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Speed plays crucial role in breaking protein's H-bonds
Date:10/30/2007

Researchers at MIT studying the architecture of proteins have finally explained why computer models of proteins behavior under mechanical duress differ dramatically from experimental observations. This work could have vast implications in bioengineering and medical research by advancing our understanding of the relationship between structure and function in these basic building blocks of life.

In a paper published as the cover article of the Oct. 16 issue of the Proceedings of the National Academies of Science (PNAS), the scientists, who work with atomistic modelsaccurate representations of nature that use fundamental laws of atomistic interactions as their basisshow for the first time the basic rupture mechanisms of protein structures when protein strands unfold in response to pressure.

We have for the first time simulated the behavior of protein structures under conditions that correspond to those in living biological systems, said Markus Buehler, the Esther and Harold E. Edgerton Assistant Professor in MITs Department of Civil and Environmental Engineering and lead researcher on the team. All the different types of proteins we studied exhibit two distinct fracture modes that are dependent on the speed at which force is applied. Now we understand that what seemed unrealistic in the earlier computer simulations was actually a consequence of deformation rates and a change in the way hydrogen bonds respond to pressure.

Researchers had puzzled over the vast difference in the amount of pressure required to unfold proteins in experimental versus computer simulation. Earlier computer models forced researchers to apply force at much faster speeds than are possible in the laboratory. As a result, these earlier models predicted that the hydrogen bonds would rupture in response to pressures so small that proteins would be unstable. This clearly isnt the case. Rather, proteins form the structural basis of most biological materials.

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Contact: Denise Brehm
brehm@mit.edu
617-253-8069
Massachusetts Institute of Technology, Department of Civil and Environmental Engineering
Source:Eurekalert

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