Protein folding by 'levels of separation': A hypothesis

FEBS Letters

Volumn 586, Issue 7, 2012, Pages 962-966

  Greene, Lesley H ^a   Grant, Terri M ^a  

^a OLD DOMINION UNIVERSITY   (United States)

Author keywords

Chymotrypsin inhibitor 2; Long range interaction; Network; Nucleation condensation model; Protein folding; Transition state

Indexed keywords

ALGORITHM; ARTICLE; BIOCHEMISTRY; COMPUTER MODEL; CONTROLLED STUDY; HYPOTHESIS; LEVELS OF SEPARATION; MATHEMATICAL MODEL; NETWORK SCIENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; SCIENCE; SIMULATION; THEORETICAL MODEL;

ANIMALS; BIOCHEMISTRY; COMPUTATIONAL BIOLOGY; HUMANS; MODELS, MOLECULAR; PEPTIDES; PLANT PROTEINS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SYSTEMS BIOLOGY;

EID: 84859265748     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2012.02.040     Document Type: Article

References (40)

1. M.K. Santra, A. Banerjee, S.S. Krishnakumar, O. Rahaman, and D. Panda Multiple-probe analysis of folding and unfolding pathways of human serum albumin Eur. J. Biochem. 271 2004 1789 1797
2. B. Nolting, and K. Andert Mechanism of protein folding Proteins Struct. Funct. Bioinform. 41 2000 288 298
3. J.B. Udgaonkar, and R.L. Baldwin NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A Nature 335 1988 694 699
4. P.S. Kim, and R.L. Baldwin Specific intermediates in the folding reactions of small protein and the mechanism of protein folding Annu. Rev. Biochem. 51 1982 459 489
5. L.S. Itzhaki, D.E. Otzen, and A.R. Fersht The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding J. Mol. Biol. 254 1995 260 288
6. N.D. Socci, J.N. Onuchic, and P.G. Wolynes Protein folding mechanisms and the multidimensional folding funnel Proteins Struct. Funct. Bioinform. 32 1998 136 158 (Pubitemid 28363897)
7. M. Oliveberg, and P.G. Wolynes The experimental survey of protein-folding energy landscapes Q. Rev. Biophys. 38 2005 245 288 (Pubitemid 44268537)
8. D.J. Watts Six Degrees: The Science of a Connected Age 2003 William Heinmann London
9. J.H. Fowler, and N.A. Christakis Dynamic spread of happiness in a large social network: longitudinal analysis over 20 years in the Framingham Heart Study BMJ 2008 337
10. C.M. Schneider, L. de Arcangelis, and H.J. Herrmann Modeling the topology of protein interaction networks Phys. Rev. E 2011 84
11. E.A. Franzosa, and Y. Xia Structural principles within the human-virus protein-protein interaction network Proc. Natl. Acad. Sci. 108 2011 10538 10543
12. S. Navlakha, and C. Kingsford Network archaeology: uncovering ancient networks from present-day Interactions PLoS Comput. Biol. 7 2011
13. C.J. Tsai, B. Ma, and R. Nussinov Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends Biochem. Sci. 34 2009 594 600
14. M. Girvan, and M.E.J. Newman Community structure in social and biological networks Proc. Natl. Acad. Sci. 99 2002 7821 7826 (Pubitemid 34650963)
15. M.E.J. Newman, and J. Park Why social networks are different from other types of networks Phys. Rev. E 2003 68
16. G. Bianconi, and A.L. Barabasi Bose-Einstein condensation in complex networks Phys. Rev. Lett. 2001 86
17. Z. Dezso, E. Almaas, A. Lukacs, B. Racz, I. Szakadat, and A.L. Barabasi Dynamics of information access on the web Phys. Rev. E 2006 73
18. A. Scala, Nunes, L.A. Amaral, and M. Barthelemy Small-world networks and the conformation space of a short lattice polymer chain Europhys. Lett. 55 2001 594 600
