title: Thermodynamic features characterizing good and bad folding sequences obtained using a simplified off-lattice protein model.
abstract: The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each beadlike amino acid interacts with the others through a contact potential controlled by a random matrix. Good folding sequences, characterized by a low native energy, display three main thermodynamical ensembles, namely, a coil-like ensemble, an unfolded globule, and a folded ensemble (plus two other states, frozen and random coils, populated only at extreme temperatures). Interestingly, the unfolded globule has some regions already structured. Poorly designed sequences, on the other hand, display a wide transition from the random coil to a frozen state. The comparison with the analytic theory of heteropolymers is discussed.
authors.affiliation: Department of Physics, University of Milano and INFN, sezione di Milano, via Celoria 16, 20133 Milano, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Amatori
authors.forename: J
authors.initials: J
authors.lastname: Ferkinghoff-Borg
authors.forename: G
authors.initials: G
authors.lastname: Tiana
authors.forename: R A
authors.initials: RA
authors.lastname: Broglia
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics; D018909:src Homology Domains
chemical_list: D011506:Proteins