding: molecular mechanics calcula-tion of the streptavidin-biotin rupture force, Science 1996, 271, 997-999.

    Google Scholar 

  24. 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.

    CAS  Google Scholar 

  25. 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.

    CAS  Google Scholar 

  26. 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.

    CAS  Google Scholar 

  27. 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.

    CAS  Google Scholar 

  28. Boresch, S.; Tettinger, F.; Karplus, M., Absolute binding free energies: a quantitative approach to their calculation, J. Phys. Chem. B 2003, 107, 9535-9551.

    CAS  Google Scholar 

  29. Tembe, B. L.; McCammon, J. A., Ligand-receptor interactions, Comp. Chem. 1984, 8, 281-283.

    CAS  Google Scholar 

  30. Hermans, J.; Shankar, S., The free energy of xenon binding to myoglobin from molecular-dynamics simulation, Isr. J. Chem. 1986, 27, 225-227.

    CAS  Google Scholar 

  31. Merz Jr., K. M., Carbon dioxide binding to human carbonic anhydrase II, J. Am. Chem. Soc. 1991, 113, 406-411.

    CAS  Google Scholar 

  32. 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.

    CAS  Google Scholar 

  33. 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.

    CAS  Google Scholar 

  34. Miyamoto, S.; Kollman, P. A., Proteins: Structure, Function and Genetics 1993, 16, 226-245.

    CAS  Google Scholar 

  35. 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.

    CAS  Google Scholar 

  36. 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.

    CAS  Google Scholar 

  37. 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.

    CAS  Google Scholar 

  38. 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.

    CAS  Google Scholar 

  39. 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.

    CAS  Google Scholar 

  40. 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.

    CAS  Google Scholar 

  41. Fersht, A., Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, Freeman: New York, 1999.

    Google Scholar 

  42. 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.

    CAS  Google Scholar 

  43. Horovitz, A., Double-mutant cycles: a powerful tool for analyzing protein structure and function, Fold. Des. 1996, 1, R121-126.

    CAS  Google Scholar 

  44. 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.

    Google Scholar 

  45. Gao, J.; Kuczera, K.; Tidor, B.; Karplus, M., Hidden thermodynamics of mutant pro-teins: A molecular dynamics analysis, Science 1989, 244, 1069-1072.

    CAS  Google Scholar 

  46. 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.

    CAS  Google Scholar 

  47. 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.

    CAS  Google Scholar 

  48. 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.

    Google Scholar 

  49. 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.

    CAS  Google Scholar 

  50. 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.

    CAS  Google Scholar 

  51. 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.

    CAS  Google Scholar 

  52. 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.

    CAS  Google Scholar 

  53. 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.

    CAS  Google Scholar 

  54. 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.

    Google Scholar 

  55. Carlsson, J.; Aqvist, J., Absolute and relative entropies from computer simulation with applications to ligand binding, J. Phys. Chem. B 2005, 109, 6448-6456.

    CAS  Google Scholar 

  56. 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.

    CAS  Google Scholar 

  57. Sagui, C.; Darden, T., Molecular dynamics simulations of biomolecules: long-range electrostatic effects, Ann. Rev. Biophys. Biomol. Struct. 1999, 28, 155-179.

    CAS  Google Scholar 

  58. Aqvist, J.; Luzhkov, V., Ion permeation mechanism of the potassium channel, Nature 2000,404,881-884.

    CAS  Google Scholar 

  59. 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.

    CAS  Google Scholar 

  60. Stote, R.; States, D.; Karplus, M., On the treatment of electrostatic interactions in bio-molecular simulation, J. Chim. Phys. 1991, 88, 2419-2433.

    CAS  Google Scholar 

  61. Warshel, A., Energetics of enzyme catalysis, Proc. Natl Acad. Sci. USA 1978, 75, 5250.

    CAS  Google Scholar 

  62. 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.

    CAS  Google Scholar 

  63. Warshel, A., Computer Modelling of Chemical Reactions in Enzymes and Solutions, John Wiley: New York, 1991.

    Google Scholar 

  64. Beglov, D.; Roux, B., Finite representation of an infinite bulk system: solvent boundary potential for computer simulations, J. Chem. Phys. 1994, 100, 9050-9063.

    CAS  Google Scholar 

  65. Im, W.; Bern èche, S.; Roux, B., Generalized solvent boundary potential for computer simulations, J. Chem. Phys. 2001, 114, 2924-2937.

