Understanding protein structure from a percolation perspective

Biophysical Journal

Volumn 97, Issue 6, 2009, Pages 1787-1794

  Deb, Dhruba ^a   Vishveshwara, Saraswathi ^a   Vishveshwara, Smitha ^b  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b United States of America   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POLYPEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL BOND; MOLECULAR INTERACTION; MOLECULAR MODEL; PROTEIN FOLDING; PROTEIN STRUCTURE;

EID: 70350031205     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.07.016     Document Type: Article

References (59)

1. Anfinsen, C. B. 1973. Principles that govern the folding of protein chains. Science. 181:223-230.
2. Watson, J. D., and F. H. Crick. 1953. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature. 171:737-738.
3. Crick, F. H., L. Barnett, S. Brenner, and R. J. Watts-Tobin. 1961. General nature of the genetic code for proteins. Nature. 192:1227-1232.
4. Khorana, H. G., H. Buchi, H. Ghosh, N. Gupta, T. M. Jacob, et al. 1966. Polynucleotide synthesis and the genetic code. Cold Spring Harb. Symp. Quant. Biol. 31:39-49.
5. Trinh, X. H., A. Trovato, F. Seno, J. R. Banavar, and A. Maritan. 2005. Geometrical model for the native-state folds of proteins. Biophys. Chem. 115:289-294.
6. Miyashita, O., P. G. Wolynes, and J. N. Onuchic. 2005. Simple energy landscape model for the kinetics of functional transitions in proteins. J. Phys. Chem. B. 109:1959-1969.
7. Ramachandran, G. N., C. Ramakrishnan, and V. Sasisekharan. 1963. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7:95-99.
8. Przytycka, T., R. Aurora, and G. D. Rose. 1999. A protein taxonomy based on secondary structure. Nat. Struct. Biol. 6:672-682.
9. Chothia, C. 1992. Proteins. One thousand families for the molecular biologist. Nature. 357:543-544.
10. Denton, M., and C. Marshall. 2001. Protein folds: laws of form revisited. Nature. 410:417.
11. Hoang, T. X., A. Trovato, F. Seno, J. R. Banavar, and A. Maritan. 2004. Geometry and symmetry presculpt the free-energy landscape of proteins. Proc. Natl. Acad. Sci. USA. 101:7960-7964.
12. Kimura, M. 1968. Evolutionary rate at the molecular level. Nature. 217:624-626.
13. King, J. L., and T. H. Jukes. 1969. Non-Darwinian evolution. Science. 164:788-798.
14. Greene, L. H., and V. A. Higman. 2003. Uncovering network systems within protein structures. J. Mol. Biol. 334:781-791.
15. Brinda, K. V., and S. Vishveshwara. 2005. A network representation of protein structures: implications for protein stability. Biophys. J. 89:4159-4170.
16. Stauffer, D. 1985. Introduction to Percolation Theory. Taylor and Francis, London, UK.
17. Derényi, I., G. Palla, and T. Vicsek. 2005. Clique percolation in random networks. Phys. Rev. Lett. 94:1-4.
18. Samudrala, R., and M. Levitt. 2000. Decoys 'R' Us: a database of incorrect protein conformations to improve protein structure prediction. Protein Sci. 9:1399-1401.
19. Yang, J. S., W. W. Chen, J. Skolnick, and E. I. Shakhnovich. 2007. All-atom ab initio folding of a diverse set of proteins. Structure. 15:53-63.
20. Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, et al. 2000. The Protein Data Bank. Nucleic Acids Res. 28:235-242.
21. Albert, R., and A.-L. Barabasi. 2002. Statistical mechanics of complex networks. Rev. Mod. Phys. 74:47-97.
22. Amaral, L. A., A. Scala, M. Barthelemy, and H. E. Stanley. 2000. Classes of small-world networks. Proc. Natl. Acad. Sci. USA. 97:11149-11152.
23. Kannan, N., and S. Vishveshwara. 1999. Identification of side-chain clusters in protein structures by a graph spectral method. J. Mol. Biol. 292:441-464.
24. Patra, S. M., and S. Vishveshwara. 2000. Backbone cluster identification in proteins by a graph theoretical method. Biophys. Chem. 84:13-25.
25. Sistla, R. K., K. V. Brinda, and S. Vishveshwara. 2005. Identification of domains and domain interface residues in multidomain proteins from graph spectral method. Proteins. 59:616-626.
26. Miyazawa, S., and R. L. Jernigan. 1985. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules. 18:534-552.
27. Miyazawa, S., and R. L. Jernigan. 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.
28. Adamcsek, B., G. Palla, I. Frakas, I. Derényi, and T. Vicsek. 2006. CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics. 22:1021-1023.
29. Sali, A., and T. L. Blundell. 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234:779-815.
