Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations.

ABSTRACT:

Background

The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations.

Objective

With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models.

Methods

Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations.

Results

SUBMITTER: Li H 

PROVIDER: S-EPMC8150535 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature