Asparagine residue

Coagulation Factors II, III, VII, IX, X, XI, and Xlla fragments, thrombin, and plasmin are classified as serine proteases because each possesses a serine residue with neighboring histidine and asparagine residues at its enzymatically active site (Table 3). Factors II, VII, IX, and X, Protein C, Protein S, and Protein Z are dependent on the presence of vitamin K [84-80-0] for their formation as biologically functionally active procoagulant glycoproteins. 

FIGURE 9.26 The carbohydrate tnoiedes of glycoproteins may be linked to the protein via (a) serine or threonine residues (in the O-linked saccharides) or (b) asparagine residues (in the N-linked saccharides), (c) N-Linked glycoproteins are of three types high mannose, complex, and hybrid, the latter of which combines structures found in the high mannose and complex saccharides. 

Structural analysis of the two pectate lyases PelC and PelE (5, 6), demonstrated that these proteins fold in a large heHx of parallel P strands. A stack of asparagine residues parallel to the helix probably plays a role in the stabUity of this structure. Identification of the structurally conserved amino adds lead to a reaHgnment of the protein sequences (7). In addition to Erwinia extracellular pectate lyases, the multiple aHgnment indudes the Bacillus subtilis pectate lyase, Aspergillus tdger and E. carotovora pectin lyases and plant proteins. 

R. Tyler-Cross and V. Schirch, Effects of amino acid sequence, buffers and ionic strength on the rate and mechanism of deamidation of asparagine residues in small peptides, J. Biol. Chem, 266, 22549 (1991). 

Radkiewicz, J. L., H. Zipse, S. Clarke, and K. N. Houk. 1996. Acclerated Racemization of Aspartic Acid and Asparagine Residues via Succinimidine Intermediates An ab initio Theoretical Exploration of Mechanism. J. Am. Chem. Soc. 118,9148. 

I-Solenoid repeats usually have several x or x x sequence patterns that correspond to the /1-strands (here, denotes an apolar residue, and x is mostly polar but can be any residue except pro line). The middle -position in x x usually has a bulky apolar residue, while -residues in positions close to turns are often alanine, glycine, serine, or threonine. These positions are also occupied by asparagine residues that stack to form H-bonded ladders inside the /1-solenoid. The strand-associated x and x x patterns are interrupted by regions enriched in polar residues and glycine (Hennetin et al., 2006). These are regions of turns and loops. The long loops frequently contain proline residues. In several /1-solenoids, the alternation of apolar and polar residues that is typical for /1-strands is not well observed and outside positions are occupied by apolar residues. 

Before doing so, we briefly examine the influence of conformation and flexibility. Indeed, formation of succinimide is limited in proteins due to conformational constraints, such that the optimal value of the and ip angles (Sect. 6.1.2) around the aspartic acid and asparagine residues should be +120° and -120°, respectively [99], These constraints often interfere with the reactivity of aspartic acid residues in proteins, but they can be alleviated to some extent by local backbone flexibility when it allows the reacting groups to approach each other and, so, favors the intramolecular reactions depicted in Fig. 6.27. When compared to the same sequence in more-flexible random coils, elements of well-formed secondary structure, especially a-helices and 13-turns, markedly reduce the rate of succinimide formation and other intramolecular reactions [90][100],... 

Asparagine residues (and glutamine residues, see below) are sites of particular instability in peptides. As will be exemplified below, rates of degradation at asparagine residues are markedly faster (tenfold and even much more) than at aspartic acid residues. As reported, the tm values for the internal asparagine in a large number of pentapeptides ranged from 6 to 507 d under... 

Another factor that influences partitioning between Pathways e and / (Fig. 6.29) is substitution at the y-amido group of asparagine. The reactivities of two octapeptide analogues, one containing an asparagine residue, the other a y-AT-methylasparagine residue (6.78, R"=H or Me, respectively, Fig. 6.31) [117], were compared. When R"=H, the ratio of Pathways elf was 45 1 at pH 7.4. However, y-A-methylalion of Asn dramatically modified the ratio of Pathways elf which, in this case, was 1 3. 

The influence of secondary structure on reactions of deamidation has been confirmed in a number of studies. Thus, deamidation was inversely proportional to the extent of a-helicity in model peptides [120], Similarly, a-hel-ices and /3-turns were found to stabilize asparagine residues against deamidation, whereas the effect of /3-sheets was unclear [114], The tertiary structure of proteins is also a major determinant of chemical stability, in particular against deamidation [121], on the basis of several factors such as the stabilization of elements of secondary structure and restrictions to local flexibility, as also discussed for the reactivity of aspartic acid residues (Sect. 6.3.3). Furthermore, deamidation is markedly decreased in regions of low polarity in the interior of proteins because the formation of cyclic imides (Fig. 6.29, Pathway e) is favored by deprotonation of the nucleophilic backbone N-atom, which is markedly reduced in solvents of low polarity [100][112],... 

A systematic study with two series of pentapeptides has afforded much information on the influence of flanking residues on asparagine reactivity [126]. In these two series, the central asparagine residue occurred in the sequences Val-Xaa-Asn-Ser-Val and Val-Ser-Asn-Xaa-Val, where Xaais one of ten different residues. In acidic solutions, the Asp peptide was the only product found, and its rate of formation was independent of the nature of the... 

M. L. Di Salvo, S. Delle Fratte, B. Maras, F. Bossa, H. T. Wright, V. Schirch, Deamidation of Asparagine Residues in a Recombinant Serine-Hydroxymethyltransferase , Arch. Biochem. Biophys. 1999, 372, 271-279. 

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