    CAS  Google Scholar 

  66. 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.

    CAS  Google Scholar 

  67. Valleau, J. P.; Card, D. N., Monte Carlo estimation of the free energy by multistage sampling, J. Chem. Phys. 1972, 57, 5457-5462.

    CAS  Google Scholar 

  68. Torrie, G. M.; Valleau, J. P., Nonphysical sampling distributions in Monte Carlo free energy estimation: umbrella sampling, J. Comput. Phys. 1977, 23, 187-199.

    Google Scholar 

  69. 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.

    CAS  Google Scholar 

  70. Pangali, C.; Rao, M.; Berne, B. J., A Monte Carlo simulation of the hydrophobic interaction, J. Chem. Phys. 1979, 71, 2975-2981.

    CAS  Google Scholar 

  71. Pratt, L. R.; Chandler, D., Theory of hydrophobic effect, J. Chem. Phys. 1977, 67, 3683-3704.

    CAS  Google Scholar 

  72. 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.

    CAS  Google Scholar 

  73. 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.

    CAS  Google Scholar 

  74. 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.

    CAS  Google Scholar 

  75. 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.

    CAS  Google Scholar 

  76. 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.

    CAS  Google Scholar 

  77. 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.

    CAS  Google Scholar 

  78. Pratt, L. R.; Pohorille, A., Hydrophobic effects and modeling of biophysical aqueous solution interfaces, Chem. Rev. 2002, 102, 2671-2692.

    CAS  Google Scholar 

  79. 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.

    CAS  Google Scholar 

  80. 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.

    CAS  Google Scholar 

  81. 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.

    CAS  Google Scholar 

  82. 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.

    CAS  Google Scholar 

  83. Dang, L. X.; Pettitt, B. M., Solvated chloride ions at contact, J. Chem. Phys. 1987, 86, 6560-6561.

    CAS  Google Scholar 

  84. 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.

    CAS  Google Scholar 

  85. 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.

    Google Scholar 

  86. 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.

    CAS  Google Scholar 

  87. Straatsma, T. P.; Berendsen, H. J. C.; Postma, J. P. M., J. Chem. Phys. 1986, 85, 6720.

    CAS  Google Scholar 

  88. Kollman, P. A., Free energy calculations: applications to chemical and biochemical phenomena, Chem. Rev. 1993, 93, 2395-2417.

    CAS  Google Scholar 

  89. 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.

    CAS  Google Scholar 

  90. 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.

    CAS  Google Scholar 

  91. 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.

    CAS  Google Scholar 

  92. 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.

    CAS  Google Scholar 

  93. 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.

    CAS  Google Scholar 

  94. 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.

    CAS  Google Scholar 

  95. Chipot, C., Rational determination of charge distributions for free energy calculations, J. Comput. Chem. 2003, 24, 409-415.

    CAS  Google Scholar 

  96. 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.

    CAS  Google Scholar 

  97. 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.

    CAS  Google Scholar 

  98. 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.

    CAS  Google Scholar 

  99. 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.

    CAS  Google Scholar 

  100. 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.

    CAS  Google Scholar 

  101. 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.

    CAS  Google Scholar 

  102. 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.

    CAS  Google Scholar 

  103. 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.

    CAS  Google Scholar 

  104. 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.

    Google Scholar 

  105. Rao, B. G.; Singh, U. C., Hydrophobic hydration: a free energy perturbation study J. Am. Chem. Soc. 1989, 111, 3125-3133.

    CAS  Google Scholar 

  106. 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.

    CAS  Google Scholar 

  107. 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.

    CAS  Google Scholar 

  108. 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.

    CAS  Google Scholar 

  109. 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.

    CAS  Google Scholar 

  110. Oostenbrink, C.; van Gunsteren, W. F., Free energies of ligand binding for structurally diverse compounds, Proc. Natl Acad. Sci. USA 2005, 102, 6750-6754.

    CAS  Google Scholar 

  111. 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.

    CAS  Google Scholar 

  112. Essex, J. W.; Reynolds, C. A.; Richards, W. G., Theoretical determination of partition coefficients, J. Am. Chem. Soc. 1992, 114, 3634-3639.

    CAS  Google Scholar 

  113. 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.

    Google Scholar 

  114. 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.

    CAS  Google Scholar 

  115. 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.

    CAS  Google Scholar 

  116. 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.

