Probing the Kinetic Network of Folding-Unfolding Transitions in Proteins

Abstract

The formation of secondary and tertiary structure elements in protein folding are intrinsically complex processes, notoriously difficult to study in a systematic manner. We construct coarse master equations for helix formation processes based on data from atomistic molecular dynamics simulations of helix-rich proteins. By carefully controlling the effects of fast, non-Markovian transitions, on one hand, and the typically limited sampling of slow relaxation processes on the other hand, we probe the underlying network of folding-unfolding transitions between the various configuration states of a protein. This systematic analysis reveals the transition states and the associated folding pathways at multiple levels, from atomistic to coarse-grained representations. We validate our approach in folding studies of short helix-forming polyalanine peptides, as well as of a larger, helix-turn-helix subdomain of a viral scaffolding protein. Our analysis of local, site-specific formation of intra- and inter-chain interactions is a first step towards understanding the elementary stages of secondary and tertiary structure formation in the folding of large proteins, and it allows a direct comparison to data from recent infrared vibrational spectroscopy studies.