Connecting Conformational Motions to Rapid Dynamics in Human Purine Nucleoside Phosphorylase

Clara F. Frost, Sree Ganesh Balasubramani, Dimitri Antoniou, Steven D. Schwartz

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

The influence of protein motions on enzyme catalysis remains a topic of active discussion. Protein motions occur across a variety of time scales, from vibrational fluctuations in femtoseconds, to collective motions in milliseconds. There have been numerous studies that show conformational 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 purine nucleoside phosphorylase (PNP) is one enzyme that contains both an important conformational motion and a rapid promoting vibration. The slower motion in this enzyme is associated with a loop motion, that when open allows substrate entry and product release but closes over the active site during catalysis. We examine the differences between an unconstrained PNP structure and a PNP structure with constraints on the loop motion. To investigate possible coupling between the slow and fast protein dynamics, we employed transition path sampling, reaction coordinate identification, electric field calculations, and free energy calculations reported here.

Original languageEnglish (US)
Pages (from-to)144-150
Number of pages7
JournalJournal of Physical Chemistry B
Volume127
Issue number1
DOIs
StatePublished - Jan 12 2023
Externally publishedYes

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

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