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Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

GMPC model and the helix-coil transition in biopolymers

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 . 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 flexibility of chain, the energies of interaction between the repeated units and the solvent molecules) (Badasyan et al., 2005; Badasyan et al., 2004). We evaluate the partition function using transfer-matrix approach. We describe the influence of solvent interaction with biopolymer, both with competing and non-competing for hydrogen bond formation ways. Handling of the problem of solvent influence on helix-coil transition we obtained dependence on energy of solvent-macromolecule interaction, how solvents change correlation length, transition temperature and interval. We obtained, that two type interaction of solvent brings to appear low temperature coil-helix transition, which we connect with cold denaturation. A consistent inclusion of osmotic pressure effects in a description of helix-coil transition for poly(L-glutamic acid) in solution with polyethylene glycol can offer an explanation of the experimentally observed linear dependence of transition temperature on osmotic pressure as well as the concurrent changes in the cooperativity of the transition (Badasyan et al., 2012). We also took into account two biopolymers side-by-side interactions. In case of effective repulsion; the shape of melting curve is two-phase with high and wide correlation length in a plateau on denaturation curve (Badasyan et al., 2009). We also took into account structural heterogeneity of biopolymers using constrained annealing approximation (Serva & Paladin, 1993).

References

    A.V. Badasyan, A. V. Grigoryan, E. Sh. Mamasakhlisov, A. S. Benight, & Morozov V. F. (2005). The helix-coil transition in heterogeneous double stranded DNA: Microcanonical method. J. Chem. Phys. 123 (doi: 10.1063/1.2727456).

    A. V. Badasyan, G. N. Hayrapetyan, Sh. A. Tonoyan, Y. Sh. Mamasakhlisov, A. S. Benight & Morozov V. F. (2009). Intersegment interactions and helix-coil transition within the generalized model of polypeptide chains approach. J. Chem. Phys. 131 (doi:10.1063/1.3216564).

    A.V. Badasyan, Sh.A. Tonoyan, A. Giacometti, R. Podgornik, V.A. Parsegian, Y. Sh. Mamasakhlisov, & Morozov V. F. (2012). Osmotic Pressure Induced Coupling between Cooperativity and Stability of a Helix-Coil Transition. Phys. Rev. Lett. 109 (doi: 10.1103/PhysRevLett.109.068101).

    V. F. Morozov, A. V. Badasyan, A. V. Grigoryan, M. A. Sahakyan, & Mamasakhlisov Y. Sh. (2004). Stacking and hydrogen bonding: DNA cooperativity at melting. Biopolymers 75, 434-439.

    M. Serva & Paladin G. (1993). Gibbs Thermodynamic Potentials for Disordered Systems. Phys. Rev. Lett. 70, 105-108.


V. F. Morozov
Sh. A. Tonoyan
L. V. Melkonyan
N. L. Poghosyan
Sh. A. Sargsyan1

Department of Molecular Physics
Yerevan State University
Yerevan, Armenia
1Department of Medical Physics
Yerevan State Medical University
Yerevan, Armenia