Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction

Proteins: Structure, Function and Genetics

Volumn 56, Issue 3, 2004, Pages 475-486

  Hsieh, Meng Juei ^a   Luo, Ray ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Ab initio; Decoys; Finite difference; Molecular mechanics; Protein folding; Surface area

Indexed keywords

PROTEIN;

AB INITIO CALCULATION; ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DIELECTRIC CONSTANT; DISULFIDE BOND; MOLECULAR INTERACTION; MOLECULAR MECHANICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; SCORING SYSTEM; SURFACE PROPERTY;

ALGORITHMS; AMINO ACID SEQUENCE; ARTIFICIAL INTELLIGENCE; COMPUTER SIMULATION; ELECTROSTATICS; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SOLVENTS; THERMODYNAMICS;

EID: 3142680776     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20133     Document Type: Article

References (86)

1. Doolittle RF. Similar amino-acid-sequences-chance or common ancestry. Science 1981;214:149-159.
2. Greer J. Comparative modeling methods-application to the family of the mammalian serine proteases. Proteins 1990;7:317-334.
3. Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 1991;9:56-68.
4. Bowie JU, Luthy R, Eisenberg DA. A method to identify protein sequences that fold into a known 3-dimensional structure. Science 1991;253:164-170.
5. Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
6. Bystroff C, Baker D. Blind predictions of local protein structure in CASP2 targets using the I-sites library. Proteins 1997;29(Suppl 1):167-171.
7. Jones DT. Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifs. Proteins 1997;29(Suppl 1):185-191.
8. Pedersen JT, Moult J. Ab initio protein folding simulations with genetic algorithms: simulations on the complete sequence of small proteins. Proteins 1997;29(Suppl 1):179-184.
9. Osguthorpe DJ. Analysis of the predicted structures of domain 1 of protein g3 (T0030) and NK-lysin (T0042). Proteins 1997;29(Suppl 1):172-178.
10. Lomize AL, Pogozheva ID, Mosberg HI. Prediction of protein structure: the problem of fold multiplicity. Proteins 1999;37(Suppl 3):199-203.
11. Samudrala R, Xia Y, Huang E, Levitt M. Ab initio protein structure prediction using a combined hierarchical approach. Proteins 1999;37(Suppl 3):194-198.
12. Lee J, Liwo A, Ripoll DR, Pillardy J, Scheraga HA. Calculation of protein conformation by global optimization of a potential energy function. Proteins 1999;37(Suppl 3):204-208.
13. Ortiz AR, Kolinski A, Rotkiewicz P, Ilkowski B, Skolnick J. Ab initio folding of proteins using restraints derived from evolutionary information. Proteins 1999;37(Suppl 3):177-185.
14. Standley DM, Eyrich VA, An YL, Pincus DL, Gunn JR, Friesner RA. Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment. Proteins 2001;45(Suppl 5):133-139.
15. Moult J. Comparison of database potentials and molecular mechanics force fields. Curr Opin Struct Biol 1997;7:194-199.
16. Lazaridis T, Karplus M. Effective energy functions for protein structure prediction. Curr Opin Struct Biol 2000;10:139-145.
17. Anfinsen CB. Principles that govern folding of protein chains. Science 1973;181:223-230.
18. Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995;5:229-235.
19. Hendlich M, Lackner P, Weitckus S, Floeckner H, Froschauer R, Gottsbacher K, Casari G, Sippl MJ. Identification of native protein folds amongst a large number of incorrect models-the calculation of low-energy conformations from potentials of mean force. J Mol Biol 1990;216:167-180.
20. Wodak SJ, Rooman MJ. Generating and testing protein folds. Curr Opin Struct Biol 1993;3:247-259.
21. Jones DT, Thornton JM. Potential energy functions for threading. Curr Opin Struct Biol 1996;6:210-216.
22. Hao MH, Scheraga HA. Designing potential energy functions for protein folding. Curr Opin Struct Biol 1999;9:184-188.
23. Park B, Levitt M. Energy functions that discriminate X-ray and near-native folds from well-constructed decoys. J Mol Biol 1996; 258:367-392.
24. Park BH, Huang ES, Levitt M. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J Mol Biol 1997;266:831-846.
25. Tobi D, Shafran G, Linial N, Elber R. On the design and analysis of protein folding potentials. Proteins 2000;40:71-85.
26. Novotny J, Bruccoleri R, Karplus M. An analysis of incorrectly folded protein models-implications for structure predictions. J Mol Biol 1984;177:787-818.
