Conformational Behavior of Flavin Adenine Dinucleotide: Conserved Stereochemistry in Bound and Free States

Abstract

Metabolic enzymes utilize the cofactor flavin adenine dinucleotide (FAD) to catalyze essential biochemical reactions. Because these enzymes have been implicated in disease pathways, it will be necessary to target them via FAD-based structural analogues that can either activate/inhibit the enzymatic activity. To achieve this, it is important to explore the conformational space of FAD in the enzyme-bound and free states. Herein, we analyze X-ray crystallographic data of the enzyme-bound FAD conformations and sample conformations of the molecule in explicit water by molecular dynamics (MD) simulations. Enzyme-bound FAD conformations segregate into five distinct groups based on dihedral angle principal component analysis (PCA). A notable feature in the bound FADs is that the adenine base and isoalloxazine ring are oppositely oriented relative to the pyrophosphate axis characterized by near trans hypothetical dihedral angle "δV" values. Not surprisingly, MD simulations in water show final compact but not perfectly stacked ring structures in FAD. Simulation data did not reveal noticeable changes in overall conformational dynamics of the dinucleotide in reduced and oxidized forms and in the presence and/or absence of ions. During unfolding-folding dynamics, the riboflavin moiety is more flexible than the adenosine monophosphate group in the molecule. Conversely, the isoalloxazine ring is more stable than the variable adenine base. The pyrophosphate group depicts an unusually highly organized fluctuation illustrated by its dihedral angle distribution. Conformations sampled from enzymes and MD are quantified. The extent to which the protein shifts the distribution from the unbound state is discussed in terms of prevalent FAD shapes and dihedral angle population.

Flavin-adenine-dinucleotide gold complex nanoparticles: chemical modeling design, physico-chemical assessment and perspectives in nanomedicine

“…For this aim, we designed a lot of experiments in which FAD-PEG was applied as complex in the nucleation of pegylated gold nanoparticles confirmed by HPLC cromatography (Figure S1-A in Supporting Information). The active isoalloxazine ring of flavin cofactors (FAD) induce one-or two-electron redox transitions in a wide range of biochemical reactions pertinent for cell bioenergetics, protein folding, cellular redox homeostasis 10,11 .…”

Deep UV dispersion and absorption spectroscopy of biomolecules

“…FAD: Similar to βNAD, FAD is also a redox protein. FAD has 4 states that enables it to accept or deliver electrons hydrogen atoms, or hydronium ions by converting among these states [29,30].…”

Revealing the transient conformations of a single flavin adenine dinucleotide using an aerolysin nanopore

“…However, X-ray crystal structures in the Protein Data Bank show that FAD adopts its intermediate conformations rather than the "stack" or "open" form within many local host enzyme environments. 10 Therefore, the various binding conformations of FAD affect the diversity of the functions of FAD-based analogues, leading to a huge inuence on the activity of related enzymes that are implicated in numerous disease pathways. 11 Although several "partially stacked" conformations of FAD were suggested by computer modelling-combined with ion mobility spectrometry (IMS), many transient intermediates and conformation distribution are still hidden in these ensemble measurements.…”