The ruggedness of protein-protein energy landscape and the cutoff for 1/ rn potentials

Bioinformatics

Volumn 25, Issue 9, 2009, Pages 1132-1136

  Ruvinsky, Anatoly M ^a   Vakser, Ilya A ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ENERGY TRANSFER; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN INTERACTION; PROTEIN STRUCTURE; REFERENCE VALUE;

ALGORITHMS; BINDING SITES; COMPUTATIONAL BIOLOGY; KINETICS; MULTIPROTEIN COMPLEXES; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION MAPPING; THERMODYNAMICS;

EID: 65449126203     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp108     Document Type: Article

References (67)

1. Abkevich,V.I. et al. (1995) Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J. Mol. Biol., 252, 460-471.
2. Alsallaq,R. and Zhou,H.X. (2007) Prediction of protein-protein association rates from a transition-state theory. Structure, 15 215-224.
3. Bahar,I. et al. (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2, 173-181.
4. Braier,P.A. et al. (1990) How the range of pair interactions governs features of multidimensional potentials. J. Chem. Phys., 93, 8745-8756.
5. Brooks,C.L. et al. (1985) Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids. J. Chem. Phys., 83, 5897-5908.
6. Bryngelson,J.D. et al. (1995) Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins, 21, 167-195.
7. Bryngelson,J.D. andWolynes,P.G. (1989) Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Phys. Chem., 93, 6902-6915.
8. Buchete,N.V. et al. (2004) Orientational potentials extracted from protein structures improve native fold recognition. Prot. Sci., 13, 862-874.
9. Camacho,C.J. and Vajda,S. (2001) Protein docking along smooth association pathways. Proc. Natl Acad. Sci. USA, 98, 10636-10641.
10. Camacho,C.J. et al. (1999) Free energy landscapes of encounter complexes in protein-protein association. Biophys. J., 76, 1166-1178.
11. Dill,K.A. (1999) Polymer principles and protein folding. Prot. Sci. 8, 1166-1180.
12. Doye,J.P.K. and Wales,D.J. (1996) The effect of the range of the potential on the structure and stability of simple liquids: From clusters to bulk, from sodium to C60. J. Phys. B At. Mol. Opt. Phys. 29, 4859-4894.
13. Doyle,R. et al. (1997) Local interactions and the optimization of protein folding. Proteins, 29, 282-291.
14. Elcock,A.H. et al. (2001) Computer simulation of protein-protein interactions. J. Phys. Chem. B, 105, 1504-1518.
15. Faisca,P.F. et al. (2005) The Go model revisited: Native structure and the geometric coupling between local and long-range contacts. Proteins, 60, 712-722.
16. Ferreiro,D.U. et al. (2007) Localizing frustration in native proteins and protein assemblies. Proc. Natl Acad. Sci. USA, 104 19819-19824.
17. Frauenfelder,H. et al. (2001) The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin. Proc. Natl Acad. Sci. USA, 98, 2370-2374.
18. Gao,Y. et al. (2007) Dockground system of databases for protein recognition studies: Unbound structures for docking. Proteins, 69, 845-851.
19. Gilson,M.K. (1995) Theory of electrostatic interactions in macromolecules. Curr. Opin. Struct. Biol., 5, 216-223.
20. Go,N. and Taketomi,H. (1978) Respective roles of short- and long-range interactions in protein folding. Proc. Natl Acad. Sci. USA, 75 559-563.
21. Govindarajan,S. and Goldstein,R.A. (1995) Optimal local propensities for model proteins. Proteins, 22, 413-418.
22. Grimsley,G.R. et al. (1999) Increasing protein stability by altering long-range Coulombic interactions. Prot. Sci., 8, 1843-1849.
23. Gromiha,M.M. and Selvaraj,S. (1999) Importance of long-range interactions in protein folding. Biophys. Chem., 77, 49-68.
24. Haluk,R. and McCammon,J.A. (1998) Correcting for electrostatic cutoffs in free energy simulations: Toward consistency between simulations with different cutoffs. J. Chem. Phys., 108, 9617-9623.
25. Harvey,S.C. (1989) Treatment of electrostatic effects in macromolecular modeling. Proteins, 5, 78-92.
26. Hinsen,K. (2008) Structural flexibility in proteins: Impact of the crystal environment. Bioinformatics, 24, 521-528.
27. Hunjan,J. et al. (2008) The size of the intermolecular energy funnel in protein-protein interactions. Proteins, 72, 344-352.
28. Hyeon,C. and Thirumalai,D. (2003) Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments?. Proc. Natl Acad. Sci. USA, 100, 10249-10253.
29. Izvekov,S. et al. (2008) Coarse-graining in interaction space: A systematic approach for replacing long-range electrostatics with short-range potentials. J. Phys. Chem., 112, 4711-4724.
30. Kaplan,I.G. (2006) Intermolecular Interactions: Physical Picture, Computational Methods and Model Potentials. John Wiley & Sons, Ltd, Chichester.
31. Khatun,J. et al. (2004) Can contact potentials reliably predict stability of proteins? J. Mol. Biol., 336, 1223-1238.
32. Klein-Seetharaman,J. et al. (2002) Long-range interactions within a nonnative protein. Science, 295, 1719-1722.
