title: Unified description of solvent effects in the helix-coil transition.
abstract: We analyze the problem of the helix-coil transition in explicit solvents analytically by using spin-based models incorporating two different mechanisms of solvent action: explicit solvent action through the formation of solvent-polymer hydrogen bonds that can compete with the intrinsic intra-polymer hydrogen bonded configurations (competing interactions) and implicit solvent action, where the solvent-polymer interactions tune biopolymer configurations by changing the activity of the solvent (non-competing interactions). The overall spin Hamiltonian is comprised of three terms: the background in vacuo Hamiltonian of the "Generalized Model of Polypeptide Chain" type and two additive terms that account for the two above mechanisms of solvent action. We show that on this level the solvent degrees of freedom can be explicitly and exactly traced over, the ensuing effective partition function combining all the solvent effects in a unified framework. In this way we are able to address helix-coil transitions for polypeptides, proteins, and DNA, with different buffers and different external constraints. Our spin-based effective Hamiltonian is applicable for treatment of such diverse phenomena as cold denaturation, effects of osmotic pressure on the cold and warm denaturation, complicated temperature dependence of the hydrophobic effect as well as providing a conceptual base for understanding the behavior of intrinsically disordered proteins and their analogues.
authors.affiliation: Materials Research Laboratory, University of Nova Gorica, Vipavska 13, SI-5000 Nova Gorica, Slovenia.
authors.forename: Artem
authors.initials: A
authors.lastname: Badasyan
authors.affiliation: Department of Molecular Physics, Yerevan State University, A. Manougian Str. 1, 375025, Yerevan, Armenia.
authors.forename: Shushanik A
authors.initials: SA
authors.lastname: Tonoyan
authors.affiliation: Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, Calle Larga S. Marta DD2137, I-30123 Venezia, Italy.
authors.forename: Achille
authors.initials: A
authors.lastname: Giacometti
authors.affiliation: Department of Theoretical Physics, J. Stefan Institute and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana - SI-1000 Ljubljana, Slovenia and Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003-9337, USA.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Podgornik
authors.affiliation: Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003-9337, USA.
authors.forename: V Adrian
authors.initials: VA
authors.lastname: Parsegian
authors.affiliation: Department of Molecular Physics, Yerevan State University, A. Manougian Str. 1, 375025, Yerevan, Armenia.
authors.forename: Yevgeni Sh
authors.initials: YSh
authors.lastname: Mamasakhlisov
authors.affiliation: Department of Molecular Physics, Yerevan State University, A. Manougian Str. 1, 375025, Yerevan, Armenia.
authors.forename: Vladimir F
authors.initials: VF
authors.lastname: Morozov
mesh_terms: D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008954:Models, Biological; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D044367:Phase Transition; D012997:Solvents / Q000737:chemistry*; D013696:Temperature; D014867:Water / Q000737:chemistry*
chemical_list: D001704:Biopolymers; D012997:Solvents; D014867:Water