Research from the Mulholland Group has revealed how two ‘textbook’ enzymes work.
Enzymes are fantastic natural catalysts, but understanding the mechanisms through which they achieve their catalytic power is very challenging experimentally. Simulations help to answer these questions by providing an atomic-level picture of how reactions happen in enzymes. Hen egg-white lysozyme breaks down bacterial cell walls by cleaving the polysaccharides. It was the first enzyme to have its structure solved by X-ray crystallography and as a result is a paradigm of enzyme mechanism shown in biochemistry textbooks. Simulations of the reaction in the enzyme, by PhD students Mike Limb (now at Google) and Ian Grant (now at Kings College London), and postdoctoral researcher Reynier Suardíaz, show that the reacting sugar is distorted – bent out of shape – in order to react, answering a question that was first raised based on the original structures, but has remained unproven until now. The simulations also show that the reaction mechanism includes an additional step, proceeding via a complex pathway of conformational rearrangement, flexing the cell wall saccharide.
QM/MM Simulations Show Saccharide Distortion is Required for Reaction in Hen Egg-White Lysozyme. Limb MAL, Suardiaz R, Grant IM, Mulholland AJ., Chemistry: a European Journal, doi: 10.1002/chem.201805250.
The 2D potential energy surface for the reaction in lysosyme from QM/MM calculations.
Simulations have also shown how a so-called ‘perfect’ enzyme changes its structure to achieve catalysis. Triosephosphate isomerase (TIM) catalyses the interconversion of glyceraldehye 3-phosphate and dihydroxyacetone phosphate, accelerating the reaction so much that it is about as fast as the diffusion limit. Work by Adrian Mulholland with Marc van der Kamp (BBSRC David Phillips Fellow, Biochemistry) and collaborators in Uppsala, Sweden and Düsseldorf and Jülich, Germany, shows that a loop of protein must close fully and snugly over the active site for the reaction to happen. This loop closure is an essential part of the catalytic cycle of the enzyme. The motion of the loop is much more complex than previously thought, however: it is not simply an ‘open and shut case’. Protein loops like this are common in enzymes and so this sort of protein motion is likely to be generally important, and should help in the design of enzyme-like catalysts.
Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case. Liao Q, Kulkarni Y, Sengupta U, Petrović D, Mulholland AJ, van der Kamp MW, Strodel B, Kamerlin SCL. J Am Chem Soc. 2018 Nov 21;140(46):15889-15903. doi: 10.1021/jacs.8b09378
The structure of TIM from MD simulations showing the flexible loop in the open position (red) and the closed position (blue).