Alanine polypeptide

We have been more concerned with the nature of the water around proteins and peptides. To this end we have investigated the structure and energetics of the solvent, both ordered and disordered around the enzyme lysozyme, in the triclinic crystal[l7d]. In addition to lysozyme, we have characterized the water structure and fluctuations in the crystal of a cyclic hexapeptide, (L-Ala-L-Pro-D-Phe)9[20]. and studied the effect of solvent on the conformation of the dipeptide of alanine[2l] and on the equilibria between extended and helical alanine polypeptides such as those discussed in the previous section[22]. The latter systems simulate aqueous solution conditions rather than crystalline environment. 

If the a hydrogen is substituted as, for example, in a-amino isobutyric acid (Aib), then the conformational energy (< >,t j) map is very restricted, and the preferred form of Aib peptides is computed to be the 310 rather than the a-helical form.150 This prediction has been verified by NMR and infrared spectroscopic measurements on solutions of oligomers of Aib.151 The stability of the 310-helix for short poly(Aib-L-alanine) polypeptides and the increased stabilization of the a-helical form with a lengthening of the chain have been demonstrated recently.152... 

A quasi-linear solute is a best-case scenario for scalability, so we first examine unfolded alanine polypeptides, (Ala) . Table 11.4 is a strong-scaling analysis for a fixed solute size, (Ala)2so, with a surface grid consisting of 350, 000 points, well beyond the... 

Figure 2 CPU time (hours) for the computation of the matrix elements of the Coulomb potential versus the number of atoms N) in a series of alanine polypeptides in a-helix form, (Ala), ...

Figure 14.2 Models of a collagen-like peptide with a mutation Gly to Ala in the middle of the peptide (orange). Each polypeptide chain is folded into a polyproline type II helix and three chains form a superhelix similar to part of the collagen molecule. The alanine side chain is accommodated inside the superhelix causing a slight change in the twist of the individual chains, (a) Space-filling model, (b) Ribbon diagram. Compare with Figure 14.1c for the change caused by the alanine substitution. (Adapted from J. Bella et al.. Science 266 75-81, 1994.)...

From a map at low resolution (5 A or higher) one can obtain the shape of the molecule and sometimes identify a-helical regions as rods of electron density. At medium resolution (around 3 A) it is usually possible to trace the path of the polypeptide chain and to fit a known amino acid sequence into the map. At this resolution it should be possible to distinguish the density of an alanine side chain from that of a leucine, whereas at 4 A resolution there is little side chain detail. Gross features of functionally important aspects of a structure usually can be deduced at 3 A resolution, including the identification of active-site residues. At 2 A resolution details are sufficiently well resolved in the map to decide between a leucine and an isoleucine side chain, and at 1 A resolution one sees atoms as discrete balls of density. However, the structures of only a few small proteins have been determined to such high resolution. 

A certain polypeptide is shown by arid hydrolysis to contain only three amino acids serine(Ser), alanine(Ala), and methionine(Met) with mole fractions of j, and respectively. Enzymatic hydrolysis yields the following fragments Ser-Ala Ser-Met Ala-Ser. Deduce the primary structure of the polypeptide. 

On complete hydrolysis, a polypeptide gives two alanine, one leucine, one methionine, one phenylalanine, and one valine residue. Partial hydrolysis gives the following fragments Ala-Phe, Leu-Met, Val-Ala, Phe-Leu. It is known that the first amino acid in the sequence is valine and the last one is methionine. What is the complete sequence of amino acids ... 

Suppose that, in the polypeptide referred to in Question 31, the first amino acid is alanine and the last one is also alanine. What is the complete sequence of amino acids ... 

C13-0119. Suppose that a polypeptide is constructed with alanine as the only monomer. What is the empirical formula of this polypeptide If the polypeptide has a molar mass of 1.20 X 10 g/mol, how many repeat units of alanine does it contain ... 

Amino acids such as glycine, alanine, or phenylalanine have been reacted to polypeptides by means of CDI in aqueous imidazole buffer.[49]... 

Amino acids containing nucleobases like uracil and adenine, as well as imidazole, such as / -(uraciM-yl)-a-alanine, j5-(adenin-9-yl)-a-alanine, and j8-(imidazol-l-yl)-a-alanine, can also be polycondensed by CDI in aqueous imidazole buffer solution at pH 6.8 at 0 °C. The polycondensation leads to low conversion (yields of polymer 1% after four days), but pure polypeptides resulted from the reaction. Thus, compared to other alternative procedures for polycondensation, that using CDI proved to be the most effective 503... 

Kallenbach and co-workers have recently demonstrated via CD spec-tropolarimetry and NMR spectrometry that a seven-residue alanine peptide adopts predominantly the PPII helical conformation in aqueous solution (Shi et al., 2002). Since alanine is nothing but backbone, such a finding indicates that the polypeptide backbone possesses an intrinsic... 

The percent conversion of the monomer to the polypeptide can be estimated by the quantity 100 (Aq - At) / Aq, where Aq and At are the integrated intensities of the ester band at the start and time t, respectively. At 40 °C, it tended to saturate at about 30 % for the Y-type films of L-NaphAla-C-i s, and L-PyrAla-G 8, although the conversion for the LB film of long-chain ester of alanine (L-Ala- Ci s) reached to 90 % [52]. This difference is considered to be due to a larger steric hindrance of the aromatic rings. 

Considerable amounts of glutamic acid, glycine, and alanine, as well as smaller quantities of aspartic acid, serine, threonine, basic amino acids, leucine, phenylalanine, and cystine have been demonstrated in a total hydrolyzate of the nondiffusible fraction by Boulanger et al. (BIO). Using Deacidite resin, they separated this material into two polypeptide fractions, acid and alkaline, and found that glutamic acid, aspartic acid, leucine, and certain cystine derivatives were the chief constituents of the former, whereas the latter contained considerable amounts of glycine, basic amino acids, and alanine. 

The results of a comprehensive 13 C CP/MAS NMR study of the structure of solid polypeptides, prepared by polymerization of amino acid N-carboxyanhydrides under various conditions, have been reported105,107. In the case of poly(L-alanine) it was found that... 

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