    CAS  Google Scholar 

  117. Eisenthal, K. B., Liquid interfaces, Acc. Chem. Res. 1993, 26, 636-643.

    CAS  Google Scholar 

  118. Pohorille, A.; Benjamin, I., Molecular dynamics of phenol at the liquid-vapor interface of water, J. Chem. Phys. 1991, 94, 5599-5605.

    CAS  Google Scholar 

  119. 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.

    CAS  Google Scholar 

  120. 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.

    Google Scholar 

  121. 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.

    CAS  Google Scholar 

  122. 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.

    CAS  Google Scholar 

  123. 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.

    Google Scholar 

  124. Overton, E., Studien über die Narkose zugleich ein Betrag zur allgemeinen Pharmakologie, Verlag von Gustav Fischer: Jena, 1901.

    Google Scholar 

  125. 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.

    Google Scholar 

  126. Wilson, M. A.; Pohorille, A., Mechanism of unassisted ion transport across membrane bilayers, J. Am. Chem. Soc. 1996, 118, 6580-6587.

    CAS  Google Scholar 

  127. . Pohorille, A. Private communication, 1999.

    Google Scholar 

  128. 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.

    CAS  Google Scholar 

  129. Roux, B., Theoretical and computational models of ion channels, Curr. Opin. Struct. Biol. 2002, 12, 182-189.

    CAS  Google Scholar 

  130. Chakrabarti, N.; Tajkhorshid, E.; Roux, B.; Pom ès, R., Molecular basis of proton block-age in aquaporins, Structure 2004, 12, 65-74.

    CAS  Google Scholar 

  131. 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.

    CAS  Google Scholar 

  132. Bern èche, S.; Roux, B., Energetics of ion conduction through the K+ channel, Nature 2001,414,73-77.

    Google Scholar 

  133. 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.

    CAS  Google Scholar 

  134. Burykin, A.; Kato, M.; Warshel, A., Exploring the origin of the ion selectivity of the KcsA potassium channel, Proteins 2003, 52, 412-426.

    CAS  Google Scholar 

  135. 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.

    CAS  Google Scholar 

  136. 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.

    CAS  Google Scholar 

  137. 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.

    CAS  Google Scholar 

  138. 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.

    CAS  Google Scholar 

  139. 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.

    CAS  Google Scholar 

  140. Tidor, B., Helix-capping interaction in λ-Cro protein — a free-energy simulation analysis, Proteins: Struct. Func. Genet. 1994, 19, 310-323.

    CAS  Google Scholar 

  141. Simonson, T.; Archontis, G.; Karplus, M., Free energy simulations come of age: protein-ligand recognition, Acc. Chem. Res. 2002, 35, 430-437.

    CAS  Google Scholar 

  142. 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.

    CAS  Google Scholar 

  143. 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.

    CAS  Google Scholar 

  144. 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.

    CAS  Google Scholar 

  145. 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.

    Google Scholar 

  146. Mongan, J.; Case, D.A.; McCammon, J.A., Constant pH molecular dynamics in generalized Born implicit solvent, J. Comp. Chem. 2004, 25, 2038-2048.

    CAS  Google Scholar 

  147. Lee, M.S.; Salsbury Jr., F.R.; Brooks III, C.L., Constant pH molecular dynamics using continuous titration coordinates, Proteins 2004, 56, 738-752.

    CAS  Google Scholar 

  148. Simonson, T., Electrostatics and dynamics of proteins, Rep. Prog. Phys. 2003, 66, 737-787.

    CAS  Google Scholar 

  149. Ichiye, T. Simulating redox proteins. in Computational Biochemistry & Biophysics, Becker, O.; Mackerell Jr., A.; Roux, B.; Watanabe, M., Eds. Marcel Dekker: New York, 2001.

    Google Scholar 

  150. Simonson, T., Gaussian fluctuations and linear response in an electron transfer protein, Proc. Natl Acad. Sci. USA 2002, 99, 6544-6549.

    CAS  Google Scholar 

  151. 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.

    CAS  Google Scholar 

  152. 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.

    CAS  Google Scholar 

  153. Warshel, A.; Chu, Z.T.; Parson, W.W., Dispersed polaron simulations of electron transfer in photosynthetic reaction centers, Science 1989, 246, 112-116.

    CAS  Google Scholar 

  154. 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.

    CAS  Google Scholar 

  155. Hummer, G.; Pratt, L.; Garcia, A. E., Free energy of ionic hydration, J. Phys. Chem. 1996,100,1206-1215.

    CAS  Google Scholar 

  156. 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.

