cNMA: A framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions

Bioinformatics

Volumn 31, Issue 12, 2015, Pages i151-i160

  Oliwa, Tomasz ^a   Shen, Yang ^a,b  

^a TOYOTA TECHNOLOGICAL INSTITUTE AT CHICAGO   (United States)

^b Texas AandM University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MULTIPROTEIN COMPLEX;

CHEMISTRY; MOLECULAR DOCKING; MOTION; PROCEDURES; PROTEIN ANALYSIS; PROTEIN CONFORMATION;

MOLECULAR DOCKING SIMULATION; MOTION; MULTIPROTEIN COMPLEXES; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING;

EID: 84931028926     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv252     Document Type: Conference Paper

References (27)

1. Atilgan A.R., et al. (2001). Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J., 80, 505-515
2. Bahar I., et al. (2010). Global dynamics of proteins: bridging between structure and function. Annu. Rev. Biophys., 39, 23-42
3. Bakan A. and Bahar I. (2009). The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc. Natl Acad. Sci. USA, 106, 14349-14354
4. Bakan A., et al. (2011). ProDy: protein dynamics inferred from theory and experiments. Bioinformatics, 27, 1575-1577
5. Bonvin A.M. (2006). Flexible protein-protein docking. Curr. Opin. Struct. Biol., 16, 194-200
6. Brooks B. and Karplus M. (1985). Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proc. Natl Acad. Sci. USA, 82, 4995-4999
7. Dasgupta B., et al. (2013). Counterbalance of ligand- and self-coupled motions characterizes multispecificity of ubiquitin. Protein Sci., 22, 168178
8. Dasgupta B., et al. (2014). Rigid-body motions of interacting proteins dominate multispecific binding of ubiquitin in a shape-dependent manner. Proteins Struct. Funct. Bioinform., 82, 7789
9. Dobbins S.E., et al. (2008). Insights into protein flexibility: the relationship between normal modes and conformational change upon protein-protein docking. Proc. Natl Acad. Sci. USA, 105, 10390-10395
10. Doruker P., et al. (2000). Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor. Proteins Struct. Funct. Bioinform., 40, 512-524
11. Eckart C. (1935). Some studies concerning rotating axes and polyatomic molecules. Phys. Rev., 47, 552-558
12. Field M. (2007). A Practical Introduction to the Simulation of Molecular Systems. Cambridge University Press, Cambridge, New York
13. Gibrat J.F. and Go N. (1990). Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion. Proteins Struct. Funct. Bioinform., 8, 258-279
14. Goh C.S., et al. (2004). Conformational changes associated with protein-protein interactions. Curr. Opin. Struct. Biol., 14, 104-109
15. Harrison R.W. (1984). Variational calculation of the normal modes of a large macromolecule: methods and some initial results. Biopolymers, 23, 2943-2949
16. Hinsen K. (1998). Analysis of domain motions by approximate normal mode calculations. Proteins Struct. Funct. Bioinform., 33, 417429
17. Hwang H., et al. (2010). Protein-protein docking benchmark version 4.0. Proteins Struct. Funct. Bioinform., 78, 31113114
18. Karplus M. and McCammon J.A. (2002). Molecular dynamics simulations of biomolecules. Nat. Struct. Mol. Biol., 9, 646-652
19. Kuhn H.W. (1955). The Hungarian method for the assignment problem. Naval Res. Logistic Q., 2, 83-97
20. Kumar S., et al. (2000). Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci. Publ. Protein Soc., 9, 10-19
21. Moal I.H. and Bates P.A. (2010). SwarmDock and the use of normal modes in protein-protein docking. Int. J. Mol. Sci., 11, 3623-3648
22. Nussinov R. and Ma B. (2012). Protein dynamics and conformational selection in bidirectional signal transduction. BMC Biol., 10, 2
23. Petrone P. and Pande V.S. (2006). Can conformational change be described by only a few normal modes?. Biophys. J., 90, 1583-1593
24. Saad Y. (1992). Numerical Methods for Large Eigenvalue Problems. Halstead Press, New York
25. Tirion M.M. (1996). Large amplitude elastic motions in proteins from a singleparameter, atomic analysis. Phys. Rev. Lett., 77, 1905-1908
26. Venkatraman V. and Ritchie D.W. (2012). Flexible protein docking refinement using pose-dependent normal mode analysis. Proteins Struct Funct. Bioinform., 80, 22622274
27. Vreven T., et al. (2013). Exploring angular distance in protein-protein docking algorithms. PLoS One, 8, e56645