Connection between slow and fast dynamics in human purine nucleoside phosphorylase.

Abstract

Protein motions occur across a variety of timescales, from vibrational fluctuations in femtoseconds, to correlated motions in picoseconds, all the way to milliseconds. There have been numerous studies that show these correlated motions may assist in catalysis, protein folding, and substrate specificity. It is also known through transition path sampling studies that rapid promoting vibrations contribute to enzyme catalysis. Human PNP (hPNP) is one enzyme that contains both a correlated motion and a rapid promoting vibration. The slower motion in this enzyme is associated with a particular loop motion that when open allows substrate entry and product release, but closes over the active site during catalysis. The work we report shows a connection between the two motions. We examine the differences between an unconstrained PNP structure, and a PNP structure with constraints on the loop motion. We employ Transition Path Sampling, reaction coordinate identification, electric field calculations, and free energy calculations to illustrate this coupling between the slow and fast protein dynamics.