title: Microsecond scale replica exchange molecular dynamic simulation of villin headpiece: an insight into the folding landscape.
abstract: Reaching the experimental time scale of millisecond is a grand challenge for protein folding simulations. The development of advanced Molecular Dynamics techniques like Replica Exchange Molecular Dynamics (REMD) makes it possible to reach these experimental timescales. In this study, an attempt has been made to reach the multi microsecond simulation time scale by carrying out folding simulations on a three helix bundle protein, Villin, by combining REMD and Amber United Atom model. Twenty replicas having different temperatures ranging from 295 K to 390 K were simulated for 1.5 µs each. The lowest Root Mean Square Deviation (RMSD) structure of 2.5 Å was obtained with respect to native structure (PDB code 1VII), with all the helices formed. The folding population landscapes were built using segment-wise RMSD and Principal Components as reaction coordinates. These analyses suggest the two-stage folding for Villin. The combination of REMD and Amber United Atom model may be useful to understand the folding mechanism of various fast folding proteins.
authors.affiliation: Bioinformatics Team, Scientific and Engineering Computing Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune - 411007, Maharashtra, India.
authors.forename: Vinod
authors.initials: V
authors.lastname: Jani
authors.forename: Uddhavesh B
authors.initials: UB
authors.lastname: Sonavane
authors.forename: Rajendra
authors.initials: R
authors.lastname: Joshi
mesh_terms: D008840:Microfilament Proteins / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D016900:Neurofilament Proteins / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D008840:Microfilament Proteins; D016900:Neurofilament Proteins; D010446:Peptide Fragments; C026615:villin; C115223:villin headpiece subdomain peptide