Citrullinated proteins

Kuhn, K. A., L. Kulik, B. Tomooka, K. J. Braschler, W. P. Arend, W. H. Robinson, and V. M. Holers. 2006. Antibodies against citrullinated proteins enhance tissue injury in experimental autoimmune arthritis. J. Clin. Invest. 116 961-973. 

Vossenaar ER, van Venrooij WJ (2004) Citrullinated proteins sparks that may ignite the fire in rheumatoid arthritis. Arthritis Res Ther 6 107-111... 

Skriner, K., Adolph, K., Jungblut, P., Burmester, G., 2006. Association of citrullinated proteins with synovial exosomes. Arthritis Rheum. 54, 3809—3814. 

Certain amino acids and their derivatives, although not found in proteins, nonetheless are biochemically important. A few of the more notable examples are shown in Figure 4.5. y-Aminobutyric acid, or GABA, is produced by the decarboxylation of glutamic acid and is a potent neurotransmitter. Histamine, which is synthesized by decarboxylation of histidine, and serotonin, which is derived from tryptophan, similarly function as neurotransmitters and regulators. /3-Alanine is found in nature in the peptides carnosine and anserine and is a component of pantothenic acid (a vitamin), which is a part of coenzyme A. Epinephrine (also known as adrenaline), derived from tyrosine, is an important hormone. Penicillamine is a constituent of the penicillin antibiotics. Ornithine, betaine, homocysteine, and homoserine are important metabolic intermediates. Citrulline is the immediate precursor of arginine. 

All defects in urea synthesis result in ammonia intoxication. Intoxication is more severe when the metabolic block occurs at reactions 1 or 2 since some covalent linking of ammonia to carbon has already occurred if citrulline can be synthesized. Clinical symptoms common to all urea cycle disorders include vomiting, avoidance of high-protein foods, intermittent ataxia, irritability, lethargy, and mental retardation. The clinical features and treatment of all five disorders discussed below are similar. Significant improvement and minimization of brain damage accompany a low-protein diet ingested as frequent small meals to avoid sudden increases in blood ammonia levels. 

Carbamyl phosphate condenses with ornithine to yield citrulline in the ornithine transcarbamylase (OTC) reaction. OTC is encoded on band p21.1 of the X chromosome, where the gene contains 8 exons and spans 85 kb of DNA. The activity of this enzyme is directly related to dietary protein. There may be tunneling of ornithine transported from the cytosol to OTC, with the availability of intramitochondrial ornithine serving to regulate the reaction. 

Patients who survive the neonatal period can be maintained with a low-protein diet and sodium benzoate. A useful therapeutic adjunct for citrullinemia and argininosuccinic aciduria is dietary arginine supplementation, which enhances the ability to eliminate nitrogen as either citrulline or argininosuccinate. Maintaining normal arginine levels also facilitates protein synthesis. 

Other PTMs may involve changes in the chemical nature of amino acids (e.g., citrullination or deimination). Because many of these modifications result in mass changes that are measurable by MS, they are amenable to detection by MS-based approaches. A number of emerging MS-based strategies allow the identification of PTMs. Several MS-based methods to determine the types and sites of protein phosphorylation and ubiquitination have been developed. Phosphorylation occurs mainly on serine, threonine, and tyrosine residues at a frequency ratio of 1800 200 1 in vertebrates.70 Although the phosphorylation of tyrosine residues occurs less frequently in the proteome, it has been extensively studied. 

Only a few important representatives of the non-proteinogenic amino acids are mentioned here. The basic amino acid ornithine is an analogue of lysine with a shortened side chain. Transfer of a carbamoyl residue to ornithine yields citrulline. Both of these amino acids are intermediates in the urea cycle (see p.l82). Dopa (an acronym of 3,4-dihydroxy-phenylalanine) is synthesized by hydroxyla-tion of tyrosine. It is an intermediate in the biosynthesis of catecholamines (see p.352) and of melanin. It is in clinical use in the treatment of Parkinson s disease. Selenocys-teine, a cysteine analogue, occurs as a component of a few proteins—e.g., in the enzyme glutathione peroxidase (see p.284). 

Figure 1.1 PTMs found on the first 30 residues of the human histone proteins. Only acetylation, methylation, deimination (formation of citrulline) and phosphorylation are shown.

