Concerted dynamic motions of an FABP4 model and its ligands revealed by microsecond molecular dynamics simulations

Yan Li, Xiang Li, Zigang Dong

Research output: Contribution to journalArticlepeer-review

9 Scopus citations

Abstract

In this work, we investigate the dynamic motions of fatty acid binding protein 4 (FABP4) in the absence and presence of a ligand by explicitly solvated all-atom molecular dynamics simulations. The dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is compared via multiple 1.2 μs simulations. In our simulations, the protein interconverts between the open and closed states. Ligand-free FABP4 prefers the closed state, whereas ligand binding induces a conformational transition to the open state. Coupled with opening and closing of FABP4, the ligand adopts distinct binding modes, which are identified and compared with crystal structures. The concerted dynamics of protein and ligand suggests that there may exist multiple FABP4-ligand binding conformations. Thus, this work provides details about how ligand binding affects the conformational preference of FABP4 and how ligand binding is coupled with a conformational change of FABP4 at an atomic level.

Original languageEnglish (US)
Pages (from-to)6409-6417
Number of pages9
JournalBiochemistry
Volume53
Issue number40
DOIs
StatePublished - Oct 14 2014

Bibliographical note

Publisher Copyright:
© 2014 American Chemical Society.

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