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Updated: Jun 20, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Intersegment interactions and helix-coil transition within the generalized model of polypeptide chains approach
A V Badasyan1, G N Hayrapetyan, Sh A Tonoyan
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)
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