title: Protein folding with implicit crowders: a study of conformational states using the Wang-Landau method.
abstract: In this paper we introduce the idea of the implicit crowding method to study the statistical mechanical behaviors of folding of β-sheet peptides. Using a simple bead-lattice model, we are able to consider, separately, the conformational entropy involving the bond angles along the backbone and the orientational entropy associated with the dihedral angles. We use a Ising-like model to partially account for the dihedral angle entropy and, implicitly, the hydrogen-bond formations. We also compare our results to recent experiments and find good quantitative agreement on the predicted folded fraction. On the basis of the predictions from the scaled particle theory, we investigate changes in the melting temperature of the protein, suggesting crowding enhanced stability for a variant of trpzip hairpin and a slight instability for the larger β-sheet designed proteins.
authors.affiliation: Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA. hoppe@drexel.edu
authors.forename: Travis
authors.initials: T
authors.lastname: Hoppe
authors.forename: Jian-Min
authors.initials: JM
authors.lastname: Yuan
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D002138:Calibration; D019277:Entropy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary
chemical_list: D010455:Peptides