Speed plays crucial role in breaking protein's H-bonds

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. Early atomistic computer models—accurate representations of nature that use fundamental natural laws as their basis—predicted that the hydrogen bonds holding proteins together would rupture in response to very small pressures, which would mean that proteins are unstable building blocks. But this clearly isn't the case; proteins form the structural basis of most biological materials. It wasn't until the MIT researchers, using large-scale computing facilities, were able to slow down the application of pressure in their models by a factor of 10 or 20, that they understood the discrepancy. At those speeds, which are much closer to the actual speeds at which pressure is applied in living cells and tissues, their study showed a change in behavior of the hydrogen bonds. The team included Xuefeng Chen, now a junior majoring in mechanical engineering, and was led by CEE Professor Markus Buehler.

Laboratory for Atomistic and Molecular Mechanics

"Hierarchies, Multiple Energy Barriers, and Robustness Govern the Fracture Mechanics of (-helical and (-sheet Protein Domains," by Theodor Ackbarow, Xuefeng Chen, Sinan Keten and Markus J. Buehler. Proceedings of the National Academies of Sciences (PNAS) Oct. 16, 2007.