Diffusion-collision model for the folding kinetics of the lambda-repressor operator-binding domain

Journal of Biomolecular Structure & Dynamics
D BashfordMartin Karplus

Abstract

The operator-binding domain of the lambda-repressor contains five alpha-helices and an extended N-terminal arm in the crystal structure determined by Pabo and Lewis reported in Nature 298, 443, 1982 (1). The four helices form a "box" enclosing a hydrophobic core with the fifth helix interacting with the equivalent helix in a dimer. With a small number of well-defined secondary structure elements (microdomains), the repressor is well suited for an analysis of its folding pathways and kinetics by use of the diffusion-collision model. In this paper, the basic elements of the model appropriate to a several microdomain protein are formulated and applied to a set of folding pathways consistent with the crystal structure of the operator-binding domain. The overall kinetics, as well as the time-dependence of intermediate states are determined as a function of the microdomain stability parameter.

References

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Citations

Apr 1, 1994·Protein Science : a Publication of the Protein Society·M Karplus, D L Weaver
Jun 5, 1987·Journal of Molecular Biology·D J StatesM Karplus
Jun 11, 2002·Journal of Molecular Biology·Suhail A IslamDavid L Weaver
May 14, 1999·Current Opinion in Structural Biology·E Alm, D Baker
Apr 10, 2008·Journal of the American Chemical Society·Katherine W Tripp, Doug Barrick
Jun 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·A T BrüngerM Karplus
May 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·A RojnuckarinS Subramaniam
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Mar 1, 1992·Proteins·K YapaM Karplus
Jul 13, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M CompianiR Casadio
Apr 1, 1994·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·G Z Archontis, E I Shakhnovich
Apr 7, 2004·Journal of Computational Chemistry·Zlatko Vasilkoski, David L Weaver
Jan 1, 1986·Annals of the New York Academy of Sciences·M Karplus
Dec 6, 2018·The Journal of Biological Chemistry·Elin KarlssonCarlo Camilloni
Jul 21, 2006·The Journal of Physical Chemistry. B·Alberto StizzaMario Compiani

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