FAD/NADH Dependent Oxidoreductases: From Different Amino Acid Sequences to Similar Protein Shapes for Playing an Ancient Function

Abstract

Flavoprotein oxidoreductases are members of a large protein family of specialized dehydrogenases, which include type II NADH dehydrogenase, pyridine nucleotide-disulphide oxidoreductases, ferredoxin-NAD+ reductases, NADH oxidases, and NADH peroxidases, playing a crucial role in the metabolism of several prokaryotes and eukaryotes. Although several studies have been performed on single members or protein subgroups of flavoprotein oxidoreductases, a comprehensive analysis on structure–function relationships among the different members and subgroups of this great dehydrogenase family is still missing. Here, we present a structural comparative analysis showing that the investigated flavoprotein oxidoreductases have a highly similar overall structure, although the investigated dehydrogenases are quite different in functional annotations and global amino acid composition. The different functional annotation is ascribed to their participation in species-specific metabolic pathways based on the same biochemical reaction, i.e., the oxidation of specific cofactors, like NADH and FADH2. Notably, the performed comparative analysis sheds light on conserved sequence features that reflect very similar oxidation mechanisms, conserved among flavoprotein oxidoreductases belonging to phylogenetically distant species, as the bacterial type II NADH dehydrogenases and the mammalian apoptosis-inducing factor protein, until now retained as unique protein entities in Bacteria/Fungi or Animals, respectively. Furthermore, the presented computational analyses will allow consideration of FAD/NADH oxidoreductases as a possible target of new small molecules to be used as modulators of mitochondrial respiration for patients affected by rare diseases or cancer showing mitochondrial dysfunction, or antibiotics for treating bacterial/fungal/protista infections.

Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies

“…In conclusion, the presented analysis highlights the importance to use fold recognition tools along the approach to a drug design problem according to a rational protocol (similar to what previously reported (29,30,49)), like the ones presented. (77)), for preventing trimer formation and stabilization, or a small molecule/peptide with high affinity for the trimer, aiming to prevent conformational changes leading to the fusion of the viral envelope with host cell plasma membranes.…”

“…CoV-Spike and ACE2 homologus protein-crystallized structures were searched by using the folding recognition methods implemented in pGenThreader and i-Tasser according to our validated protocols (27)(28)(29)(30).…”

“…The sequences of the retrieved 48 crystallized structures (with reference to those crystallized structures indicated with "Certain" or "High" confidence level in pGenThreader output) were aligned by using ClustalW (31) implemented in the Jalview package (32). The 3D coordinates from the 48 crystallized structures were superimposed for comparative purposes by using PyMOL (33) according to our validated protocols (29,34).…”

“…The proposed complete IgG chimeric antibodies were obtained by superimposing the above cited m396 and the resulting engineered FAB portions, in complex with SARS-CoV-1/2 RBD, to the 3D atomic model of a crystallized IgG, available on the PDB (1igt.pdb, (48)) by using SPDBV and PyMOL, according to our validated protocols (29,30,49), that allow to model missing residues, solving clashes and breaks in the backbone.…”

Biological Application and Disease of Oxidoreductase Enzymes

“…Oxidoreductases, which includes oxidase, oxygenase, peroxidase, dehydrogenase, and others, are enzymes that catalyze redox reaction in living organisms and in the laboratory [1]. Interestingly, oxidoreductases catalyze reaction involving oxygen insertion, hydride transfer, proton extraction, and other essential steps.…”