Methods of Protein Iodination
Erwin Regoeczi in Iodine-Labeled Plasma Proteins, 2019
An acyl group is the univalent group, , where R is any organic group attached to one bond of the bivalent carbonyl group ,. The alkyl group has already been defined in Section C.1.a. An aryl group is an organic group derived from an aromatic hydrocarbon by the removal of a hydrogen (e.g., the phenyl group, C6H5-, derived from benzene, C6H6). Amines are organic derivatives of ammonia (NH3) formed by the replacement of one, two, or three of the hydrogen atoms by an alkyl or aryl group; correspondingly, the resulting aliphatic and aromatic (and other) amines are classified as primary (RNH2), secondary (R2NH), or tertiary (R3N) amines. Amides are carboxylic acid derivatives obtained by the replacement of the OH group of an acid by an amino group (NH2). Azo compounds are organic compounds which contain the group, -N:N-, attached to two alkyl or aryl groups (e.g., azobenzene, C6H5-N:N-C6H5). In contrast, only one of the two N atoms bonded together in diazo compounds is attached to a carbon of an organic structure (RN=N, see further below). Imines, containing the grouping, -CH=N-, arise from the condensation of primary amines with aldehydes (or ketones) through the loss of H2O. Imides are nitrogen analogs of anhydrides:
Formation of Peptide Bonds — Proteases as “Activating Systems”
Willi Kullmann in Enzymatic Peptide Synthesis, 1987
The principle of carboxyl activation is ubiquitious in the field of peptide or protein synthesis both in vivo and in vitro. A typical species of an activated acyl group donor is the so-called active ester of the form RCOO—R′ (R′ = alkyl, acyl, aryl). In ribosomal protein synthesis the peptidyl-t-RNA represents an active peptide ribosyl ester which exhibits strong acylating power, and, as a consequence, is readily aminolyzed by an incoming amino acyl-t-RNA.3This ester type activation is also widely used in the field of chemical peptide synthesis. (For a comprehensive review see Reference 4). Carboxyl activation is not only accomplished via active oxygen-based esters; thus during nonribosomal peptide biosynthesis of microbial antibiotics, which is mediated by a multienzyme complex, and to a minor extent during the chemosynthesis of peptides, thioesters play the role of an energy-rich acyl-group donor.4,5
Myocardial Metabolism During Diabetes Mellitus
Grant N. Pierce, Robert E. Beamish, Naranjan S. Dhalla in Heart Dysfunction in Diabetes, 2019
The defect in energy metabolism in the heart during diabetes has also been suggested to involve carnitine. Carnitine and associated cofactors are essential constituents in fatty acid oxidation. Without carnitine, metabolism of fatty moieties would be significantly impaired. Its central role in fatty acid metabolism is depicted in Figure 9. The fatty acyl group combines with coenzyme A in the cytoplasm of the cell to form acyl-CoA. Acyl-CoA can pass through the freely permeable outer mitochondrial membrane but it cannot move through the more selective permeability barrier offered by the inner mitochondrial membrane. The function of carnitine is to transport the acyl-CoA group across the inner mitochondrial membrane. Carnitine acyl-transferase, an enzyme bound to both sides of the inner mitochondrial membrane, catalyzes the formation of acyl-carnitine and coenzyme A from free carnitine and acyl-CoA. The acyl-carnitine can pass through the inner mitochondrial membrane in exchange for free carnitine through the action of the membrane-bound carnitine/acyl-carnitine translocase protein.98 The carnitine acyl-transferase enzyme which is bound to the inner surface of the inner mitochondrial membrane then catalyzes the reformation of free carnitine and acyl-CoA from the transported acyl-carnitine and coenzyme A. The acyl-CoA which is now located within the cristae is available for β-oxidation and subsequent metabolism and energy production.
Standardizing and increasing the utility of lipidomics: a look to the next decade
Published in Expert Review of Proteomics, 2020
Yuqin Wang, Eylan Yutuc, William J Griffiths
Like other neutral lipids TAG can be ionized as [M+ NH4]+ ions. MS/MS of the [M+ NH4]+ ion leads to the loss of fatty acids (RCO2H) and NH3 leaving a series of [M + H-RCO2H]+ ions [64]. These ions will reveal the fatty acyl groups attached to the glycerol backbone, although not their positions or location of double bonds. This is illustrated in Figures 1B – D where the [M+ NH4]+ ion at 874.79 will fragment to give [M + H-R1CO2H]+, [M + H-R2CO2H]+ and [M + H-R3CO2H]+ at m/z 603.53, 573.49 and 577.52. This allows molecular species level identification as TG 16:1_18:0_18:2. Loss of R2CO2H at the second carbon of glycerol is often, but not always, less facile than at other positions, allowing a tentative identification of this acyl group. Diacylglycerols (DG) fragment through similar mechanisms to TAG. If the alkali metal adducts [M+ Na]+ or [M+ Li]+ are fragmented the dominant fragment-ions correspond to the loss of the fatty acids with the metal attached to the residual ion. However, fragmentation of [M+ Na]+ ions is less facile than of [M+ NH4]+ ions.
Cumulus cell acetyl-CoA metabolism from acetate is associated with maternal age but only partially with oocyte maturity
Published in Systems Biology in Reproductive Medicine, 2022
Sharon Anderson, Peining Xu, Alexander J. Frey, Jason R. Goodspeed, Mary T. Doan, John J. Orris, Nicolle Clements, Michael J. Glassner, Nathaniel W. Snyder
Cumulus cells incubated with either [13C6]-glucose, [13C5]-glutamine, or [13C2]-acetate for one hour were analyzed for isotopologue enrichment of the central carbon intermediate acetyl-CoA. Isotopologue enrichment, calculated with FluxFix (10), gives the relative molar % of the product detected derived from the labeled substrate in the given incubation conditions. Thus, in this context, the isotopologue notation describes how many labeled carbons are in the analyte of interest corresponding to M + 0 as the unlabeled acetyl-CoA, M + 1 containing one 13C, M + 2 containing two 13C atoms (Figure 1). M + 2 represents the maximum labeling of the acyl-group (the acetyl group) in acetyl-CoA. Mean isotopologue enrichment of M + 2 acetyl-CoA (mean, standard deviation) was for glucose (3.6, 7.7), for glutamine (9.4, 6.2), and for acetate was (20.7, 13.9) (Figure 2).
Quorum sensing pathways in Gram-positive and -negative bacteria: potential of their interruption in abating drug resistance
Published in Journal of Chemotherapy, 2019
Shafiul Haque, Dinesh K. Yadav, Shekhar C. Bisht, Neelam Yadav, Vineeta Singh, Kashyap Kumar Dubey, Arshad Jawed, Mohd Wahid, Sajad Ahmad Dar
QS signal degradation in Gram-negative bacteria is mostly caused by various AHL degrading enzymes which are categorized into two classes: AHL acylases and AHL lactonases.177 Enzymatic activity of AHL acylases and lactonases involves the cleavage of amide linkage of AHLs and inactivation of lactone ring, respectively.178 Syntheses of acylases were first reported in Variovorax paradoxus178 which degrades the AHL through alkaline hydrolysis of acyl group as an energy source. Xu et al.179 reported a porcine acylase I showing hydrolytic activity for both, the C4-HSL and C8-HSL. An enzyme with potent AHL lactonase activity has been isolated from B. thuringiensis, which displays the ability to attenuate pathogenicity of Erwinia carotova.180