Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Generalized Model of Polypeptide Chain (GMPC) as One-Dimensional Potts-Like Model With Many-Particle Interactions and Theory of Helix-Coil Transition In Biopolymers

We summarize the results of our theoretical investigations of helix-coil transition both in single-strand (polypeptides) and two-strand (polynucleotides) macromolecules. The Hamiltonian of the Generalized Model of Polypeptide Chain (GMPC) is introduced to describe the system in which the conformations are correlated over some dimensional range Δ. The Hamiltonian does not contain any parameter designed especially for helix-coil transition and uses pure molecular microscopic parameters (the energy of hydrogen bond formation, reduced partition function of repeated unit, the number of repeated units fixed by one hydrogen bond, the energies of interaction between the repeated units and the solvent molecules). To calculate averages we evaluate the partition function using two different methods: (i) random surfaces, and (ii) transfer-matrix approach. An important problem of equivalence between GMPC and many particle one-dimensional Potts model is solved. A number of problems were solved using this unified approach. Thus, we succeed to describe the influence of solvents, both competing and non-competing for hydrogen bond formation with biopolymers, studied the helix-coil transition in circular closed (cc) DNA, considered stacking and hydrogen bonding simultaneously, took into account structural inhomogeneity of biopolymers.

We obtained, that solvents change transition temperature and interval in different ways, depending on energy of solvent-macromolecule interaction; the transition in ccDNA takes place in a wide temperature interval and fine structure is smoothed; stacking on the background of H-bonding increases stability and decreases cooperativity of melting; DNA heterogeneity increases stability and decreases cooperativity, we could analytically derive well known formulae for transition temperature and interval.

Vladimir F. Morozovz*
Yevgeni Sh. Mamasakhlisov
Artem V. Badasyan
Arsen V. Grigoryan
Artem V. Tsarukyan

Yerevan State University
Department of Molecular Physics
1. A. Manougian Str., 375025

*Phone: (374 1) 55 43 41
Fax: (374 1) 55 46 41
Email: morozov@ysu.am