Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models

Journal of Structural and Functional Genomics

Volumn 12, Issue 2, 2011, Pages 137-147

  Zimmermann, Michael T ^a   Leelananda, Sumudu P ^a   Gniewek, Pawel ^a,b   Feng, Yaping ^a   Jernigan, Robert L ^a   Kloczkowski, Andrzej ^a,c,d  

^a IOWA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF WARSAW   (Poland)

^c THE RESEARCH INSTITUTE AT NATIONWIDE CHILDREN S HOSPITAL   (United States)

^d THE OHIO STATE UNIVERSITY COLLEGE OF MEDICINE   (United States)

Author keywords

4 Body potentials; Elastic network models; Multibody potentials; Protein dynamics; Protein structure prediction; Protein structure refinement

Indexed keywords

ANALYTIC METHOD; ARTICLE; ENERGY YIELD; ENTROPY; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR WEIGHT; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; PROTEIN DETERMINATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; STATISTICAL ANALYSIS; ALGORITHM; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN CONFORMATION; THERMODYNAMICS;

AMINO ACID; PROTEIN;

ALGORITHMS; AMINO ACIDS; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; ENTROPY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS;

EID: 80054031361     PISSN: 1345711X     EISSN: 15700267     Source Type: Journal    
DOI: 10.1007/s10969-011-9113-3     Document Type: Article

References (54)

