Biopolym. Cell. 2010; 26(2):146-152.
http://dx.doi.org/10.7124/bc.000151
Bioinformatics
New technique of identifying the hierarchy of dynamic domains in proteins using a method of molecular dynamics simulations
1Yesylevskyy S. O.
  1. Institute of Physics, NAS of Ukraine
    46, Prospect Nauki, Kyiv, Ukraine, 03028

Abstract

Despite a large number of existing domain identification techniques there is no universally accepted method, which identifies the hierarchy of dynamic domains using the data of molecular dynamics (MD) simulations. The aim of this work is to develop such technique. Methods. The dynamic domains are identified by eliminating systematic motions from MD trajectories recursively in a model-free manner. Results. The technique called the Hierarchical Domain-Wise Alignment (HDWA) to identify hierarchically organized dynamic domains in proteins using the MD trajectories has been developed. Conclusion. A new method of domain identification in proteins is proposed.
Keywords: dynamic domains, domain identification, Hierarchical Domain-Wise Alignment, molecular dynamics
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References

[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 FX, Marques O, Sanejouand YH. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 2000;41(1):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 Bioinformatics 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.