33. Lafuente,E. et al. (2002) Long-range RNA-RNA interactions between distant regions of the hepatitis C virus internal ribosome entry site element. J. Gen. Virol., 83, 1113-1121.
34. Loncharich,R.J. and Brooks,B.R. (1989) The effects of truncating long-range forces on protein dynamics. Proteins, 6, 32-45.
35. Lukatsky,D.B. et al. (2006) Statistically enhanced self-attraction of random patterns. Phys. Rev. Lett., 97, 178101.
36. Miller,D.W. and Dill,K.A. (1997) Ligand binding to proteins: The binding landscape model. Prot. Sci., 6, 2166-2179.
37. Miller,M.A. et al. (1999) Structural relaxation in Morse clusters: energy landscapes. J. Chem. Phys., 110, 328-334.
38. Minh,D.D.L. et al. (2005) The entropic cost of protein-protein association: A case study on acetylcholinesterase binding to fasciculin-2. Biophys. J.: Biophys. Lett., 89, L25-L27.
39. Nevo,R. et al. (2005) Direct measurement of protein energy landscape roughness. EMBO Rep., 6, 482-486.
40. Norberg,J. and Nilsson,L. (2000) On the truncation of long-range electrostatic interactions in DNA. Biophys. J., 79, 1537-1553.
41. O'Toole,N. and Vakser,I.A. (2008) Large-scale characteristics of the energy landscape in protein-protein interactions. Proteins, 71 144-152.
42. Pappu,R.V. et al. (1999) A potential smoothing algorithm accurately predicts transmembrane helix packing. Nat. Struct. Biol. 6, 50-55.
43. Ruvinsky,A.M. (2007) Calculations of protein-ligand binding entropy of relative and overall molecular motions. J. Comput. Aided Mol. Des. 21, 361-370.
44. Ruvinsky,A.M. and Kozintsev,A.V. (2005a) The key role of atom types, reference states, and interaction cutoff radii in the knowledge-based method: New variational approach. Proteins, 58, 845-851.
45. Ruvinsky,A.M. and Kozintsev,A.V. (2005b) New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy J. Comput. Chem., 26, 1089-1095.
46. Ruvinsky,A.M. and Vakser,I.A. (2008a) Interaction cutoff effect on ruggedness of protein-protein energy landscape. Proteins, 70 1498-1505.
47. Ruvinsky,A.M. and Vakser,I.A. (2008b) Chasing funnels on protein-protein energy landscapes at different resolutions. Biophys. J., 95, 2150-2159.
48. Sagui,C. and Darden,T.A. (1999) Molecular dynamics simulations of biomolecules: Long-range electrostatic effects. Ann. Rev. Biophys. Biomol. Struct., 28, 155-179.
49. Stillinger,F.H. and Stillinger,D.K. (1990) Cluster optimization simplified by interaction modification. J. Chem. Phys., 93, 6106-6107.
50. Sutto,L. et al. (2007) Consequences of localized frustration for the folding mechanism of the IM7 protein. Proc. Natl Acad. Sci. USA 104, 19825-19830.
51. Tirion,M.M. (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett., 77, 1905-1908.
52. Tobi,D. and Elber,R. (2000) Distance-dependent, pair potential for protein folding: Results from linear optimization. Proteins, 41 40-46.
53. Tobi,D. et al. (2000) On the design and analysis of protein folding potentials. Proteins, 40, 71-85.
54. Tovchigrechko,A. and Vakser,I.A. (2001) How common is the funnel-like energy landscape in protein-protein interactions? Prot. Sci., 10, 1572-1583.
55. Tovchigrechko,A. and Vakser,I.A. (2005) Development and testing of an automated approach to protein docking. Proteins, 60, 296-301.
56. Tovchigrechko,A. et al. (2002) Docking of protein models. Prot. Sci., 11, 1888-1896.
57. Tsai,C.-J. et al. (1999) Folding funnels, binding funnels, and protein function. Prot. Sci., 8, 1181-1190.
58. Vakser,I.A. (1996) Long-distance potentials: An approach to the multiple-minima problem in ligand-receptor interaction. Prot. Eng. 9, 37-41.
59. Vakser,I.A. and Jiang,S. (2002) Strategies for modeling the interactions of the transmembrane helices of G-protein coupled receptors by geometric complementarity using the GRAMM computer algorithm. Methods Enzymol. 343, 313-328.
60. Vakser,I.A. et al. (1999) A systematic study of low-resolution recognition in protein-protein complexes. Proc. Natl Acad. Sci. USA 96, 8477-8482.
61. Vendruscolo,M. and Domany,E. (1998) Pairwise contact potentials are unsuitable for protein folding. J. Chem. Phys., 109, 11101-11108.
62. Vendruscolo,M. et al. (1999) Protein folding in contact map space. Phys. Rev. Lett., 82, 656-659.
63. Wang,J. and Verkhivker,G.M. (2003) Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding. Phys. Rev. Lett., 90, 188101.
64. Wang,J. et al. (2007) Optimal specificity and function for flexible biomolecular recognition. Biophys. J., 92, L109-L111.
65. Wawak,R.J. et al. (1992) Application of the diffusion equation method of global optimization to water clusters. J. Phys. Chem., 96, 5138-5145.
66. Whitfield,T.W. and Straub,J.E. (2002) Gravitational smoothing as a global optimization strategy. J. Comput. Chem., 23, 1100-1102.
67. Wolynes,P.G. (2005) Recent successes of the energy landscape theory of protein folding and function. Quart. Rev. Biophys., 38, 405-410.