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

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