F. Pontiggia, G. Colombo, C. Micheletti and H. Orland
Anharmonicity and self-similarity of the free energy landscape of protein G
Phys. Rev. Lett. 98, art. No. 048102 (2007)
Link to online article. ABSTRACT
The near-native free-energy landscape of protein G is investigated through 0.4 $\mu$s-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.