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.
All Science Journal Classification (ASJC) codes
- Computer Science Applications
- Physical and Theoretical Chemistry