Distinguish Protein Decoys by Using a Scoring Function Based on a New AMBER Force Field, Short Molecular Dynamics Simulations, and the Generalized Born Solvent Model

Proteins: Structure, Function and Genetics

Volumn 55, Issue 3, 2004, Pages 620-634

  Lee, Mathew C ^a   Duan, Yong ^a  

^a UNIVERSITY OF DELAWARE   (United States)

Author keywords

Computational structure prediction; Deliberately misfolded proteins; Potential energy function; Protein folding; Z scores

Indexed keywords

PROTEIN; PROTEIN DECOY; UNCLASSIFIED DRUG;

AMBER FORCE FIELD; ARTICLE; CHEMOTAXONOMY; COMPUTER MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; ENERGY; GENERALIZED BORN SOLVENT MODEL; INTERMETHOD COMPARISON; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR PHYSICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN STRUCTURE; SCORING SYSTEM; SEQUENCE ANALYSIS; STATISTICAL SIGNIFICANCE; STRUCTURE ANALYSIS;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; MODELS, CHEMICAL; PROTEIN CONFORMATION; PROTEIN FOLDING; SOLVENTS;

EID: 2442480826     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10470     Document Type: Article

References (53)

1. Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181:223-230.
2. Sohl JL, Jaswal SS, Agard DA. Unfolded conformations of alpha-lytic protease are more stable than its native state. Nature 1998;395:817-819.
3. Lazaridis T, Karplus M. Effective energy functions for protein structure prediction. Curr Opin Struct Biol 2000;10:139-145.
4. Lazaridis T, Archontis G, Karplus M. Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics. Adv Protein Chem 1995;47:231-306.
5. Karplus M, Shakhnovich EI. Protein folding: theoretical studies of thermodynamics and dynamics. In: Creighton T, editor. Protein folding. New York: WH Freeman; 1992. p 127-195.
6. Bryngelson JD, Wolynes PG. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J Phys Chem B 1989;93:6902-6915.
7. 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.
8. Vajda S, Sippl M, Novotny J. Empirical potentials and functions for protein folding and binding. Curr Opin Struct Biol 1997;7:222-228.
9. Sippl MJ. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990;213:859-883.
10. Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995;5:229-235.
11. Dominy BN, Brooks CL. Identifying native-like protein structures using physics-based potentials. J Comput Chem 2002;23:147-160.
12. Price DJ, Brooks CL III. Modern protein force fields behave comparably in molecular dynamics simulations. J Comput Chem 2002;23:1045-1057.
13. 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.
14. Novotny J, Bruccoleri R, Karplus M. An analysis of incorrectly folded protein models. Implications for structure predictions. J Mol Biol 1984;177:787-818.
15. 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.
16. Samudrala R, Levitt M. Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 2000;9:1399-1401.
17. Simons KT, Bonneau R, Ruczinski II, Baker D. Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins 1999;37:171-176.
18. Kihara D, Lu H, Kolinski A, Skolnick J. TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc Natl Acad Sci USA 2001;98:10125-10130.
19. Vorobjev YN, Hermans J. Free energies of protein decoys provide insight into determinants of protein stability. Protein Sci 2001;10:2498-2506.
20. Vorobjev YN, Hermans J. Free energies of protein decoys provide insight into determinants of protein stability. Protein Sci 2002;11:994.
21. Vila J, Williams RL, Vasquez M, Scheraga HA. Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor. Proteins 1991;10:199-218.
22. Vieth M, Kolinski A, Brooks CL, 3rd, Skolnick J. Prediction of the folding pathways and structure of the GCN4 leucine zipper. J Mol Biol 1994;237:361-367.
23. Lazaridis T, Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 999;288:477-487.
24. Liu Y, Beveridge DL. Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model. Proteins 2002;46:128-146.
25. Vorobjev YN, Hermans J. ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model. Biophys Chem 1999;78:195-205.
26. 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.
27. Lee MR, Duan Y, Kollman PA. Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece. Proteins 2000;39:309-316.
28. Roux R, Simonson T. Implicit solvent models. Biophys Chem 1999;78:1-20.
29. Williams RL, Vila J, Perrot G, Scheraga HA. Empirical solvation models in the context of conformational energy searches: application to bovine pancreatic trypsin inhibitor. Proteins 1992;14:110-119.
30. Wang Y, Zhang H, Li W, Scott RA. Discriminating compact nonnative structures from the native structure of globular proteins. Proc Natl Acad Sci USA 1995;92:709-713.
31. Wang Y, Zhang H, Scott RA. A new computational model for protein folding based on atomic solvation. Protein Sci 1995;4:1402-1411.
32. Monge A, Lathrop EJ, Gunn JR, Shenkin PS, Friesner RA. Computer modeling of protein folding: conformational and energetic analysis of reduced and detailed protein models. J Mol Biol 1995;247:995-1012.
33. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagone G, Profeta S, Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 1984;106:765-784.
34. Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 1990;112:6127-6129.
35. Petrey D, Honig B. Free energy determinants of tertiary structure and the evaluation of protein models. Protein Sci 2000;9:2181-2191.
36. Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996;118:11225-11236.
37. Zhang L, Gallicchio E, Friesner RA, Levy RM. Solvent models for protein-ligand binding: comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations. J Comput Chem 2001;22:591-607.
38. Ghosh A, Rapp CS, Friesner RA. Generalized Born model based on a surface integral formulation. J Phys Chem B 1998;102:10983-10990.
39. Holm L, Sander C. Evaluation of protein models by atomic solvation preference. J Mol Biol 1992;225:93-105.
40. Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997;268:209-225.
41. Sternberg MJ, Bates PA, Kelley LA, MacCallum RM. Progress in protein structure prediction: assessment of CASP3. Curr Opin Struct Biol 1999;9:368-373.
42. Xia Y, Huang ES, Levitt M, Samudrala R. Ab initio construction of protein tertiary structures using a hierarchical approach. J Mol Biol 2000;300:171-185.
43. Samudrala R, Xia Y, Levitt M, Huang ES. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Pac Symp Biocomput 1999:505-516.
44. Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998;282:740-744.
45. Daura X, van Gunsteren WF, Mark AE. Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations. Proteins 1999;34:269-280.
46. Katz M, Papadopoulos P, Bruno G. Leveraging standard core technologies to programmatically build linux cluster appliances. IEEE International Conference on Cluster Computing 2002;47-54.
47. Case DA, Pearlman DA, Caldwell JW, Cheatham TE III, Wang J, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, et al. AMBER 7. San Francisco: University of California San Francisco; 2002.
48. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
49. Hawkins GD, Cramer CJ, Truhlar DG. Pairwise solute descreening of solute charges from a dielectric medium. Chem Phys Lett 1995;246:122-129.
50. Hawkins GD, Cramer CJ, Truhlar DG. Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute charges from a dielectric medium. J Phys Chem 1996;100:19824-19839.
51. Srinivasan J, Trevathan MW, Beroza P, Case DA. Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects. Theor. Chem Acc 1999;101:416-434.
52. Zhang L, Skolnick J. What should the Z-score of native protein structures be? Protein Sci 1998;7:1201-1207.
53. Moult J, Pedersen JT, Judson R, Fidelis K. A large-scale experiment to assess protein structure prediction methods. Proteins 1995;23:ii-v.