IIIT Hyderabad Publications |
|||||||||
|
Molecular Dynamics Studies to Investigate Thermostability of Mutant LipasesAuthors: Ramya Cherukupalli,Monika Sharma,N. Madhusudan Rao,Harjinder Singh,Abhijit Mitra Conference: Bioconvene 2007, International conference on Bioinformatics and Drug Discovery, December 20-22, 2007 : University of Hyderabad, Hyderabad Date: 2008-06-07 Report no: IIIT/TR/2008/23 AbstractInvestigation of factors governing thermostability can give valuable insights in understanding the structural and physio-chemical basis of protein stability. Experimental thermostability studies can be complemented by Molecular Dynamics (MD) simulations to analyze the behavior of atoms with a fine grained time resolution. Double mutant (DM: N166Y, A132D) and triple mutant (TM: N166Y, A132D, L114P) of B.subtilis lipase, generated by directed evolution approaches are observed to be more thermostable, with the DM and the TM respectively showing 100-fold and 300-fold increase in their half-lives with respect to the wild type. Crystal structures showed subtle changes like stacking of tyrosine residues, peptide plane flipping and a better anchoring of the terminus, explaining the structural basis for enhanced thermostability. We present initial results of MD simulation studies, of the three systems, carried out with GROMACS software using OPLS-AA force-field. Systems were energy-minimized using steepest descent, followed by constrained dynamic evolution for 200ps and free evolution for 5ns. All simulations were carried out at 300K. The observations in the simulations of systems are indicative of differential roles of respective mutations in DM and TM. One such interesting case is observed in TM, where breaking up of pi-stacking of Y166 and Y25 in crystal structure seems to be compensated by close proximity (2.6)of Y166 to carbonyl carbon of L160 residue. Centre for Computational Natural Sciences and Bioinformatics |
||||||||
Copyright © 2009 - IIIT Hyderabad. All Rights Reserved. |