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Mechanical Resistance of Proteins Explained Using Simple Molecular Models

Daniel K. West ^* , David J. Brockwell  , Peter D. Olmsted ^* , Sheena E. Radford   and Emanuele Paci ^* 

^* School of Physics & Astronomy, School of Biochemistry & Microbiology, and Institute of Molecular Biophysics, University of Leeds, Leeds, United Kingdom

Correspondence: Address reprint requests to Dr. Emanuele Paci, Tel.: 44-113-343-3806; E-mail: e.paci{at}leeds.ac.uk.

Recent experiments have demonstrated that proteins unfold when two atoms are mechanically pulled apart, and that this process is different to 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 others "soft." Mechanical resistance originates from the presence of barriers on the energy landscape; 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 rationalize the effect of the location of importation/degradation tags on the rates of mitochondrial import or protein degradation in vivo.

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