Lysine side chain

Factor XIII. Factor XIII circulates in the blood as a zymogen composed of two pairs of different polypeptide chains designated A and B. Inert Factor XIII has a molecular weight of 350,000 daltons and is converted to its active transglutaminase form in the presence of thrombin and calcium. Activated Factor XIII, Xllla, induces an irreversible amide exchange reaction between the y-glutamine and S-lysine side chains of adjacent fibrin... 

Reaction between a peptide group and a lysine side chain... 

The inhibition of C a2+-ATPase at the active site by ATP-Im or ADP-Im with the participation of Ca2+ is illustrated by the following model. In the reaction of ATP-imidazolide with the carboxylate of Asp 351, a mixed anhydride is formed with the aspartate residue, followed by presumably nucleophilic attack of a lysine side chain, thereby displacing the nucleotide and leading to an intramolecular crosslink.[1]... 

RNase A is a basic protein with an isoelectric point (pi) of 9.45 and a net positive charge in neutral solution.35 However, the conversion of positively charged lysine side chains to polar, but neutrally charged, methylol adducts would be expected to lower the pi of formalin-treated RNase A. To explore this further, RNase A was treated with 5% formalin and analyzed by isoelectric focusing (IEF) gel electrophoresis. Figure 15.5a shows that the pi values were shifted into the pH 6.0-7.4 range. Figure 15.5b shows the results of IEF... 

Protein functional groups able to react with anhydrides include the oc-amines at the N-terminals, the s-amine of lysine side chains, cysteine sulfhydryl groups, the phenolate ion of tyrosine residues, and the imidazolyl ring of histidines. However, acylation of cysteine, tyrosine, and histidine side chains forms unstable complexes that are easily reversible to regenerate the original group. Only amine functionalities of proteins are stable to acylation with anhydride reagents (Fraenkel-Conrat, 1959 Smyth, 1967). 

Figure 4.33 Benzidine can be diazotized with sodium nitrite and HC1 for reaction with proteins through their tyrosine, histidine, or lysine side-chain groups.

It should be noted that the majority of the derivatization techniques modify the peptide s N-terminus. The reason is that the N-terminal amine group is easier to modify than the C-terminal carboxyl group. Also, due to differences in pKa value in the e-amino group of lysine, there are possible reaction that modify the N-terminus only, while the lysine side chains remain intact. Modifications of carboxyl groups... 

The chemical structure of 2,5-hexanedione suggested that it could react with lysine side-chain amino groups in proteins to form pyrroles (see Figure 2-7). In vitro experiments showed that this was, in fact, the case, and that the modified proteins can undergo secondary reactions to yield oxidized and polymeric products (DeCaprio et al. 1982 Graham et al. 1982). Oral administration of 2,5-hexanedione produced evidence that this process can take place in vivo as demonstrated by the detection of 2,5-dimethylpyrrole adducts in serum and axonal cytoskeletal proteins (DeCaprio and O Neill 1985). When a series of... 

One simple case of disordered structure involves many of the long charged side chains exposed to solvent, particularly lysines. For example, 16 of the 19 lysines in myoglobin are listed as uncertain past C8 and 5 of them for all atoms past C/J (Watson, 1969) for ribonuclease S Wyckoff et al. (1970) report 6 of the 10 lysine side chains in zero electron density in trypsin the ends of 9 of the 13 lysines refined to the maximum allowed temperature factor of 40 (R. Stroud and J. Chambers, personal communication) and in rubredoxin refined at 1.2 A resolution the average temperature factor for the last 4 atoms in the side chain is 9.2 for one of the four lysines versus 43.6, 74.4, and 79.3 for the others. Figure 57 shows the refined electron density for the well-ordered lysine and for the best of the disordered ones in ru-... 

---