Research

High-Temperature unfolding of a trp-Cage mini-protein: a molecular dynamics simulation study

Aswin Sai Narain Seshasayee

Centre for Biotechnology, Anna University, Chennai 600025, India

author email corresponding author email

Theoretical Biology and Medical Modelling 2005, 2:7doi:10.1186/1742-4682-2-7

Published:	11 March 2005

Abstract

Background

Trp cage is a recently-constructed fast-folding miniprotein. It consists of a short helix, a 3,10 helix and a C-terminal poly-proline that packs against a Trp in the alpha helix. It is known to fold within 4 ns.

Results

High-temperature unfolding molecular dynamics simulations of the Trp cage miniprotein have been carried out in explicit water using the OPLS-AA force-field incorporated in the program GROMACS. The radius of gyration (Rg) and Root Mean Square Deviation (RMSD) have been used as order parameters to follow the unfolding process. Distributions of Rg were used to identify ensembles.

Conclusion

Three ensembles could be identified. While the native-state ensemble shows an Rg distribution that is slightly skewed, the second ensemble, which is presumably the Transition State Ensemble (TSE), shows an excellent fit. The denatured ensemble shows large fluctuations, but a Gaussian curve could be fitted. This means that the unfolding process is two-state. Representative structures from each of these ensembles are presented here.