Mechanical resistance of proteins explained using simple molecular models

¹ University of Leeds

^* To whom correspondence should be addressed. E-mail: e.paci{at}leeds.ac.uk.

Submitted on July 19, 2005
Revised on August 12, 2005
Accepted on 26 September 2005

	Abstract

Recent experiments have demonstrated that proteins unfold when two atoms are mechanically pulled apart, and that they unfold differently when heated or when a chemical denaturant is added to the solution. Experiments have also shown that the response of proteins to external forces is very diverse, some of them being hard and some others soft. Mechanical resistance originates from the presence of barriers on the energy landscape in the direction of the applied force; together, experiment and simulation have demonstrated that unfolding occurs through alternative pathways when different pairs of atoms undergo mechanical extension. Here we use simulation to probe the mechanical resistance of six structurally diverse proteins when pulled in different directions. For this, we use two very different models: a detailed, transferable one, and a coarse-grained, structure-based one. The coarse-grained model gives results that are surprisingly similar to the detailed one and qualitatively agree with experiment; i.e., the mechanical resistance of different proteins or of a single protein pulled in different directions can be predicted by simulation. The results demonstrate the importance of pulling direction relative to the local topology in determining mechanical stability, and rationalise the effect of the location of importation/degradation tags on the rates of mitochondrial import or protein degradation in vivo.

Key Words: energy landscape, mechanical unfolding, molecular models, protein structure and topology, simulation, structure-based models

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