Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations

Lipi Thukral,Jeremy C Smith,Isabella Daidone,Nikolay V Dokholyan

doi:10.1371/journal.pcbi.1002137

Abstract

Small globular proteins and peptides commonly exhibit two-state folding kinetics in which the rate limiting step of folding is the surmounting of a single free energy barrier at the transition state (TS) separating the folded and the unfolded states. An intriguing question is whether the polypeptide chain reaches, and leaves, the TS by completely random fluctuations, or whether there is a directed, stepwise process. Here, the folding TS of a 15-residue β-hairpin peptide, Peptide 1, is characterized using independent 2.5 μs-long unbiased atomistic molecular dynamics (MD) simulations (a total of 15 μs). The trajectories were started from fully unfolded structures. Multiple (spontaneous) folding events to the NMR-derived conformation are observed, allowing both structural and dynamical characterization of the folding TS. A common loop-like topology is observed in all the TS structures with native end-to-end and turn contacts, while the central segments of the strands are not in contact. Non-native sidechain contacts are present in the TS between the only tryptophan (W11) and the turn region (P7-G9). Prior to the TS the turn is found to be already locked by the W11 sidechain, while the ends are apart. Once the ends have also come into contact, the TS is reached. Finally, along the reactive folding paths the cooperative loss of the W11 non-native contacts and the formation of the central inter-strand native contacts lead to the peptide rapidly proceeding from the TS to the native state. The present results indicate a directed stepwise process to folding the peptide.

Highlights

In recent years, extensive investigation has been undertaken of the folding of small proteins and peptides that can be approximated as two-state folders
The six trajectories were used to evaluate the free energy landscape of the system using two progress variables based on the native topology of the peptide: the R parameter, containing information on the backbone, and the fraction of native contacts (r) containing information on the sidechain packing (Figure 1b)
It has been shown that for two-state peptides, such as the present, global coordinates based on the native topology fully satisfy the criteria needed to accurately identify and describe transition state ensemble (TSE) [25]

Summary

Introduction

Extensive investigation has been undertaken of the folding of small proteins and peptides that can be approximated as two-state folders. In these systems, only two stable populations are detected (folded and unfolded), separated by a single effective free energy barrier with only one kinetically important transition state (TS), the reaching of which can be considered as the rate limiting step [1]. To obtain insight at residuelevel detail, w-values are commonly used to investigate the formation of side-chain interactions in the TSE by mutating residues and assessing the effect on folding kinetics. It has been shown that not all conformations obtained in MD simulations by using the wvalue as a restraint belong to the TS [21]

Methods

Results

Conclusion