Thompson, P.R. and Fast, W. (2006) Histone citrullination by protein arginine deiminase is arginine methylation a green light or a roadblock ACS Chemical Biology, 1, 433-441. 

PAD4 is a Ca -dependent enzyme that catalyzes the conversion of protein arginine residues to citrulline. (a) Ribbon representation of the PAD4/benzoyl-L-arginine amide complex (PDB code Iwda) in the presence of the ions (green spheres). 

A series of supernatant transfer studies uncovered the fact that HC also produce NO, and in relatively large quantities (Curran et al., 1989). A supernatant generated from KC 8 hr after exposure to LPS and interferon-gamma (IFN-y) stimulated HC -NO biosynthesis and caused a simultaneous decrease in protein synthesis. As seen in the coculture model, a 6- to 8-hr delay in measurable NOj + N03 synthesis was seen in the HC exposed to conditioned KC supernatant. However, unlike KC or KC + HC where equimolar concentrations of citrulline were released into the culture supernatant, no increase in citrulline release paralleled the N02 + N03 synthesis by stimulated HC. It is most likely that the citrulline enters the HC urea cycle and is not secreted. 

Timbrell et al. (1996) reported that much higher hydrazine concentrations were required in rat hepatocyte cultures in comparison to plasma concentrations in male Sprague-Dawley rats to elicit the following hepatic/hepatocellular effects lactate dehydrogenase leakage, ATP and GST depletion, increase in citrulline level, protein synthesis inhibition, taurine leakage and triglyceride accumulation. 

Some 300 additional amino acids have been found in cells. They have a variety of functions but are not constituents of proteins. Ornithine and citrulline... 

FIGURE 3-8 Uncommon amino acids, (a) Some uncommon amino acids found in proteins. All are derived from common amino acids. Extra functional groups added by modification reactions are shown in red. Desmosine is formed from four Lys residues (the four carbon backbones are shaded in yellow). Note the use of either numbers or Creek letters to identify the carbon atoms in these structures, (b) Ornithine and citrulline, which are not found in proteins, are intermediates in the biosynthesis of arginine and in the urea cycle. 

Formation of citrulline Ornithine and citrulline are basic amino acids that participate in the urea cycle. [Note They are not incorporated into cellular proteins, because there are no codons for these amino acids (see p. 429).] Ornithine is regenerated with each turn of the urea cycle, much in the same way that oxaloacetate is regenerated by the reactions of the citric acid cycle (see p 109). The release of the high-energy phosphateof carbamoyl phosphate as inorganic phosphate drives the reaction in the forward direction. The reaction product, citrulline, is trans ported to the cytosol. 

Correct answer = D. Methionine is the precursor of cysteine. An increase in gluconeogenesis releases increased ammonia and results in increased urea production. The essential amino acids leucine and lysine are ketogenic. Ornithine and citrulline are amino acids that are intermediates in the urea cycle, but are not found in tissue proteins. 

About half of the NPN of milk is accounted for by urea. Orotic acid is a particular hallmark of the milks of ruminants milks of other species contain little if any of it (Larson and Hegarty 1977). The free amino acids constituting the a-amino N fraction in Table 1.6 include those that are also found in proteins, as well as ornithine, citrulline, and cx-amino butyric acid. Quantitative analyses of the mixture of free amino acids have been published (Deutsch and Samuelsson 1958 Armstrong and Yates 1963 Rassin et al. 1978). 

The 216-residue hen egg yolk storage protein phosvitin contains 123 serine residues, most of which have been phosphorylated (Eq. 2-16).295 A basic protein of the myelin sheath of neurons contains as many as 6 specific residues of citrulline (Eq. 2-19).296 An adhesive protein from the foot of a marine mollusk contains -80 repeated sequences containing hydroxy-proline 2,3-dihydroxyproline and 3,4-dihydroxyphenylalanine (Dopa) 297/298... 

Natural amino acids, normally not contained in proteins, but which are effective in medicine, include citrulline, ornithine, and dihydroxypheny-lalanine. These aie not listed hi Tables 2 and 3. Citrulline (Cit) with an isoelectric point of 5.9 was isolated by Koga in 1914 by Odake in 1914 and by Wada in 1930. It has the formula... 

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