Loop Motion in Triosephosphate Isomerase is not a Simple Open and Shut Case

Qinghua Liao, Yashraj Kulkarni, Ushnish Sengupta, Dusan Petrovic, Adrian Mulholland, Marc Van der Kamp, Birgit Strodel, Shina Caroline Lynn Kamerlin

Research output: Contribution to journalArticle (Academic Journal)peer-review

21 Citations (Scopus)
438 Downloads (Pure)

Abstract

Conformational changes are crucial for the catalytic action of many enzymes. A prototypical and well-studied example is loop opening and closure in triosephosphate isomerase (TIM), which is thought to determine the rate of catalytic turnover in many circumstances. Specifically, TIM loop 6 ‘grips’ the phosphodianion of the substrate and, together with a change in loop 7, sets up the TIM active site for efficient catalysis. Crystal structures of TIM typically show an open or a closed conformation of loop 6, with the tip of the loop moving ~7 Å between conformations. Many studies have interpreted this motion as a two-state, rigid-body transition. Here, we use extensive molecular dynamics simulations, with both conventional and enhanced sampling techniques, to analyze loop motion in apo and substrate-bound TIM in detail, using five crystal structures of the dimeric TIM from S. cerevisiae. We find that loop 6 is highly flexible and samples multiple conformational states. Empirical valence bond simulations of the first reaction step show that slight displacements away from the fully closed loop conformation can be sufficient to abolish much of the catalytic action; full closure is required for efficient reaction. The conformational change of the loops in TIM is thus not a simple ‘open and shut’ case, and is crucial for its catalytic action. Our detailed analysis of loop motion in a highly efficient enzyme highlights the complexity of loop conformational changes and their role in biological catalysis.
Original languageEnglish
Pages (from-to)15889-15903
Number of pages15
JournalJournal of the American Chemical Society
Volume140
Issue number46
Early online date26 Oct 2018
DOIs
Publication statusPublished - 21 Nov 2018

Structured keywords

  • BrisSynBio
  • Bristol BioDesign Institute

Keywords

  • SYNTHETIC BIOLOGY

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