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Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case

Author:
Liao, Qinghua, Kulkarni, Yashraj, Sengupta, Ushnish, Petrović, Dušan, Mulholland, Adrian J., van der Kamp, Marc W., Strodel, Birgit, Kamerlin, Shina Caroline Lynn
Source:
Journal of the American Chemical Society 2018 v.140 no.46 pp. 15889-15903
ISSN:
1520-5126
Subject:
Saccharomyces cerevisiae, active sites, catalytic activity, crystal structure, molecular dynamics, sampling, simulation models, triose-phosphate isomerase
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 Saccharomyces 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 most of the catalytic activity; 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.
Agid:
6220128