27. Novotny J, Rashin AA, Bruccoleri RE. Criteria that discriminate between native proteins and incorrectly folded models. Proteins 1988;4:19-30.
28. Vorobjev YN, Hermans J. Free energies of protein decoys provide insight into determinants of protein stability. Protein Sci 2001;10: 2498-2506.
29. Vorobjev YN, Almagro JC, Hermans J. 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 1998;32:399-413.
30. Lazaridis T, Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 1999;288:477-487.
31. Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152.
32. Gatchell DW, Dennis S, Vajda S. Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins 2000;41:518-534.
33. Fan ZZ, Hwang JK, Warshel A. Using simplified protein representation as a reference potential for all-atom calculations of folding free energy. Theor Chem Acc 1999;103:77-80.
34. Lee MR, Tsai J, Baker D, Kollman PA. Molecular dynamics in the endgame of protein structure prediction. J Mol Biol 2001;313:417-430.
35. Felts AK, Gallicchio E, Wallqvist A, Levy RM. Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized Born solvent model. Proteins 2002;48:404-422.
36. Dominy BN, Brooks CL. Identifying native-like protein structures using physics-based potentials. J Comput Chem 2002;23:147-160.
37. Hassan SA, Mehler EL. A critical analysis of continuum electrostatics: the screened Coulomb potential-implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins. Proteins 2002;47:45-61.
38. Feig M, Brooks CL. Evaluating Casp4 predictions with physical energy functions. Proteins 2002;49:232-245.
39. Luo R, David L, Gilson MK. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comput Chem 2002;23:1244-1253.
40. Lu Q, Luo RA. Poisson-Boltzmann dynamics method with the non-periodic boundary condition. J Chem Phys 2003;119:11035-11047.
41. Lu Q, Luo R. Optimization of the main chain torsional term for protein simulations. Manuscript in preparation.
42. Zauhar RJ. The incorporation of hydration forces determined by continuum electrostatics into molecular mechanics simulations. J Comput Chem 1991;12:575-583.
43. Sharp K. Incorporating solvent and ion screening into molecular dynamics using the finite-difference Poisson-Boltzmann method. J Comput Chem 1991;12:454-468.
44. Niedermeier C, Schulten K. Molecular dynamics simulations in heterogeneous dielectrica and Debye-Huckel media-application to the protein bovine pancreatic trypsin inhibitor. Mol Simul 1992;8:361-387.
45. Gilson MK, McCammon JA, Madura JD. Molecular dynamics simulation with a continuum electrostatic model of the solvent. J Comput Chem 1995;16:1081-1095.
46. Im W, Beglov D, Roux B. Continuum solvation model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Comput Phys Commun 1998;111:59-75.
47. Friedrichs M, Zhou RH, Edinger SR, Friesner RA. Poisson-Boltzmann analytical gradients for molecular modeling calculations. J Phys Chem B 1999;103:3057-3061.
48. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A 2nd generation forcefield for the simulation of proteins, nucleic-acids, and organic-molecules. J Am Chem Soc 1995;117:5179-5197.
49. Wang JM, Cieplak P, Kollman PA. How well does a restrained electrostatic potential (Resp) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 2000;21:1049-1074.
50. McQuarrie DA. Statistical mechanics. New York: Harper & Row; 1973.
51. Warwicker J, Watson HC. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. J Mol Biol 1982;157: 671-679.
52. Klapper I, Hagstrom R, Fine R, Sharp K, Honig B. Focusing of electric fields in the active site of Cu, Zn superoxide dismutase. Proteins 1986;1:47-79.
53. Sitkoff D, Sharp KA, Honig B. Accurate calculation of hydration free energies using macroscopic solvation models. J Phys Chem 1994;98:1978-1988.
54. Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J Am Chem Soc 1998;120:9401-9409.
55. Lee FS, Chu ZT, Bolger MB, Warshel A. Calculations of antibody antigen interactions-microscopic and semimicroscopic evaluation of the free-energies of binding of phosphorylcholine analogs to Mcpc603. Protein Eng 1992;5:215-228.
56. Lee FS, Chu ZT, Warshel A. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the Polaris and Enzymix programs. J Comput Chem 1993;14:161-185.
57. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG. Funnels, pathways, and the energy landscape of protein-folding-a synthesis. Proteins 1995;21:167-195.
58. Dill KA, Bromberg S, Yue KZ, Fiebig KM, Yee DP, Thomas PD, Chan HS. Principles of protein-folding-a perspective from simple exact models. Protein Sci 1995;4:561-602.
59. Honig B, Sharp K, Yang A-S. Macroscopic models of aqueous solutions: biological and chemical applications. J Phys Chem 1993;97:1101-1109.
60. Mardis K, Luo R, David L, Potter M, Glemza A, Payne G, Gilson MK. Modeling molecular recognition: theory and application. J Biomol Struct Dyn 2000;S1:89-94.
61. Kollman PA, Massova I, Reyes C, Kuhn B, Huo SH, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 2000;33:889-897.
62. Hockney RW, Eastwood JW. Computer simulation using particles. Bristol, UK. Adam Hilger; 1988.
63. van Gunsteren WF, Berendsen HJC. Algorithms for macromolecular dynamics and constraint dynamics. Mol Phys 1977;34:1311-1327.
64. Ryckaert J-P, Ciccotti G, Berendsen HJC. Numerical integration of cartesian equations of motion of a system with constraints-molecular dynamics of N-Alkanes. J Comput Phys 1977;23:327-341.
65. Lee MR, Kollman PA. Free-energy calculations highlight differences in accuracy between X-ray and NMR structures and add value to protein structure prediction. Structure 2001;9:905-916.
66. Darden T, York D, Pedersen L. Particle mesh Ewald-an N · log(N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089-10092.
67. Holm L, Sander C. Evaluation of protein models by atomic solvation preference. J Mol Biol 1992;225:93-105.
68. Moult J, Pedersen JT, Judson R, Fidelis K. A large-scale experiment to assess protein-structure prediction methods. Proteins 1995;23:R2-R4.
69. Levitt M. Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 1992;226:507-533.
70. Samudrala R, Levitt M. Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 2000;9:1399-1401.
71. Simons KT, Bonneau R, Ruczinski I, Baker D. Ab initio protein structure prediction of Casp III targets using Rosetta. Proteins 1999;37:171-176.
72. Feig M, MacKerell AD, Brooks CL. Force field influence on the observation of pi-helical protein structures in molecular dynamics simulations. J Phys Chem B 2003;107:2831-2836.
73. Kabsch W, Sander C. Dictionary of protein secondary structure-pattern- recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
74. Warshel A, Russell ST. Calculations of electrostatic interactions in biological-systems and in solutions. Q Rev Biophys 1984;17:283-422.
75. Schutz CN, Warshel A. What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins 2001; 44:400-417.
76. MacKerell A, Bashford D, Bellott M, Dunbrack R, Evanseck J, Field M, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau F, Mattos C, Michnick S, Ngo T, Nguyen D, Prodhom B, Reiher W, Roux B, Schlenkrich M, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-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.
77. Jorgensen WL, Tirado-Rives J. The OPLS potential function for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 1988;110:1657-1666.
78. Cieplak P, Caldwell J, Kollman P. Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and n-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases. J Comput Chem 2001;22:1048-1057.
79. Burgi R, Kollman PA, van Gunsteren WF. Simulating proteins at constant pH: an approach combining molecular dynamics and Monte Carlo simulation. Proteins 2002;47:469-480.
80. Wen EZ, Hsieh MJ, Kollman PA, Luo R. Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces. J Mol Graph Mod, Forthcoming.
81. a shifts in small molecules and HIV protease: electrostatics and conformation. J Am Chem Soc 1998;120:6138-6146.
82. Gilson MK. Modeling protonation equilibria in biomolecules. In: van Gunsteren WF, Weiner PK, Wilkinson AJ, editors. Computer simulations of biomolecular systems. Volume 3. Dordrecht: Kluwer/Escom; 1997. p 199-222.
83. Luo R, David L, Hung H, Devaney J, Gilson MK. Strength of solvent exposed salt-bridges. J Phys Chem 1999;103:727-736.
84. Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 2001;105:6474-6487.
85. Okur A, Strockbine B, Hornak V, Simmerling C. Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins. J Comput Chem 2003;24:21-31.
86. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 2003;24:1999-2012.