Proline helix

Fig. 11. Ribbon diagram of the GFCC /1-sheet face in Dl. The tt cation stacking motif and structural differences observed in the edge /3-strand are shown. /3-bulges (B1 or B2) and the left handed poly proline helix (PPII) in GHR D2 are denoted with arrows. Residues at the end of the /3-strand GDI that participated in cytokine contacts are labeled on the figure. IFNAR2 Gys-12 which forms a disulfide bond with cysteine on /3-strand is also labeled.

Figure 1.4. Chiral supramolecular structures (a) a-helix of polypeptides, (b) poly-prolin-helix of collagene, and (c) deoxyribonucleic acid (DNA) Z = D-Deoxyribose, P = phosphoric acid, A — adenine, G = guanine, C = cytosine, T = thymine (from [8]).

Fhe amino acid side chains project out from the a helix (see Figure 2.2e) and do not interfere with it, except for proline. The last atom of the proline side... 

Figure 14.1 Each polypeptide chain in the collagen molecule folds into an extended polyproline type II helix with a rise per turn along the helix of 9.6 A comprising 3.3 residues. In the collagen molecule three such chains are supercoiled about a common axis to form a 3000-A-long rod-like molecule. The amino acid sequence contains repeats of -Gly-X-Y- where X is often proline and Y is often hydroxyproline. (a) Ball and stick model of two turns of one polypeptide chain.

Proline is the only amino acid in Table 27.1 that is a secondary amine, and its presence in a peptide chain introduces an amide nitrogen that has no hydrogen available for hydrogen bonding. This disrupts the network of hydrogen bonds and divides the peptide into two separate regions of a helix. The presence of proline is often associated with a bend in the peptide chain. 

The tendencies of the amino acids to stabilize or destabilize a-helices are different in typical proteins than in polyamino acids. The occurrence of the common amino acids in helices is summarized in Table 6.1. Notably, proline (and hydroxyproline) act as helix breakers due to their unique structure, which fixes the value of the —N—C bond angle. Helices can be formed from either... 

Surveys of the frequency with which various residues appear in helices and sheets show that some residues, such as alanine, glutamate, and methionine, occur much more frequently in a-helices than do others. In contrast, glycine and proline are the least likely residues to be found in an a-helix. Likewise, certain residues, including valine, isoleucine, and the aromatic amino acids, are more likely to be found in /3-sheets than other residues, and aspartate, glutamate, and proline are much less likely to be found in /3-sheets. 

The a-helical parts of myoglobin and other proteins stop whenever a proline residue is encountered in the chain. Why is proline never present in a protein o -helix ... 

So far, the CD of poIy(L-proline) n has been interpreted without ambiguity for a rather strong left-handed helix ... 

One may conclude that the rate-determining step of the renaturation is at least partly influenced by the cis-trans isomerization of the peptide bond the secondary nitrogen atom of which arises from proline. Otherwise, only the entropy-controlled slow nuclea-tion should be observed kinetically. The covalent bridging through Lys-Lys, therefore, gives rise not only to thermodynamic stabilization of the triple helix but also to kinetic properties which have hitherto been observed in the case of type III procollagen146) and its aminoterminal fragment Col 1-3144). 

Because of these observations, comparative experiments with peptides of different proline content in a solvent less polar than water, are recommended. (Pro-Pro-Gly)n and (Pro-Ala-Gly)n, in methanol/acetic add (volume ratio 9 1) show a temperature-induced triple helix-coil transition which is characterized by the following parameters92,150) (Pro-Pro-Gly)n AH°s = -1.9 kJ/rnol tripeptide AS° = -5.4 J tnor1 K (Pro-Ala-Gly) A HI = -0.9 kJ/mol tripeptide A 5° = -3.8 J mol-1 K ... 

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