30. Rohl, C. A., and D. Baker. 2002. De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J. Am. Chem. Soc. 124:2723-2729.
31. Kannan, N., S. Selvaraj, M. M. Gromiha, and S. Vishveshwara. 2001. Clusters in alpha/beta barrel proteins: implications for protein structure, function, and folding: a graph theoretical approach. Proteins. 43:103-112.
32. Lesk, A. M., C. I. Branden, and C. Chothia. 1989. Structural principles of alpha/beta barrel proteins: the packing of the interior of the sheet. Proteins. 5:139-148.
33. Wodak, S. J., I. Lasters, F. Pio, and M. Claessens. 1990. Basic design features of the parallel alpha beta barrel, a ubiquitous protein-folding motif. Biochem. Soc. Symp. 57:99-121.
34. Murzin, A. G., A. M. Lesk, and C. Chothia. 1994. Principles determining the structure of beta-sheet barrels in proteins. II. The observed structures. J. Mol. Biol. 236:1382-1400.
35. Bharat, T. A., S. Eisenbeis, K. Zeth, and B. Hocker. 2008. A beta alpha-barrel built by the combination of fragments from different folds. Proc. Natl. Acad. Sci. USA. 105:9942-9947.
36. Banavar, J. R., and A. Maritan. 2007. Physics of proteins. Annu. Rev. Biophys. Biomol. Struct. 36:261-280.
37. Kuwajima, K., H. Yamaya, S. Miwa, S. Sugai, and T. Nagamura. 1987. Rapid formation of secondary structure framework in protein folding studied by stopped-flow circular dichroism. FEBS Lett. 221:115-118.
38. Goto, Y., and A. L. Fink. 1990. Phase diagram for acidic conformational states of apomyoglobin. J. Mol. Biol. 214:803-805.
39. Chyan, C. L., C. Wormald, C. M. Dobson, P. A. Evans, and J. Baum. 1993. Structure and stability of the molten globule state of guinea-pig alpha-lactalbumin: a hydrogen exchange study. Biochemistry. 32:5681-5691.
40. Luthey-Schulten, Z., B. E. Ramirez, and P. G. Wolynes. 1995. Helix-coil, liquid crystal and spin glass transitions of a collapsed heteropolymer. J. Phys. Chem. 99:2177-2185.
41. Levitt, M., M. Gerstein, E. Huang, S. Subbiah, and J. Tsai. 1997. Protein folding: the endgame. Annu. Rev. Biochem. 66:549-579.
42. Ferreiro, D. U., J. A. Hegler, E. A. Komives, and P. G. Wolynes. 2007. Localizing frustration in native proteins and protein assemblies. Proc. Natl. Acad. Sci. USA. 104:19819-19824.
43. Goldstein, H. 1950. Classical Mechanics. Addison-Wesley, Reading, MA.
44. Go, N., T. Noguti, and T. Nishikawa. 1983. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. USA. 80:3696-3700.
45. Brooks, B., and M. Karplus. 1985. Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proc. Natl. Acad. Sci. USA. 82:4995-4999.
46. Levitt, M., C. Sander, and P. S. Stern. 1985. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol. 181:423-447.
47. Ma, J. 2005. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure. 13:373-380. (Pubitemid 40342876)
48. Van Wynsberghe, A. W., and Q. Cui. 2006. Interpreting correlated motions using normal mode analysis. Structure. 14:1647-1653.
49. Tirion, M. M. 1996. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1905-1908.
50. Bahar, I., A. R. Atilgan, and B. Erman. 1997. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:173-181.
51. Yang, L.-W., and C.-P. Chng. 2008. Coarse-grained models reveal functional dynamics - I. Elastic network models - theories, comparisons and perspectives. Bioinform. Bio. Insights. 2:25-45.
52. Hinsen, K. 1998. Analysis of domain motions by approximate normal mode calculations. Proteins. 33:417-429. (Pubitemid 28516346)
53. Bahar, I., B. Erman, R. L. Jernigan, A. R. Atilgan, and D. G. Covell. 1999. Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function. J. Mol. Biol. 285:1023-1037.
54. Keskin, O., I. Bahar, D. Flatow, D. G. Covell, and R. L. Jernigan. 2002. Molecular mechanisms of chaperonin GroEL-GroES function. Biochemistry. 41:491-501. (Pubitemid 34062018)
55. Xu, C., D. Tobi, and I. Bahar. 2003. Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T< - >R2 transition. J. Mol. Biol. 333:153-168.
56. Cui, Q., G. Li, J. Ma, and M. Karplus. 2004. A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. J. Mol. Biol. 340:345-372.
57. Wang, Y., A. J. Rader, I. Bahar, and R. L. Jernigan. 2004. Global ribosome motions revealed with elastic network model. J. Struct. Biol. 147:302-314.
58. Lockless, S. W., and R. Ranganathan. 1999. Evolutionarily conserved pathways of energetic connectivity in protein families. Science. 286:295-299.
59. Dima, R. I., and D. Thirumalai. 2006. Determination of network of residues that regulate allostery in protein families using sequence analysis. Protein Sci. 15:258-268.