title: From polymers to proteins: the effect of side chains and broken symmetry on the formation of secondary structures within a Wang-Landau approach.
abstract: We use a micro-canonical Wang-Landau technique to study the equilibrium properties of a single flexible homopolymer where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and non-consecutive monomers interact via a square-well potential. To mimic the characteristics of a protein-like system, the model is then refined in two different directions. Firstly, by allowing partial overlap between consecutive beads, we break the spherical symmetry and thus provide a severe constraint on the possible conformations of the chain. Alternatively, we introduce additional spherical beads at specific positions in the direction normal to the backbone, to represent the steric hindrance of the side chains in real proteins. Finally, we consider also a combination of these two ingredients. In all three systems, we obtain the full phase diagram in the temperature-interaction range plane and find the presence of helicoidal structures at low temperatures in the intermediate range of interactions. The effect of the range of the square-well attraction is highlighted, and shown to play a role similar to that found in simple liquids and polymers. Perspectives in terms of protein folding are finally discussed.
authors.affiliation: Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy. tatjana.skrbic@unive.it achille.giacometti@unive.it.
authors.forename: Tatjana
authors.initials: T
authors.lastname: Škrbić
authors.affiliation: Material Research Laboratory, University of Nova Gorica, SI-5270 Ajdovscina, Slovenia. artem.badasyan@ung.si.
authors.forename: Artem
authors.initials: A
authors.lastname: Badasyan
authors.affiliation: Center for Computational Physics Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan St., Hanoi, Vietnam. hoang@iop.vast.ac.vn.
authors.forename: Trinh Xuan
authors.initials: TX
authors.lastname: Hoang
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. rudolf.podgornik@ijs.si.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Podgornik
authors.affiliation: Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy. tatjana.skrbic@unive.it achille.giacometti@unive.it.
authors.forename: Achille
authors.initials: A
authors.lastname: Giacometti
mesh_terms: D008958:Models, Molecular; D011108:Polymers / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: D011108:Polymers; D011506:Proteins