1. Qu X, Swanson R, Day R, Tsai J (2009) A guide to template based structure prediction. Curr Protein Pept Sci 10:270-285
2. Kihara D, Chen H, Yang YD (2009) Quality assessment of pro-tein structure models. Curr Protein Pept Sci 10:216-228
3. Skolnick J, Jaroszewski L, Kolinski A, Godzik A (1997) Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci 6:676-688 (Pubitemid 27120064)
4. Skolnick J, Brylinski M (2009) FINDSITE: a combined evolu-tion/structure- based approach to protein function prediction. BriefBioinform 10:378-391
5. Kryshtafovych A, Fidelis K (2009) Protein structure prediction and model quality assessment. Drug Discov Today 14:386-393
6. Bellows ML, Floudas CA (2010) Computational methods for de novo protein design and its applications to the human immuno-deficiency virus 1, purine nucleoside phosphorylase, ubiquitin specific protease 7, and histone demethylases. Curr Drug Targets 11:264-278
7. Mandell DJ, Kortemme T (2009) Computer-aided design of functional protein interactions. Nat Chem Biol 5:797-807
8. Mandell DJ, Kortemme T (2009) Backbone flexibility in com-putational protein design. Curr Opin Biotechnol 20:420-428
9. Gerlt JA, Babbitt PC (2009) Enzyme (re)design: lessons from naturalevolutionandcomputation. CurrOpinChemBiol13:10-18
10. Vajda S, Kozakov D (2009) Convergence and combination of methods in protein-protein docking. Curr Opin Struct Biol 19: 164-170
11. de Azevedo WF, Dias R (2008) Computational methods for calculation of ligand-binding affinity. Curr Drug Targets 9: 1031-1039
12. Vakser IA, Kundrotas P (2008) Predicting 3D structures of pro-tein-protein complexes. Curr Pharm Biotechnol 9:57-66
13. Ritchie DW (2008) Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci 9:1-15
14. Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE (2009) Long-timescale molecular dynamics simulations of protein structure and function. Curr Opin Struct Biol 19:120-127
15. Roccatano D (2008) Computer simulations study ofbiomolecules in non-aqueous or cosolvent/water mixture solutions. Curr Pro-tein Pept Sci 9:407-426
16. Fawzi NL, Yap EH, Okabe Y, Kohlstedt KL, Brown SP, Head-Gordon T (2008) Contrasting disease and nondisease protein aggregation by molecular simulation. Acc Chem Res 41:1037-1047
17. Rumfeldt JAO, Galvagnion C, Vassall KA, Meiering EM (2008) Conformational stability and folding mechanisms of dimeric proteins. Prog Biophys Mol Biol 98:61-84
18. Samudrala R, Moult J (1998) An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 275:895-916 (Pubitemid 28077703)
19. Lu H, Skolnick J (2001) A distance-dependent atomic knowl-edge-based potential for improved protein structure selection. Proteins 44:223-232 (Pubitemid 32702231)
20. Zhou H, Zhou Y (2002) Distance-scaled, finite ideal-gas refer-ence state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 11: 2714-2726 (Pubitemid 35191145)
21. Miyazawa S, Jernigan RL (1986) Estimation of effective inter-residue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 18:534-552
22. Miyazawa S, Jernigan RL (1996) Residue\-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256:623-644 (Pubitemid 26107211)
23. Sippl MJ (1990) Calculation of conformational ensembles from potentials of mena force: an approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 213:859-883 (Pubitemid 20213222)
24. Tanaka S, Scheraga HA (1976) Medium- and long-range inter-action parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 9:945-950
25. Betancourt M, Thirumalai D (1999) Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci 8:361-369 (Pubitemid 29072436)
26. Munson P, Singh RK (1997) Statistical significance of hierar-chical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment. Protein Sci 6:1467-1481 (Pubitemid 27299047)
27. Li X, Liang J (2005) Geometric cooperativity and anticooper-ativity of three-body interactions in native proteins. Proteins 60:46-65 (Pubitemid 40734749)
28. Krishnamoorthy B, Tropsha A (2003) Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinformatics 19:1540-1548 (Pubitemid 37038870)
29. Feng Y, Kloczkowski A, Jernigan RL (2007) Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys. Proteins 68:57-66 (Pubitemid 46876534)
30. Feng Y, Kloczkowski A, Jernigan R (2010) Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials. BMC Bioinform 11:92-95
31. Bahar I, Kaplan M, Jernigan RL (1997) Short-range conforma-tional energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins 29:292-308 (Pubitemid 27484221)
32. Gniewek P, Leelananda SP, Kolinski A, Jernigan RL, Klocz-kowski A (2011) Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models. Proteins 79:1923-1929
33. Samudrala R, Levitt M (2000) Decoys ''R'' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 9:1399-1401 (Pubitemid 30602295)
34. Gilis D (2004) Protein decoy sets for evaluating energy functions. J Biomol Struct Dyn 21:725-736
35. Pokarowski P, Kloczkowski A, Jernigan RL, Kothari NS, Pok-arowska M, Kolinski A (2005) Inferring ideal amino acid inter-action forms from statistical protein contact potentials. Proteins 59:49-57 (Pubitemid 40316477)
36. Kennedy J, Eberhart RC (1995) Particle swarm optimization. In: Proceedings of IEEE international conference on neural net-works, pp 1942-1948
37. Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977) The Protein Data Bank: a computer-based archival file for macro-molecular structures. J Mol Biol 112:535-542 (Pubitemid 8109216)
38. Yang LW, Eyal E, Chennubhotla C, Jee J, Gronenborn AM, Bahar I (2007) Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions. Structure 15:741-749 (Pubitemid 46876711)
39. Yang L, Song G, Carriquiry A, Jernigan RL (2008) Close cor-respondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic net-work modes. Structure 16:321-330 (Pubitemid 351215213)
40. Yang LW, Eyal E, Bahar I, Kitao A (2009) Principal component analysis of native ensembles of biomolecular structures (PCA-NEST): insights into functional dynamics. Bioinformatics 25:606-614
41. Bahar I, Atilgan AR, Erman B (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter har-monic potential. Fold Des 2:173-181 (Pubitemid 127740467)
42. Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80:505-515
43. Bahar I, Rader AJ (2005) Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 15:586-592 (Pubitemid 41393491)
44. Tama F, Brooks CL (2006) Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annu Rev Biophys Biomol Struct 35:115-133 (Pubitemid 43877372)
45. Jernigan RL, Kloczkowski A (2007) Packing regularities in biological structures relate to their dynamics. Methods Mol Biol 350:251-276
46. Dubois PF, Greenbaum A, Rodrigue GH (1979) Approximating the inverse of a matrix for use in iterative algorithms on vector processors. Computing 22:257-268 (Pubitemid 10416992)
47. Qiang E, Rader AJ, Chennubhotla C, Yang LW, Bahar I (2006) The Gaussian network model: theory and applications in normal mode analysis. Theory and applications to biological and chem-ical systems. Chapman & Hall, pp 41-64
48. Sen TZ, Feng Y, Garcia JV, Kloczkowski A, Jernigan RL (2006) The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models. J Chem Theory Comput 2:696-704
49. Gerstein M, Krebs W (1998) A database of macromolecular motions. Nucleic Acids Res 26:4280-4290 (Pubitemid 28418388)
50. Mirzaie M, Eslahchi C, Pezeshk H, Sadeghi M (2009) A distance-dependent atomic knowledge-based potential and force for dis-crimination ofnative structures from decoys. Proteins 77:454-463
51. Brooks BR, Janezic D, Karplus M (1995) Harmonic-analysis of large systems. 1. Methodology. J Comput Chem 16:1522-1542
52. Lu MY, Ma JP (2011) Normal mode analysis with molecular geometry restraints: bridging molecular mechanics and elastic models. Arch Biochem Biophys 508:64-71
53. Carugo O, Pongor S (2001) A normalized root mean square distance for comparing protein three dimensional structures. Protein Sci 10:1470-1473 (Pubitemid 32568114)
54. Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J. Mol Biol 147:195-197