Dynamics of the WPD Loop of the Yersinia Protein Tyrosine Phosphatase

¹ The Rockefeller University

^* To whom correspondence should be addressed. E-mail: stebbins{at}rockefeller.edu.

Submitted on December 22, 2005
Revised on February 16, 2006
Accepted on 2 May 2006

	Abstract

The bacterial protein tyrosine phosphatase YopH is an essential virulence determinant in Yersinia spp., causing gastrointestinal diseases and the plague. Like eukaryotic PTPases, YopH catalyzes the hydrolysis of the phosphate moiety of phosphotyrosine within a highly conserved binding pocket, which is also characterized by the closure of the so-called "WPD loop" upon ligand binding. In this study, we investigate the conformational changes and dynamics of the WPD loop by molecular dynamics simulations. Consistent with experimental observation, our simulations show that the WPD loop of YopH is intrinsically flexible and fluctuates between the open and closed conformation with a frequency of ~4 ns for the apo, native protein. The region of helix 4 spanning loop 384-392, which has been revealed experimentally as a second substrate-binding site in YopH, is found to be highly associated with the WPD loop and stabilize the loop in the closed, active conformation, providing a structural basis for the cooperation of the second-substrate binding site in substrate recognition. Loop L4 (residues 323-327) is shown to involve in a parallel, correlated motion mode with the WPD loop that contributes the stabilization of a more extended open conformation. In addition, we have detected the loop re-opening in the ligand-bound protein complex applying the locally enhanced sampling (LES) method. The dynamic behavior of the WPD loop for the C403S mutant differs from the wild-type YopH remarkably. These results shed light on the role of the WPD loop in PTPase-mediated catalysis, and are useful in structure-based design for novel, selective YopH inhibitors as antibacterial drugs.

Key Words: Essential dynamics analysis, Locally enhanced sampling, Yersinia virulence factor, conformational transition, molecular dynamics simulations