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Research GBB Molecular Dynamics Group Research

Understanding protein folding

Understanding and predicting how proteins fold is fundamental to protein science. The study of protein folding is occurring at multiple levels. Drs. Xue is testing the effectiveness of alternative approaches to accelerate the folding of small peptides such as the inclusion of low levels of co-solvents or denaturants in accelerating the folding.This work builds on the computational chaperone approach developed by Dr. Fan in which the environment is modulated over time. Such work is not only helping to define conditions that promote rapid folding but also shedding light on the alternative mechanisms by which folding chaperones may work and co solvents and denaturants may interact with peptides. As part of an EC network on emergent complexity Dr. Rampioni (in collaboration with Dr. Nerukh of Cambridge University) is attempting to identify critical events during the folding and unfolding of peptides based on an analysis of velocity correlation matrices.In particular the work is aimed at revealing conditions that give rise to the successful folding transitions and to identify possible transition states. Dr. Periole in collaboration with Prof. Vendruscolo of Cambridge University as part of an EC research training Network of Protein, Folding Misfolding and Disease has also been working to understand the nature of folding transition states by analyzing the properties of a proposed transition state ensemble of the Spectrin SH3 and of a WW domain.Closely related to the work on folding Dr. Fan and Dr. Periole in collaboration with researchers from Columbia University, New York, have investigated the use of alternative approaches for refining protein structures based on homology that combine sampling using replica-exchange methods with a series of recently developed scoring functions.


Periole, X. and Mark, A.E.

Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent

J. Chem. Phys. 126 (2007) 014903


Fan, H. and Mark, A.E.

Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures

Protein Science 15 (2006) 441-448


Fan, H., Wang, X., Zhu, J., Robillard, G.T. and Mark, A.E.

Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface

Proteins 64 (2006) 863 - 873


Fan, H. and Mark, A.E.

Refinement of homology-based protein structures by molecular dynamics simulation techniques
Protein Sci. 13 (2004) 211-220


Fan, H. and Mark, A.E.

Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology-based protein structures

Protein Science 13 (2004) 992-999

Last modified:19 January 2018 2.08 p.m.