title: Anharmonicity and self-similarity of the free energy landscape of protein G.
abstract: The near-native free-energy landscape of protein G is investigated through 0.4-micros-long atomistic molecular dynamics simulations in an explicit solvent. A theoretical and computational framework is used to assess the time dependence of salient thermodynamical features. While the quasiharmonic character of the free energy is found to degrade in a few ns, the slow modes display a very mild dependence on the trajectory duration. This property originates from a striking self-similarity of the free-energy landscape embodied by the consistency of the principal directions of the local minima, where the system dwells for several ns, and of the virtual jumps connecting them.
authors.affiliation: International School for Advanced Studies and CNR-INFM Democritos, Via Beirut 2-4, 34014 Trieste, Italy.
authors.forename: F
authors.initials: F
authors.lastname: Pontiggia
authors.forename: G
authors.initials: G
authors.lastname: Colombo
authors.forename: C
authors.initials: C
authors.lastname: Micheletti
authors.forename: H
authors.initials: H
authors.lastname: Orland
mesh_terms: D003198:Computer Simulation; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D009419:Nerve Tissue Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry*
chemical_list: C029152:G-substrate; D009419:Nerve Tissue Proteins; D012997:Solvents