Protein dynamics and catalysis: The problems of transition state theory and the subtlety of dynamic control

J. R.E.T. Pineda, S. D. Schwartz

Research output: Contribution to journalArticlepeer-review

31 Scopus citations

Abstract

This manuscript describes ongoing research on the nature of chemical reactions in enzymes. We will investigate how protein dynamics can couple to chemical reaction in an enzyme. We first investigate in some detail why transition state theory cannot fully describe the dynamics of chemical reactions catalysed by enzymes. We describe quantum theories of chemical reaction in condensed phase including studies of how the symmetry of coupled vibrational modes differentially affects reaction dynamics. We make reference to previous work in our group on a variety of condensed phase chemical reactions (liquid and crystalline) and a variety of enzymatically catalysed reactions including the reactions of lactate dehydrogenase and purine nucleoside phosphorylase. All the protein motions we have studied have been quite rapid. We will propose methods to find motions over a broad range of time-scales in enzymes that couple to chemical catalysis. We report recent findings which show that conformational fluctuations in lactate dehydrogenase can strongly affect its ability to catalyse reactions through protein motion, and that only a tiny minority of conformations appear to be catalytically competent.

Original languageEnglish (US)
Pages (from-to)1433-1438
Number of pages6
JournalPhilosophical Transactions of the Royal Society B: Biological Sciences
Volume361
Issue number1472
DOIs
StatePublished - Aug 29 2006

Keywords

  • Catalysis
  • Promoting vibration
  • Protein dynamics

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

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