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

Accepted version
Peer-reviewed

Type

Article

Change log

Authors

Joseph, JA 
Whittleston, CS 
Wales, DJ 

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.

Description

Keywords

Kinetics, Molecular Dynamics Simulation, Protein Folding, Protein Structure, Secondary, Proteins, Thermodynamics, Tryptophan

Journal Title

Journal of Chemical Theory and Computation

Conference Name

Journal ISSN

1549-9618
1549-9626

Volume Title

12

Publisher

American Chemical Society
Sponsorship
J.A.J. acknowledges financial support from the Gates Cambridge Trust.