170 GMPC model and the helix–coil transition in biopolymers

Abstract

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 flexibility of chain, the energies of interaction between the repeated units and the solvent molecules) (Badasyan et al., 2005, 2004). We evaluate the partition function using transfer-matrix approach. We describe the influence of solvent interaction with biopolymer, both with competing and noncompeting for hydrogen bond formation ways. On handling 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 results in 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 the case of effective repulsion; the shape of the 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).