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Molecular dynamics investigations for understanding protein folding mechanism of a small two-helix proteinAuthors: Monika Sharma,Harjinder Singh,Abhijit Mitra Conference: Discussion Meeting on Theoretical Chemistry (TCS-2009), Jan 18-22, 2009 organized by IISc and JNCASR, Bangalore, India Date: 2009-08-28 Report no: IIIT/TR/2009/93 AbstractThe study of protein folding has greatly advanced in recent years with the development of various experimental and computational techniques. The way a protein folds, is dictated by the sequence of protein, followed by the stochastic search of many conformations available to it. Therefore, the understanding of time dependent behavior of folding requires detailed information on the fluctuations and conformational changes. The energy landscapes of all proteins are rugged with all the possible conformations rolling down to one or more 3D thermodynamic stable forms. For single domain domains, the energy landscapes are relatively simpler than or domains and the former fold faster than latter.1,2 Our efforts to understand protein folding focus on one such helix domain hbSBD, subunit-binding domain of mammalian mitochondrial branched-chain -ketoacid dehydrogenase complex (BCKD). It is a two-helix protein, and thus, a good candidate for observation of downhill folding mechanism.3 We have performed explicit solvent molecular dynamics simulations to observe its dynamic behavior. Centre for Computational Natural Sciences and Bioinformatics |
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