New technique of identifying the hierarchy of dynamic domains in proteins using a method of molecular dynamics simulations

Biopolymers and Cell

Volumn 26, Issue 2, 2010, Pages 146-152

  Yesylevskyy, S O ^a  

^a INSTITUTE OF PHYSICS   (Ukraine)

Author keywords

Domain identification; Dynamic domains; Hierarchical Domain Wise Alignment; Molecular dynamics

Indexed keywords

PROTEIN;

ARTICLE; MOLECULAR DYNAMICS; PROTEIN ANALYSIS; PROTEIN DOMAIN; SIMULATION; STRUCTURE ANALYSIS;

EID: 77952168957     PISSN: 02337657     EISSN: 19936842     Source Type: Journal    
DOI: 10.7124/bc.000151     Document Type: Article

References (28)

1. Janin J., Wodak S. J. Protein modules and protein-protein interaction. Introduction. Adv Protein Chem. 2002. 61. P. 1-8.
2. Janin J., Wodak S. J. Structural domains in proteins and their role in the dynamics of protein function. Prog. Biophys. Mol. Biol. 1983. 42, N 1. P. 21-78.
3. Ito K., Uyeda T. Q., Suzuki Y., Sutoh K., Yamamoto K. Requirement of domain-domain interaction for conformational change and functional ATP hydrolysis in myosin. J. Biol. Chem. 2003. 278, N 33. P. 31049-31057.
4. Popp S., Packschies L., Radzwill N., Vogel K. P., Steinhoff H. J., Reinstein J. Structural dynamics of the DnaK-peptide complex. J. Mol. Biol. 2005. 347, N 5. P. 1039-1052.
5. Zhang X. J., Wozniak J. A., Matthews B. W. Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. J. Mol. Biol. 1995. 250, N 4. P. 527-552.
6. Gerstein M., Anderson B. F., Norris G. E., Baker E. N., Lesk A. M., Chothia C. Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces. J. Mol. Biol. 1993. 234, N 2. P. 357-372.
7. Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C. J., Hofmann K., Bairoch A. The PROSITE database, its status in 2002. Nucl. Acids Res. 2002. 30, N 1. P. 235-238.
8. Nagar B., Bornmann W. G., Pellicena P., Schindler T., Veach D. R., Miller W. T., Clarkson B., Kuriyan J. Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571). Cancer Res. 2002. 62, N 15. P. 4236-4243.
9. Schmitt L., Tampe R. Structure and mechanism of ABC transporters. Curr. Opin Struct. Biol. 2002. 12, N 6. P. 754-760.
10. Fischer K. F., Marqusee S. A rapid test for identification of autonomous folding units in proteins. J. Mol. Biol. 2000. 302, N 3. P. 701-712.
11. Anselmi C., Bocchinfuso G., Scipioni A., De Santis P. Identification of protein domains on topological basis. Biopolymers. 2001. 58, N 2. P. 218-229.
12. Nichols W. L., Rose G. D., Ten Eyck L. F., Zimm B. H. Rigid domains in proteins: an algorithmic approach to their identification. Proteins. 1995. 23, N 1. P. 38-48.
13. Wriggers W., Schulten K. Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins. 1997. 29, N 1. P. 1-14.
14. Hayward S., Berendsen H. J. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins. 1998. 30, N 2. P. 144-154.
15. Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins. 1998. 33, N 3. P. 417-429.
16. Hinsen K., Thomas A., Field M. J. Analysis of domain motions in large proteins. Proteins. 1999. 34, N 3. P. 369-382.
17. Tama F., Gadea F. X., Marques O., Sanejouand Y. H. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins. 2000. 41, N 1. P. 1-7.
18. Kundu S., Sorensen D. C., Phillips G. N., Jr. Automatic domain decomposition of proteins by a Gaussian Network Model. Proteins. 2004. 57, N 4. P. 725-733.
19. Sista R., Brinda K. V., Vishveshwara S. Identification of domains and domain interface residues in multidomain proteins from graph spectral method. Proteins: Structure, Function, and Bioinformatics. 2005. 59, N 3. P. 616-626.
20. Yesylevskyy S. O., Kharkyanen V. N., Demchenko A. P. Hierarchical clustering of the correlation patterns: New method of domain identification in proteins. Biophys. Chem. 2006. 119, N 1. P. 84-93.
21. Yesylevskyy S. O., Kharkyanen V. N., Demchenko A. P. Dynamic protein domains: identification, interdependence and stability. Biophys. J. 2006. 91, N 2. P. 670-685.
22. Yesylevskyy S. O., Kharkyanen V. N., Demchenko A. P. The change of protein intradomain mobility on ligand binding, is it a commonly observed phenomenon?. Biophys. J. 2006. 91, N 8. P. 3002-3013.
23. Yesylevskyy S. O., Kharkyanen V. N., Demchenko A. P. The blind search for the closed states of hinge-bending proteins. Proteins: Structure, Function, and Bioinformatics. 2007. 71, N 2. P. 831-843.
24. Yesylevskyy S. O., Kharkyanen V. N. New approaches to slow dynamics of protein domains. Ukr. J. Phys. 2009. 54, N 1-2. P. 109-116.
25. Menor S. A., de Graff A. M. R., Thorpe M. F. Hierarchical plasticity from pair distance fluctuations. Phys. Biol. 2009. 6, N 3. P. 036017.
26. Berendsen H. J. C. Bio-molecular dynamics comes of age. Science. 1996. 271, N 5251. P. 954-955.
27. Lange O. F., Grubmuller H. Generalized correlation for biomolecular dynamics. Proteins: Structure, Function, and Bio-informatics. 2006. 62, N 4. P. 1053-1061.
28. Amadei A., Linssen A. B. M., Berendsen H. J. C. Essential dynamics of proteins. Prot. Struct. Funct. Genet. 1993. 17, N 4. P. 412-425.