    CAS  Google Scholar 

  157. 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.

    CAS  Google Scholar 

  158. 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.

    CAS  Google Scholar 

  159. Mulholland, A., Modelling enzyme reaction mechanisms, specificity and catalysis, Drug Disc. Today 2005, 10, 1393-13402.

    CAS  Google Scholar 

  160. 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.

    CAS  Google Scholar 

  161. 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.

    CAS  Google Scholar 

  162. 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.

    CAS  Google Scholar 

  163. Voth, G. A., Computer simulation of proton solvation and transport in aqueous and biomolecular systems, Acc. Chem. Res. 2006, 39, 143-150.

    CAS  Google Scholar 

  164. 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.

    Google Scholar 

  165. 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.

    Google Scholar 

  166. 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.

    CAS  Google Scholar 

  167. 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.

    CAS  Google Scholar 

  168. 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.

    CAS  Google Scholar 

  169. Roux, B., The art of dissecting the function of a potassium channel, Neuron Sep 2005, 47,777-778.

    CAS  Google Scholar 

  170. Roux, B., Ion conduction and selectivity in K+ channels, Annu. Rev. Biophys. Biomol. Struct. 2005, 34, 153-171.

    CAS  Google Scholar 

  171. Bohannon, John, Distributed computing. Grassroots supercomputing., Science May 2005,308,810-813.

    CAS  Google Scholar 

  172. Shirts, M.; Pande, V., Screen savers of the world unite!, Science 2000, 290, 1903-1904.

    CAS  Google Scholar 

  173. 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.

    Google Scholar 

  174. 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.

    CAS  Google Scholar 

  175. Ferrenberg, A. M.; Swendsen, R. H., Optimized Monte Carlo data analysis, Phys. Rev. Lett. 1989, 63, 1195-1198.

    CAS  Google Scholar 

  176. 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.

    CAS  Google Scholar 

  177. Sheinerman, F. B.; Brooks, C. L., Calculations on folding of segment B1 of streptococcal protein G., J. Mol. Biol. May 1998, 278, 439-456.

    CAS  Google Scholar 

  178. 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.

    CAS  Google Scholar 

  179. 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.

    CAS  Google Scholar 

  180. Mitsutake, A.; Sugita, Y.; Okamoto, Y., Generalized-ensemble algorithms for molecular simulations of biopolymers, Biopolymers 2001, 60, 96-123.

    CAS  Google Scholar 

  181. Sugita, Y.; Okamoto, Y., Replica-exchange molecular dynamics method for protein folding, Chem. Phys. Lett. 1999, 314, 141-151.

    CAS  Google Scholar 

  182. 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.

    CAS  Google Scholar 

  183. 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.

    CAS  Google Scholar 

  184. Rhee, Y. M.; Pande, V. S., Multiplexed-replica exchange molecular dynamics method for protein folding simulation, Biophys. J. 2003, 84, 775-786.

    CAS  Google Scholar 

  185. 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.

    CAS  Google Scholar 

  186. García, A. E.; Sanbonmatsu, K. Y., Exploring the energy landscape of a beta hairpin in explicit solvent., Proteins 2001, 42, 345-354.

    Google Scholar 

  187. Lifson, S.; Roig, A., Theory of helix-coil transition in polypeptides, J. Chem. Phys. 1961,34,1963-1974.

    Google Scholar 

  188. Qian, H.; Schellman, J.A., Helix-coil theories: a comparative study for finite length polypeptides, J. Phys. Chem. 1992, 96, 3987-3994.

    CAS  Google Scholar 

  189. 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.

    CAS  Google Scholar 

  190. Wu, X.; Wang, S., Helix folding of an alanine-based peptide in explicit water, J. Phys. Chem. B 2001, 105, 2227-2235.

    CAS  Google Scholar 

  191. Sugita, A. Kitao; Okamoto, Y., Multidimensional replica-exchange method for free-energy calculations, J. Chem. Phys. 2000, 113, 6042-6051.

    CAS  Google Scholar 

  192. 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.

    CAS  Google Scholar 

  193. Jang, S. Shin; Pak, Y., Replica-exchange method using the generalized effective potentia, Phys. Rev. Lett. 2003, 91, 058305-4.

    Google Scholar 

  194. 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.

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints 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

Publish with us

Policies and ethics