Investigation of PTP1B activation mechanism computational methods

Abstract

Protein tyrosine phosphatase 1B (PTP1B) is a negative regulator of insulin and leptin signaling, and is a major molecular target for the treatment of type II diabetes and obesity. WPD loop is a key element in the mechanism of PTP1B catalysis. In the apo form of the enzyme, WPD loop is usually in an “open” conformation, whereas it closes over the active site upon substrate binding. Here, targeted molecular dynamics (TMD) simulations are reported to examine the transition of the WPD loop from the open to closed states as well as the effect of this motion on the PTP1B conformational activation mechanism. Targeting potential was applied to the WPD loop only and to the whole protein in different sets of simulations. Residue-residue interactions and dihedral angles that contribute to the WPD loop conformational transition were identified. Two major conformational transitions between the open and closed states of WPD loop were observed using PCA and K-means clustering analysis of the Cα atoms in all TMD simulations, except TMD4 simulation. The first transition was the backbone dihedral angle rotation of Ser187 or Pro188 at the WPD loop C-terminus. The second transition was the simultaneous rotations of Trp179 and Arg221 sidechain dihedral angles, and the formation of a polar interaction between the WPD loop and the Arg221 sidechain. A third subtle conformational change, which was not observed in the clustering analysis, was the rotation of the backbone dihedral angle between Asp181 and Phe182 backbone dihedral angles, resulting in the formation of hydrogen bonds between Asp181-Gly183 and between Phe182-Gln262 at. It was also was found that WPD loop closing motion was hindered due to the alternative conformations of the Arg221 and the closed conformation of the R loop. Hydrophobic interactions between the WPD loop and the regions around it, such as the active site, helices α3, α6, α7, loop between β9-β10 (loop11) and S loop were also investigated and it was found that these regions may act as steric hinderance that could influence the WPD loop closure during the simulations. Elucidating the detailed mechanism of PTP1B conformational activation will guide future drug design efforts toward type II diabetes and obesity.