Substrate—enzyme fluctuation correlations

One result from the analysis of the MD simulation was the proposal of a new enzymic pathway for hydrolysis by lysozyme. We begin with a description of the alternative mechanism, and the basis on which it was proposed. The energetics of the individual GlcNAc units in the lysozyme cleft are then presented, followed by a graphical representation of the correlation between the atomic fluctuations of the substrate and those of the enzyme. Of particular interest is the fact that the binding interactions stabilize a bound state conformation for the two glycosides involved in hydrolysis that is optimum for catalysis by the alternative mechanism and which differs from the conformations of the other glycosides. These conformational features are described in the final two sections. 

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