Application of MM/PBSA colony free energy to loop decoy discrimination: Toward correlation between energy and root mean square deviation

Protein Science

Volumn 14, Issue 4, 2005, Pages 889-901

  Fogolari, Federico ^a   Tosatto, Silvio C E ^b  

^a UNIVERSITY OF UDINE   (Italy)

^b UNIVERSITY OF PADOVA   (Italy)

Author keywords

Colony energy; Implicit solvent; Loop decays; MM PBSA; Poisson Boltzmann

Indexed keywords

SOLVENT;

ACCURACY; ARTICLE; CALCULATION; CONFORMATIONAL TRANSITION; ENERGY; MODEL; MOLECULAR MECHANICS; PRIORITY JOURNAL; THERMODYNAMICS;

AMINO ACIDS; DATA INTERPRETATION, STATISTICAL; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 15244349255     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.041004105     Document Type: Article

References (65)

1. Ajay and Murcko, M.A. 1995. Computational methods to predict binding free energy in ligand-receptor complexes. J. Med. Chem. 38: 4953-4967.
2. Anfinsen, C.B. 1973. Principles that govern the folding of protein chains. Science 181: 23-230.
3. Baginski, M., Fogolari, F., and Briggs, J.M. 1997. Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA. J. Mol. Biol. 274: 253-267.
4. Bashford, D. and Case, D.A. 2000. Generalized born models of macromolecular solvation effects. Ann. Rev. Phys. Chem. 51: 129-152.
5. Berrera, M., Molinari, H., and Fogolari, F. 2003. Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. BMC Bioinformatics 4: 8.
6. Blokzijl, W. and Engberts, J.B.F.N. 1993. Hydrophobic effects. Opinions and facts. Angew. Chem. Int. Ed. Engl. 32: 1545-1579.
7. Bonneau, R. and Baker. D. 2001. Ab initio protein structure prediction: Progress and prospects. Ann. Rev. Biophys. Biomol. Struct. 30: 173-189.
8. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., and Karplus, M. 1983. Charmm: A program for macromolecular energy minimization and dynamics calculations. J. Comput. Chem. 4: 187-217.
9. Canutescu, A.A., Shelenkov, A.A., and Dunbrack, R.L. 2003. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 12: 2001-2014.
10. Davis, M.E. and McCammon, J.A. 1991a. Electrostatic in biomolecular structure and dynamics. Chem. Rev. 90: 509-521.
11. -. 1991b. Dielectric boundary smoothing in finite difference solutions of the Poisson equation: An approach to improve accuracy and convergence. J. Comp. Chem. 12: 909-912.
12. de Bakker, P.I.W., De Pristo, M.A., Burke, D.F., and Blundell, T.L. 2003. Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the amber force field with the generalized born solvation model. Proteins 51: 21-40.
13. Doig, A.J. and Sternberg, M.J. 1995. Side-chain conformational entropy in protein folding. Protein Sci. 4: 2247-2251.
14. Dominy, B.N. and Brooks III, C.L. 2002. Identifying native-like protein structures using physics-based potentials. J. Comput. Chem. 23: 147-160.
15. Eisenberg, D. and McLachlan, A.D. 1986. Solvation energy in protein folding and binding. Nature 319: 199-203.
16. Feig, M. and Brooks III, C.L. 2002. Evaluating casp4 predictions with physical energy functions. Proteins 49: 232-245.
17. Finkelstein, A.V. and Janin, J. 1989. The price of lost freedom: Entropy of bimolecular complex formation. Protein Eng. 3: 1-3.
18. Fogolari, F. and Briggs, J.M. 1997. On the variational approach to the Poisson-Boltzmann free energies. Chem. Phys. Lett. 281: 135-139.
19. Fogolari, F., Zuccato, P., Esposito, G., and Viglino, P. 1999. Biomolecular electrostatics with the linearized Poisson-Boltzmann equation. Biophys. J. 76: 1-16.
20. Fogolari, F., Esposito, G., Viglino, P., and Molinari, H. 2001. Molecular mechanics and dynamics of biomolecules using a solvent continuum model. J. Comput. Chem. 22: 1830-1842.
21. Fogolari, F., Brigo, A., and Molinari, H. 2002. The Poisson-Boltzmann equation for biomolecular electrostatics: A tool for structural biology. J. Mol. Recogn. 15: 377-392.
22. -. 2003. Protocol for MM/PBSA molecular dynamics simulations of proteins. Biophys. J. 85: 159-166.
23. Fraternali, F. and Van Gunsteren, W.F. 1996. An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution. J. Mol. Biol. 256: 939-948.
24. Gatchell, D.W., Dennis, S., and Vajda, S. 2000. Discrimination of near native protein structures from misfolded models by empirical free energy functions. Proteins 41: 518-534.
25. Gilson, M.K., Given, J.A., Bush, B.L., and McCammon, J.A. 1997. The statistical-thermodynamic basis for computation of binding affinities: A critical review. Biophys J. 72: 1047-1069.
26. Hill, T. 1956. An introduction to statistical mechanics. Dover Publications, New York.
27. Holm, L. and Sander, C. 1992. Evaluation of protein models by atomic solvation preference. J. Mol. Biol. 225: 93-105.
28. Honig, B. and Nicholls, A. 1995. Classical electrostatic in biology and chemistry. Science 268: 1144-1149.
29. Honig, B. and Yang, A.-S. 1995. Free energy balance in protein folding. Adv. Prot. Chem. 46: 27-58.
30. Honig, B., Sharp, K., and Yang, A.-S. 1993. Macroscopic models of aqueous solution: Biological and chemical applications. J. Phys. Chem. 97: 1101-1109.
31. Hsieh, M.-J. and Luo, R. 2004. Physical scoring function based on amber force field and Poisson-Boltzmann implicit solvent for protein structure prediction. Proteins 56: 475-486.
