Anharmonicity and self-similarity of the free energy landscape of protein G.
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.
Pontiggia
F
F
International School for Advanced Studies and CNR-INFM Democritos, Via Beirut 2-4, 34014 Trieste, Italy.
Colombo
G
G
Micheletti
C
C
Orland
H
H
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*
C029152:G-substrate; D009419:Nerve Tissue Proteins; D012997:Solvents