TCB Publications - Abstract

Jan Saam, Elena Rosini, Gianluca Molla, Klaus Schulten, Loredano Pollegioni, and Sandro Ghisla. O2-reactivity of flavoproteins: Dynamic access of dioxygen to the active site and role of a H+ relay system in D-amino acid oxidase. Journal of Biological Chemistry, 285:24439-24446, 2010. (PMC: 2915680)

SAAM2010 Molecular dynamics simulations and implicit ligand sampling methods have identified trajectories and sites of high affinity for O2 in the protein framework of the flavoprotein D-amino acid oxidase (DAAO). A specific dynamic channel for the diffusion of O2 leads from solvent to the flavin Si-side (amino acid substrate and product bind on the Re-side). Based on this, amino acids that flank the putative O2 high affinity sites have been exchanged with bulky residues in order to introduce steric constraints. In Gly52Val-DAAO, the valine side chain occupies the site that in wild-type DAAO has the highest O2 affinity. In this variant the reactivity of the reduced enzyme with O${_2}$ is decreased $\leq$ 100-fold and the turnover number $\approx$1000-fold thus verifying the concept. In addition, the simulations have identified a chain of 3 water molecules that might serve in relying a H+ from the product iminoacid =NH2+ group bound on the flavin Re-side to the incipient peroxide on the Si-side. This function would be comparable to that of a similarly located histidine in the flavoprotein glucose oxidase.

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