32. Kollman, P.A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Duan, Y., Wang, W., Donini, O., et al. 2000. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc. Chem. Res. 33: 889-897.
33. Lazaridis, T. and Karplus, M. 2000. Effective energy functions for protein structure prediction. Curr. Op. Struct. Biol. 10: 139-145.
34. Lee, M.R. and Kollman, P.A. 2001. Free-energy calculations highlight differences in accuracy between x-ray and NMR structures and add value to protein structure prediction. Structure 9: 905-916.
35. α RMSD structure predictions on two small proteins, hp-36 and s15. J. Am. Chem. Soc. 123: 1040-1046.
36. Levy, R.M., Zhang, L.Y., Gallicchio, E., and Felts, A.K. 2003. On the nonpolar hydration free energy of proteins: Surface area and continuum solvent models for the solute-solvent interaction energy. J. Am. Chem. Soc. 125: 9523-9530.
37. Lu, B.Z., Chen, W.Z., Wang, C.X., and Xu, X.-J. 2002. Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation. Proteins 48: 497-504.
38. 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., et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102: 3586-3616.
39. Madura, J.D., Davis, M.E., Gilson, M.K., Wade, R., Luty, B.A, and McCammon, J.A. 1994. Biological applications of electrostatics calculations and Brownian dynamics simulations. Rev. Comp. Chem. 5: 229-267.
40. Madura, J.D., Briggs, J.M., Wade, R., Davis, M.E., Luty, B.A., Ilin, A., Antosiewicz, J.A., Gilson, M.K., Bagheri, B., Ridgway Scott, L., et al. 1995. Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian Dynamics program. Comput. Commun. Phys. 91: 57-95.
41. Marcus, R.A. 1955. Calculation of thermodynamic properties of polyelectrolytes. J. Chem. Phys. 23: 1057-1068.
42. Nicholls, A., Sharp, K.A., and Honig, B. 1991. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11: 281-296.
43. Novotny, J., Bruccoleri, R., and Karplus, M. 1984. An analysis of incorrectly folded protein models. Implications for structure predictions. J. Mol. Biol. 177: 787-818.
44. Park, B. and Levitt, M. 1996. Energy functions that discriminate x-ray and near-native folds from well-constructed decoys. J. Mol. Biol. 258: 367-392.
45. Petrey, D. and Honig, B. 2000. Free energy determinants of tertiary structure and the evaluation of protein models. Protein Sci. 9: 2181-2191.
46. Qiu, D., Shenkin, P., Hollinger, F., and Still, W. 1997. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate born radii. J. Phys. Chem. 101: 3005-3014.
47. Roux, B. and Simonson, T. 1999. Implicit solvent models. Biophys. Chem. 78: 1-20.
48. Samudrala, R. and Levitt, M. 2000. Decoys 'r' us: A database of incorrect protein conformations to improve protein structure prediction. Protein Sci. 9: 1399-1401.
49. Samudrala, R. and Moult, J. 1998. A graph-theoretic algorithm for comparative modelling of protein structure. J. Mol. Biol. 279: 287-302.
50. Schapira, M., Totrov, M., and Abagyan, R. 1999. Prediction of the binding energy for small molecules, peptides, and proteins. J. Mol. Recogn. 12: 177-190.
51. Schutz, C.N. and Warshel, A. 2001. What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins 44: 400-417.
52. Sharp, K.A., and Honig, B. 1990. Calculating total electrostatic energies with the non-linear Poisson-Boltzmann equation. J. Phys. Chem. 94: 7684-7692.
53. Simonson, T. 1999. Dielectric relaxation in proteins: Microscopic and macroscopic models. Int. J. Quant. Chem. 73: 45-57.
54. Srinivasan, J., Cheatham III, T.E., Cieplak, P., Kollman, P.A., and Case, D.A. 1998. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J. Am. Chem. Soc. 120: 9401-9409.
55. Tosatto, S.C.E., Bindewald, E., Hesser, J., and Maenner, R. 2002. A divide and conquer approach to fast loop modeling. Protein Eng. 15: 279-286.
56. Vajda, S., Sippl, M., and Novotny, J. 1997. Empirical potentials and functions for protein folding and binding. Curr. Op. Struct. Biol. 7: 222-228.
57. Vorobjev, Y.N. and Hermans, J. 2001. Free energies of protein decoys provide insight into determinants of protein stability. Protein Sci. 10: 2498-2506.
58. Vorobjev, Y.N., Almagro, J.C., and Hermans, J. 1998. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Proteins 32: 399-413.
59. Vriend, G. 1990. What if: A molecular modeling and drug design program. J. Mol. Graph. 8: 52-54.
60. Wang, Y., Zhang, H., Li, W., and Scott, R.A. 1995. Discriminating compact nonnative structures from the native structure of globular proteins. Proc. Natl. Acad. Sci. 92: 709-713.
61. Xiang, Z., Soto, S.C., and Honig, B. 2002. Evaluating free energies: The colony energy and its application to the problem of loop prediction. Proc. Natl. Acad. Sci. 99: 7432-7437.
62. Zhang, C., Liu, S., Zhou, H., and Zhou, Y. 2004a. Accurate and efficient loop selections by the dfire-based all-atom statistical potential. Protein Sci. 13: 391-399.
63. -. 2004b. An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci. 13: 400-411.
64. Zhou, H.X. 1994. Macromolecular electrostatic energy within the nonlinear Poisson-Boltzmann equation. J. Chem. Phys. 100: 3152-3162.
65. Zhou, H. and Zhou, Y. 2002. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 11: 2714-2726.