Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines
- Abteilung Physikalische Chemie, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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Communicated by Gerhard Ertl, Max Planck Society for the Advancement of Science, Berlin, Germany, April 4, 2007 (received for review January 23, 2007)
Abstract
Analyzing nonlinear conformational relaxation dynamics in elastic networks corresponding to two classical motor proteins, we find that they respond by well defined internal mechanical motions to various initial deformations and that these motions are robust against external perturbations. We show that this behavior is not characteristic for random elastic networks. However, special network architectures with such properties can be designed by evolutionary optimization methods. Using them, an example of an artificial elastic network, operating as a cyclic machine powered by ligand binding, is constructed.
Footnotes
- To whom correspondence should be sent at the present address: Nanobiology Laboratories, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan. E-mail: togashi{at}phys1.med.osaka-u.ac.jp
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Author contributions: Y.T. and A.S.M. designed research; Y.T. and A.S.M. performed research; Y.T. analyzed data; and Y.T. and A.S.M. wrote the paper.
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The authors declare no conflict of interest.
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This article contains supporting information online at www.pnas.org/cgi/content/full/0702950104/DC1.
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↵ † The described evolutionary optimization algorithm allows us to construct only the networks with a single soft mode. It can be, however, easily modified for the design of networks with two or more soft modes, separated by a gap from the rest of the spectrum.
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Freely available online through the PNAS open access option.
- © 2007 by The National Academy of Sciences of the USA
