Amino Acid Environment Affinity Model Based on Graph Attention Network

ABSTRACTRefsum disease is an inborn error of metabolism that is characterised by a defect in peroxisomal α-oxidation of the branched-chain fatty acid phytanic acid. The disorder presents with late-onset progressive retinitis pigmentosa and polyneuropathy and can be diagnosed biochemically by elevated levels of phytanic acid in plasma and tissues of patients. To date, no cure exists for Refsum disease, but phytanic acid levels in patients can be reduced by plasmapheresis and a strict diet.In this study, we reconstructed a fibroblast-specific genome-scale model based on the recently published, FAD-curated model, based on Recon3D reconstruction. We used transcriptomics (available via GEO database with identifier GSE138379), metabolomics, and proteomics data (available via ProteomeXchange with identifier PXD015518), which we obtained from healthy controls and Refsum disease patient fibroblasts incubated with phytol, a precursor of phytanic acid.Our model correctly represents the metabolism of phytanic acid and displays fibroblast-specific metabolic functions. Using this model, we investigated the metabolic phenotype of Refsum disease at the genome-scale, and we studied the effect of phytanic acid on cell metabolism. We identified 53 metabolites that were predicted to discriminate between Healthy and Refsum disease patients, several of which with a link to amino acid metabolism. Ultimately, these insights in metabolic changes may provide leads for pathophysiology and therapy.

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Recent Advances in the Chemistry of Covalently Bound Flavin Coenzymes

Zeitschrift für Naturforschung B ◽

10.1515/znb-1972-0920 ◽

1972 ◽

Vol 27 (9) ◽

pp. 1069-1071 ◽

Cited By ~ 11

Author(s):

W. C. Kenney ◽

W. H. Walker ◽

E. B. Kearney ◽

R. Seng ◽

T. P. Singer ◽

...

Keyword(s):

Amino Acid ◽

Absorption Band ◽

Performic Acid ◽

Cysteic Acid ◽

Hypsochromic Shift ◽

Ninhydrin Reaction ◽

Acid Environment ◽

Definite Proof ◽

Covalently Bound

Following elucidation of the structures of the flavin components of succinate dehydrogenase (SD) as N (3) -histidyl-8α-FAD and of monoamine oxidase (MAO) as cysteinyl-8α-FAD and determination of the peptide sequences around the flavin sites of these enzymes, attention has been focused on the covalently bound FAD of Chromatium cytochrome c-552. As documented in preliminary communications, the FAD moiety of this enzyme is also substituted at the 8α-position, as judged from ESR hyderfine structure of the free radical cation and the characteristic hypsochromic shift of the second absorption band of the neutral flavoquinone in purified preparations of the flavin. Definite proof has come from the liberation of 8-carbxyriboflavin on performic acid treatment of the enzyme. In regard to ESR and optical spectra and the tendency of the purified flavin (liberated by proteolysis) to undergo autooxidation with a further hypsochromic shift of the second absorption band and increased fluorescence, the flavin resembles the MAO flavin. The fact that fluorescence is >90% quenched at all pH values even at the FMN level and doees not vary with pH between 3.2 and 8 also suggests a thioether linkage as in cysteinyl riboflavin. In many respects, however, the Chromatium flavin differs from cysteinyl riboflavin. Highly purified preparations from tryptic-chymotryptic digests give a positive chloroplatinic test. Electrophoresis clearly shows the presence of carboxyl and amino groups but the peptide gives no characteristic ninhydrin reaction and amino acid analysis of performic acid oxidized samples yields cysteic acid and threonine in amounts less than equimolar to the flavin. The amino acid environment around the flavin may account for these results although a linkage other than a thioether remains a possibility.

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