19. M. Vendruscolo, N.V. Dokholyan, E. Paci, and M. Karplus Small-world view of the amino acids that play a key role in protein folding Phys. Rev. E 2002 65
20. N.V. Dokholyan, L. Li, F. Ding, and E.I. Shakhnovich Topological determinants of protein folding Proc. Natl. Acad. Sci. USA 99 2002 8637 8641 (Pubitemid 34693612)
21. L.H. Greene, and V.A. Higman Uncovering network systems within protein structures J. Mol. Biol. 334 2003 781 791 (Pubitemid 37433891)
22. F. Rao, and A. Caflisch The protein folding network J. Mol. Biol. 342 2004 299 306 (Pubitemid 39099290)
23. A.R. Atilgan, P. Akan, and C. Baysal Small-world communication of residues and significance for protein dynamics Biophys. J. 86 2004 85 91 (Pubitemid 38067438)
24. G. Bagler, and S. Sinha Network properties of protein structures Physica A 346 2005 27 33
25. K.V. Brinda, and S. Vishveshwara A network representation of protein structures: implications for protein stability Biophys. J. 89 2005 4159 4170 (Pubitemid 41725636)
26. V.A. Higman, and L.H. Greene Elucidation of conserved long-range interaction networks in proteins and their significance in determining protein topology Phys. A Stat. Mech. Appl. 368 2006 595 606 (Pubitemid 43831508)
27. C. Bode, I.A. Kovacs, M.S. Szalay, R. Palotai, T. Korcsmaros, and P. Csermely Network analysis of protein dynamics FEBS Lett. 581 2007 2776 2782 (Pubitemid 46874391)
28. N.T. Doncheva, K. Klein, F.S. Domingues, and M. Albrecht Analyzing and visualizing residue networks of protein structures Trends Biochem. Sci. 36 2011 179 182
29. A. Del Sol, H. Fujihashi, and R. Nusinov Residues critical for maintaining short paths in network communication mediate signalling in proteins Mol. Syst. Biol. 2006 2006
30. M.M.G. Krishna, L. Hoang, Y. Lin, and S.W. Englander Hydrogen exchange methods to study protein folding Methods 34 2004 51 64 (Pubitemid 38993208)
31. M.D. Winn, C.C. Ballard, K.D. Cowtan, E.J. Dodson, P. Emsley, P.R. Evans, R.M. Keegan, E.B. Krissinel, A.G.W. Leslie, and A. McCoy Overview of the CCP4 suite and current developments Acta Crystallogr. Sect. D 67 2011 235 242
32. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, and N.S. Pannu Crystallography and NMR system: A new software suite for macromolecular structure determination Acta Crystallogr. Sect. D, Biol. Crystallogr. 54 1998 905 921
33. I.N. Shindyalov, and P.E. Bourne Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Eng. 11 1998 739 747 (Pubitemid 28434482)
34. V. Daggett Protein folding-simulation Chem. Rev. 106 2006 1898 1916 (Pubitemid 43792785)
35. A.R. Fersht Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications Proc. Natl. Acad. Sci. 92 1995 10869 10873
36. A.R. Fersht, A. Matouschek, and L. Serrano The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding J. Mol. Biol. 224 1992 771 782
37. S.A. Kauffman The Origins of Life: A New View. Origins or Order: Self-Orgaization and Selection in Evolution 1993 Oxford University Press NY pp. 287-342
38. D. Deb, S. Vishveshwara, and S. Vishveshwara Understanding protein structure from a percolation perspective Biophys. J. 97 2009 1787 1794
39. S. Carmi, S. Havlin, S. Kirkpatrick, Y. Shavitt, and E. Shir A model of internet topology using k-shell decomposition Proc. Natl. Acad. Sci. USA 104 2007 11150 11154 (Pubitemid 47175109)
40. J. Shao, S.V. Buldyrev, L.A. Braunstein, S. Havlin, and H.E. Stanley Structure of shells in complex networks Phys. Rev. E 80 2009 036105