TITLE:
Folding and Unfolding Simulations of a Three-Stranded Beta-Sheet Protein
AUTHORS:
Seung-Yeon Kim
KEYWORDS:
Protein, Folding, Unfolding, Computer Simulation
JOURNAL NAME:
Journal of Materials Science and Chemical Engineering,
Vol.4 No.1,
January
11,
2016
ABSTRACT: Understanding the folding processes of a
protein into its three-dimensional native structure only with its amino-acid
sequence information is a long-standing challenge in modern science. Two- hundred
independent folding simulations (starting from non-native conformations) and two-
hundred independent unfolding simulations (starting from the folded native
structure) are performed using the united-residue force field and Metropolis
Monte Carlo algorithm for betanova (three-stranded antiparallel beta-sheet
protein). From these extensive computer simulations, two representative folding
pathways and two representative unfolding pathways are obtained in the reaction
coordinates such as the fraction of native contacts, the radius of gyration,
and the root- mean-square deviation. The folding pathways and the unfolding
pathways are similar each other. The largest deviation between the folding
pathways and the unfolding pathways results from the root-mean-square deviation
near the folded native structure. In general, unfolding computer simulations could
capture the essentials of folding simulations.