A targeted molecular dynamics study of WPD loop movement in PTP1B

Targeted molecular dynamics was used to examine the mechanism of WPD loop closure in PTP1B, which is essential for the activity of the enzyme. Two important regions are identified: the R-loop (residues 113–118), which assists in substrate binding, and the S-loop (residues 198–209), which undergoes a conformational change that appears to be vital for the movement of the WPD loop. The S-loop is adjacent to the α3-helix, and its conformational change is coupled with a change of interactions between the α3- and α7-helices. This latter observation is of particular interest in connection with a novel class of allosteric inhibitors of PTP1B [Wiesmann et al., Nat. Struc. Mol. Biol. 11 (2004) 730–737]. These compounds prevent the closure of the WPD loop, forcing the enzyme to remain in a catalytically inactive conformation, by blocking the rearrangement of the α3-helix relative to the α7-helix.