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J Chem Phys. 2009 Sep 21;131(11):115104. doi: 10.1063/1.3216564.

Intersegment interactions and helix-coil transition within the generalized model of polypeptide chains approach.

Author information

  • 1Department of Molecular Physics, Yerevan State University, A. Manougian Str. 1, 375025 Yerevan, Armenia. abenight@pdx.edu

Abstract

The generalized model of polypeptide chains is extended to describe the helix-coil transition in a system comprised of two chains interacting side-by-side. The Hamiltonian of the model takes into account four possible types of interactions between repeated units of the two chains, i.e., helix-helix, helix-coil, coil-helix, and coil-coil. Analysis reveals when the energy I(hh)+I(cc) of (h-h, c-c) interactions overwhelms the energy I(hc)+I(ch) of mixed (h-c, c-h) interactions, the correlation length rises substantially, resulting in narrowing of the transition interval. In the opposite case, when I(hh)+I(cc)<I(hc)+I(ch), nontrivial behavior of the system is predicted where an intermediate plateau appears on the denaturation curve. For the latter case, calculations of the number of junctions and the average length of helical segments indicate rearrangement of helical segments at the transition point. Conceptual links are established with experimentally oriented theories of Ghosh and Dill [J. Am. Chem. Soc. 131, 2306 (2009)] and Skolnick and Holtzer [Biochemistry 25, 6192 (1986)], providing a potential explanation for both favorable helix formation and disfavored intersegment interactions from the same theoretical perspective.

PMID:
19778153
[PubMed - indexed for MEDLINE]
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