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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 weaker and shorter-ranged interaction leads to the population-shift model. We further postulate that the protein binding to small ligand tends to proceed via the population-shift model, whereas the protein docking to macromolecules such as DNA tends to fit the induced-fit model.

journal_name

Proc Natl Acad Sci U S A

journal_title

Proceedings of the National Academy of Sciences of the United States of America

authors

Okazaki K,Takada S

doi

10.1073/pnas.0802524105

subject

Has Abstract

pub_date

2008-08-12 00:00:00

pages

11182-7

issue

32

eissn

0027-8424

issn

1091-6490

pii

0802524105

journal_volume

105

pub_type

杂志文章

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