Structure, Thermodynamics, and Folding Pathways for a Tryptophan Zipper as a Function of Local Rigidification.

Publication Year
2016

Type

Journal Article
Abstract

We investigate how the underlying potential energy landscape for a tryptophan zipper changes as indole rings, peptide bonds, termini, and trigonal planar centers are systematically grouped into local rigid bodies. The local rigid body framework results in a substantial computational speedup by effectively reducing the total number of degrees of freedom. Benchmarks are presented for the thermodynamics and folding mechanism. In general, the melting transition, as well as the precise sequence of folding events, is accurately reproduced with conservative local rigidification. However, aggressive rigidification leads to increased topological frustration and a concomitant slowing down of the global kinetics. Our results suggest that an optimal choice of local rigidification, and perhaps a hierarchical approach, could be very useful for investigating complex pathways in biomolecules.

Journal
Journal of chemical theory and computation
Volume
12
Issue
12
Pages
6109-6117
ISSN Number
1549-9626
Alternate Journal
J Chem Theory Comput
PMID
27809512