Amino-acid residues proline

Though 85% of the amino acid residues in the SF protein are compact with small side chains (glycine, alanine, and serine), near both the N- and C-termini of the SF chain, several quite bulky amino acid residues (proline, histidine, trypthophan) are present in the SF primary structure [100], At first glance, the possibility that y-CDs (9-10A channel diameter) have completely threaded over SF protein chains to form the SF-y-CD IC seems unlikely. However, there is precedence for such an observation in the study of the complexation of propylene oxide-fe-ethylene oxide-fe-propylene oxide (PPO-PEO-PPO) block copolymer with a-CD [101], As pointed out in this study, PPO and PEO homopolymers are known to form CD-ICs only with (3- and a-CDs, respectively. Nevertheless, it was observed there that a-CDs are able to thread over the bulkier PPO end-blocks and complex with the central PEO... 

The amino acid composition of collagen is distinctive. Glycine constitutes approximately one-third of the amino acid residues. Proline and 4-hydroxyproline may account for as much as 30% of a collagen molecule s amino acid composition. Small amounts of 3-hydroxyproline and 5-hydroxylysine also occur. (Specific proline and lysine residues in collagen s primary sequence are hydroxylated within the rough ER after the polypeptides have been synthesized. These reactions, which are discussed in Chapter 19, require the antioxidant ascorbic acid.)... 

Proline is one amino acid which would be expected to profoundly influence the reactivity of a peptide substrate. Proline restricts the possible conformations of a peptide chain and in addition is unable to act as a hydrogen bond donor. Both of these factors could affect peptide bond cleavage by hindering substrate binding or by preventing proper catalysis. Alternately, favorable interaction could take place between the enzyme and a prolyl residue, due either to a favorable hydrophobic interaction with the prolyl side chain or because proline restricts the peptide conformation to one which is favorable. That these effects are important is accentuated by the fact that at every subsite the cleavage probability of a substrate with a proline residue is significantly different from the mean (0.148). This is true for no other amino acid residue. Proline is favorable at P4 and P3 and unfavorable at all other subsites (P2 P3) ... 

Collagen Collagen is an extracellular structural protein 1052 amino acid residues. Collagen has an minsnal amino acid composidon it is about one-third glycine and is rich in proline. Note diat it also lacks Cys and Trp and is deficient in aromadc amino acid residues in general. 

ENZYMATIC ANALYSIS WITH CARBOXYPEPTIDASES. Carboxypeptidases are enzymes that cleave amino acid residues from the C-termini of polypeptides in a successive fashion. Four carboxypeptidases are in general use A, B, C, and Y. Carboxypeptidase A (from bovine pancreas) works well in hydrolyzing the C-terminal peptide bond of all residues except proline, arginine, and lysine. The analogous enzyme from hog pancreas, carboxypeptidase B, is effective only when Arg or Lys are the C-terminal residues. Thus, a mixture of carboxypeptidases A and B liberates any C-terminal amino acid except proline. Carboxypeptidase C from citrus leaves and carboxypeptidase Y from yeast act on any C-terminal residue. Because the nature of the amino acid residue at the end often determines the rate at which it is cleaved and because these enzymes remove residues successively, care must be taken in interpreting results. Carboxypeptidase Y cleavage has been adapted to an automated protocol analogous to that used in Edman sequenators. 

Since the proline residue in peptides facilitates the cyclization, 3 sublibraries each containing 324 compounds were prepared with proline in each randomized position. Resolutions of 1.05 and 2.06 were observed for the CE separation of racemic DNP-glutamic acid using peptides with proline located on the first and second random position, while the peptide mixture with proline preceding the (i-alamine residue did not exhibit any enantioselectivity. Since the c(Arg-Lys-0-Pro-0-(i-Ala) library afforded the best separation, the next deconvolution was aimed at defining the best amino acid at position 3. A rigorous deconvolution process would have required the preparation of 18 libraries with each amino acid residue at this position. 

The improvements in resolution achieved in each deconvolution step are shown in Figure 3-3. While the initial library could only afford a modest separation of DNB-glutamic acid, the library with proline in position 4 also separated DNP derivatives of alanine and aspartic acid, and further improvement in both resolution and the number of separable racemates was observed for peptides with hydrophobic amino acid residues in position 3. However, the most dramatic improvement and best selectivity were found for c(Arg-Lys-Tyr-Pro-Tyr-(3-Ala) (Scheme 3-2a) with the tyrosine residue at position 5 with a resolution factor as high as 28 observed for the separation of DNP-glutamic acid enantiomers. 

The intramembrane segments consist of 21-25 amino acid residues with overrepresentation of the hydrophobic residues Phe, He, Leu, Val, Trp, Tyr, but also of Pro and Cys. This may suggest that S-S bridge formation is part of stabilizing intramembrane structures. Prolines or glycines break the continuity of membrane... 

On the other hand, resonance assignments for CP of threonine and serine, and C and Cy of hydroxy proline, were difficult to make, because of their proximity to carbohydrate carbon resonances. In most cases then, the resonances were assigned on the basis of the effects of pH on the chemical shifts of those resonances. It was shown that the chemical shifts for the carbohydrate carbon resonances were virtually unaffected (AS 0.4 p.p.m.) when going from the cationic state (pH 2) to the anionic state (pH 11) of the amino acid residues. The chemical shifts of C and CP of the amino acid residues, however, shifted considerably (up to 3.1 and 6.6 p.p.m. for C" and CP, respectively see Table VI). 

N-linked glycosylation is sequence specific, involving the transfer of a pre-synthesized oligosaccharide chain to an asn residue found in a characteristic sequence Asn-X-Ser, or Asn-X-Thr or Asn-X-Cys, where X represents any amino acid residue, with the exception of proline. An additional glycosylation determinant must also apply, as not all potential N-linked sites are glycosylated in some proteins. The pre-synthesized oligosaccharide side chain then undergoes... 

The SH3 domain consists of approximately 60 amino acid residues and is C-terminal to the unique domain. Its five P strands form a globular structure whose N- and C-termini are in proximity to each other. SH3 domains mediate both intermolecular and intramolecular interactions, targeting short amino acid sequences that consist of specific proline-rich motifs in a left-handed helix - polyproline... 

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