Conformational selection and induced changes along the catalytic cycle of Escherichia coli dihydrofolate reductase

Thomas R. Weikl, David D. Boehr

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

Protein function often involves changes between different conformations. Central questions are how these conformational changes are coupled to the binding or catalytic processes during which they occur, and how they affect the catalytic rates of enzymes. An important model system is the enzyme dihydrofolate reductase (DHFR) from Escherichia coli, which exhibits characteristic conformational changes of the active-site loop during the catalytic step and during unbinding of the product. In this article, we present a general kinetic framework that can be used (1) to identify the ordering of events in the coupling of conformational changes, binding, and catalysis and (2) to determine the rates of the substeps of coupled processes from a combined analysis of nuclear magnetic resonance R2 relaxation dispersion experiments and traditional enzyme kinetics measurements. We apply this framework to E. coli DHFR and find that the conformational change during product unbinding follows a conformational-selection mechanism, that is, the conformational change occurs predominantly prior to unbinding. The conformational change during the catalytic step, in contrast, is an induced change, that is, the change occurs after the chemical reaction. We propose that the reason for these conformational changes, which are absent in human and other vertebrate DHFRs, is robustness of the catalytic rate against large pH variations and changes to substrate/product concentrations in E. coli. Proteins 2012;.

Original languageEnglish (US)
Pages (from-to)2369-2383
Number of pages15
JournalProteins: Structure, Function and Bioinformatics
Volume80
Issue number10
DOIs
StatePublished - Oct 1 2012

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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