Elucidating The Nature Of The Streptomyces Plicatusβ-hexosaminidase-bound Intermediate Using Ab Initiornmolecular Dynamics Simulations

摘要

By using all-atom ab initio molecular dynamics simulations, the solution pK_a of the oxazolinium ion intermediate formed during the Streptomyces plicatus β-hexosaminidase (SpHex)-catalyzed hydrolysis of β-D-N-acetylglucosaminides is estimated as pK_a = 7.7. The structure and protonation state of the enzyme-bound intermediate have also been investigated, using hybrid QM/MM methods. The protonation state and conformational properties of the enzyme bound intermediate are found to be sensitive to the protonation state of a number of ionisable residues (other than the aspartate-glutamate catalytic dyad) suggesting that the microscopic electrostatic environment of SpHex not only perturbs the relative magnitudes of the pK_a values of the Asp side chain carboxylate and oxazolinium ion but also that SpHex binds its intermediate in a distorted conformation with respect to its ground-state conformation in solution.