O2 Reactivity of Flavoproteins

Abstract

Molecular dynamics simulations and implicit ligand sampling methods have identified trajectories and sites of high affinity for O 2 in the protein framework of the flavoprotein D-amino-acid oxidase (DAAO). A specific dynamic channel for the diffusion of O 2 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 O 2 high affinity sites have been exchanged with bulky residues to introduce steric constraints. In G52V DAAO, the valine side chain occupies the site that in wild-type DAAO has the highest O 2 affinity. In this variant, the reactivity of the reduced enzyme with O 2 is decreased >100-fold and the turnover number ≈1000-fold thus verifying the concept. In addition, the simulations have identified a chain of three water molecules that might serve in relaying a H ؉ from the product imino acid ‫؍‬NH 2 ؉ group bound on the flavin Reside to the developing peroxide on the Si-side. This function would be comparable with that of a similarly located histidine in the flavoprotein glucose oxidase.

Modulating O2 Reactivity in a Fungal Flavoenzyme

“…Therefore, Phe-397 side chain displacements are not necessary along the O 2 diffusion compared with the alcohol diffusion. The results showing O 2 access to the AAO active site through a (narrow) hydrophobic channel are in agreement with recent reports describing specific (unique or multiple) O 2 diffusion channels in cholesterol oxidase (33,34), D-amino acid oxidase (35), and other flavo-oxidases (32), in contrast with the traditional hypothesis assuming free diffusion of O 2 through proteins. The existence of channel gates has also been described in some of the above flavo-oxidases, e.g.…”

“…In D-amino acid oxidase, O 2 and the reducing amino acid substrate react with the flavin ring at opposite sides (si and re, respectively) and access the cofactor by different pathways (35). In contrast, in AAO (and glucose oxidase), both oxidizing and reducing substrates would occupy nearly the same position for catalysis (at the re-side of flavin).…”

“…The mechanism of O 2 reduction at the active site of GMC oxidoreductases is still not fully understood (28 -31). O 2 access to the flavoenzyme active site has also been considered in recent studies (32)(33)(34)(35). However, only preliminary investigations on the AAO reaction with O 2 have been performed to date (36), although the physiological (environmental) role of this oxidase is oxygen activation in lignocellulose decay.…”

Engineering of pyranose 2-oxidase for modified oxygen reactivity

“…A positive charge around the flavin reaction site, which can be provided by amino acid residues [15,26,[29][30][31][32] or bound substrate and/or product [33][34][35][36], can influence this. Channels leading from the surface to the active site may affect oxidase reactivity [37,38]. Altering the oxygen reactivity is of considerable interest as shown in recent reviews [15,28] and works of Krondorfer et al [39], Sygmund et al [40], Leferink et al [41], and others [42][43][44].…”

Fluorescent protein barrel fluctuations and oxygen diffusion pathways in mCherry

“…25 Recent developments in efficient computational sampling methods have allowed thorough scanning of the possible pathways for gas diffusion in the interior of proteins. [26][27][28][29] For example, such computational investigations have proved useful in understanding gas diffusion in many protein systems such as molecular dioxygen pathways via dynamic oxygen access channels in flavoproteins, [30][31][32] ammonia transport in carbamoyl phosphate synthetase, [33][34][35] and gas diffusion and channeling in hemoglobin. 28,36 In this paper, we use explicit solvent all-atom molecular dynamics (MD) simulations to investigate the protein barrel fluctuations in mCherry, which is one of the most useful monomeric variants of RFP.…”