Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms.

ABSTRACT: Allostery, the coupling between ligand binding and protein conformational change, is the heart of biological network and it has often been explained by two representative models, the induced-fit and the population-shift models. Here, we clarified for what systems one model fits better than the other by performing molecular simulations of coupled binding and conformational change. Based on the dynamic energy landscape view, we developed an implicit ligand-binding model combined with the double-basin Hamiltonian that describes conformational change. From model simulations performed for a broad range of parameters, we uncovered that each of the two models has its own range of applicability, stronger and longer-ranged interaction between ligand and protein favors the induced-fit model, and wea

SUBMITTER: Okazaki K 

PROVIDER: S-EPMC2516237 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature