Deriving protein dynamical properties from weighted protein contact number

Proteins: Structure, Function and Genetics

Volumn 72, Issue 3, 2008, Pages 929-935

  Lin, Chih Peng ^a   Huang, Shao Wei ^a   Lai, Yan Long ^a   Yen, Shih Chung ^a   Shih, Chien Hua ^a   Lu, Chih Hao ^a   Huang, Cuen Chao ^a   Hwang, Jenn Kang ^a  

^a NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

Author keywords

B factors; Protein contact number; Protein dynamics

Indexed keywords

PROTEIN;

ACCURACY; ARTICLE; ATOM; COMPARATIVE STUDY; CORRELATION COEFFICIENT; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN STRUCTURE; STRUCTURE ACTIVITY RELATION; X RAY CRYSTALLOGRAPHY;

AMINO ACIDS; CARBON; CHONDROITIN LYASES; CYTOCHROME C GROUP; DATABASES, PROTEIN; MODELS, MOLECULAR; MOLECULAR WEIGHT; PROTEINS; SUCCINATE DEHYDROGENASE;

EID: 47349097554     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21983     Document Type: Article

References (27)

1. Levitt M, Warshel A. Computer simulation of protein folding. Nature 1975;253:694-698.
2. Warshel A. Bicycle-pedal model for the first step in the vision process. Nature 1976;260:679-683.
3. McCammon JA, Gelin BR, Karplus M. Dynamics of folded proteins. Nature 1977;267:585-590.
4. Warshel A. Molecular dynamics simulations of biological reactions. Acc Chem Res 2002;35:385-395.
5. Rueda M, Ferrer-Costa C, Meyer T, Perez A, Camps J, Hospital A, Gelpi JL, Orozco M. A consensus view of protein dynamics. Proc Natl Acad Sci USA 2007;104:796-801.
6. Tirion MM. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 1996;77:1905-1908.
7. Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 1997;2:173-181.
8. Ming D, Kong Y, Lambert MA, Huang Z, Ma J. How to describe protein motion without amino acid sequence and atomic coordinates. Proc Natl Acad Sci USA 2002;99:8620-8625.
9. Micheletti C, Banavar JR, Maritan A Conformations of proteins in equilibrium. Phys Rev Lett 2001;87:088102.
10. Canino LS, Shen T, McCammon JA. Changes in flexibility upon binding: application of the self-consistent pair contact probability method to protein-protein interactions. J Chem Phys 2002;117:9927-9933.
11. Pandey BP, Zhang C, Yuan X, Zi J, Zhou Y. Protein flexibility prediction by an all-atom mean-field statistical theory. Protein Sci 2005;14:1772-1777.
12. Halle B. Flexibility and packing in proteins. Proc Natl Acad Sci USA 2002;99:1274-1279.
13. Noguchi T, Akiyama Y. PDB-REPRDB: a database of representative protein chains from the protein data bank (PDB) in 2003. Nucleic Acids Res 2003;31:492-493.
14. Team RDC. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2007.
15. Yang LW, Rader AJ, Liu X, Jursa CJ, Chen SC, Karimi HA, Bahar I. oGNM: online computation of structural dynamics using the Gaussian network model. Nucleic Acids Res 2006;34:W24-W31.
16. Henrick K, Thornton JM. PQS: a protein quaternary structure file server. Trends Biochem Sci 1998;23:358-361.
17. Xu Q, Canutescu A, Obradovic Z, Dunbrack RL, Jr. ProtBuD: a database of biological unit structures of protein families and superfamilies. Bioinformatics 2006;22:2876-2882.
18. Budiman ME, Knaggs MH, Fetrow JS, Alexander RW. Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase. Proteins 2007;68:670-689.
19. Zheng W, Liao JC, Brooks BR, Doniach S. Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model. Proteins 2007;67:886-896.
20. Ming D, Kong Y, Wakil SJ, Brink J, Ma J. Domain movements in human fatty acid synthase by quantized elastic deformational model. Proc Natl Acad Sci USA 2002;99:7895-7899.
21. Yang LW, Bahar I. Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure 2005;13:893-904.
22. Brooks B, Karplus M. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 1983;80:6571-6575.
23. Levitt M, Sander C, Stern PS. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol 1985;181:423-447.
24. Kidera A, Go N. Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data. J Mol Biol 1992;225:457-475.
25. Lee FS, Chu ZT, Warshel A. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs. J Comp Chem 1993;14:161-185.
26. Fan Z-Z, Hwang J-K, Warshel A. Using simplified protein representaion as a reference potential for all-atom calculations of folding free energy. Theor Chem Acc 1999;103:77-80.
27. Shih CH, Huang SW, Yen SC, Lai YL, Yu SH, Hwang JK. A simple way to compute protein dynamics without a mechanical model. Proteins 2007;68:34-38.