High temperature unfolding simulations of the TRPZ1 peptide

¹ MRC - Centre for Protein Engineering

^* To whom correspondence should be addressed. E-mail: gs{at}mrc-lmb.cam.ac.uk.

Submitted on September 21, 2007
Revised on November 2, 2007
Accepted on 3 January 2008

	Abstract

We report high temperature molecular dynamics simulations of the unfolding of the TRPZ1 peptide using an explicit model for the solvent. The system has been simulated for a total of 6 µs with 100 ns minimal continuous stretches of trajectory. The populated states along the simulations are identified by monitoring multiple observables, probing both the structure and the flexibility of the conformations. The un/folding transition pathways are analysed. The unfolding process of the peptide occurs in two steps because of the accumulation of a metastable on-pathway intermediate state stabilised by two native backbone hydrogen bonds assisted by non-native hydrophobic interactions between the tryptophan side chains. Analysis of the un/folding kinetics and classical commitment probability calculations on the conformations extracted from the transition pathways show that the rate limiting step for unfolding is the disruption of the ordered native hydrophobic packing (TRP-zip motif) leading from the native to the intermediate state. But, the speed of the folding process is mainly determined by the transition from the completely unfolded state to the intermediate and specifically by the closure of the hairpin loop driven by formation of two native backbone hydrogen bonds and hydrophobic contacts between tryptophan residues. The temperature dependence of the unfolding time provides an estimate of the unfolding activation enthalpy that is in agreement with experiments. The unfolding time extrapolated to room temperature is in agreement with the experimental data, as well, thus providing a further validation to the analysis reported here.

Key Words: TRP-Zipper, intermediate state, molecular dynamics simulation, peptide folding, transition state