How to mark off paths on the protein energy landscape

Abstract

Protein folding has run the gamut from complexity, to simplicity, and in a way, back to complexity. In the beginning, there were the slow and complex folding mechanisms of multidomain proteins involving multiple parallel or sequential intermediates en route to the native state (1). Then followed small proteins that can fold by a rapid two-state mechanism (2). Finally, when the single leftover activation barrier was reduced as much as possible through protein engineering, energy landscape roughness was revealed in folding kinetics (3). Landscape roughness temporarily traps very fast folders as they navigate many pathways toward the native state (4). The article by Noe et al. (5) in this issue of PNAS shows how molecular dynamics simulations can be used very efficiently to create a roadmap of the pathways on which a protein explores the energy landscape.