Stretching lattice models of protein folding
- §Bell Laboratories, Lucent Technologies, 700 Mountain Avenue, Murray Hill, NJ 07974; ¶Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021; **Department of Physics-0319, University of California at San Diego, La Jolla, CA 92093-0319; and ‡‡School of Chemical Sciences, University of Illinois, Urbana, IL 61801
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Contributed by Peter G. Wolynes
Abstract
A new class of experiments that probe folding of individual protein domains uses mechanical stretching to cause the transition. We show how stretching forces can be incorporated in lattice models of folding. For fast folding proteins, the analysis suggests a complex relation between the force dependence and the reaction coordinate for folding.
Footnotes
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↵ ‖ To whom reprint requests should be sent at present address: Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021. e-mail: soccin{at}rockefeller.edu.
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↵ †† A detailed description of the model can be found in refs. 8–10. The energy function used is a contact energy in which monomers that are nearest neighbors on the lattice are considered in contact. There are two terms, one of which is the number of like contacts, N l, (i.e., contacts between monomers of the same type) and the other of which is the number of unlike contacts, N u. The contact part of the energy is then: E cont = NlEl + N u E u. E l and E u set the strengths of like and unlike contacts, respectively. In this work they are −3 and −1, respectively. The sequence used was ABABBBCBACBABABACACBACAACAB.
- Copyright © 1999, The National Academy of Sciences
