A-helix configuration

The winter flounder antifreeze protein (AFP), characterized by Sicheri and Yang [42], consists of 37 residues of eight amino acids in an a-helix configuration. The AFP protein was synthesized by the conjoining of the Aa residues determined in the glycine mold, with the exception of the two residues at each of the termini, FIOOC-Asp Thr and Ala Arg-NP and the synthesized protein fragment is left with open amidic surfaces on the... 

Table 3 results compare the importance of different devices used in the SPLIT algorithm. Chosen smoothing procedure is very important, while main filter procedure is next in importance. Subroutines FILTER, CHARGE-BREAK, TURN-BREAK (Methods) and routine for finding maximum preference for the a-helix configuration were all eliminated to examine the importance of the main filter procedure. Automatic choice of decision constants for each tested protein helps to improve the prediction accuracy and the improvement is most obvious when Ajj and Qp parameters are compared in the presence of the decision constants device (first row) and in its absence (fourth row). 

One letter amino acid codes are used in the second column (AA). Predicted structure (PS) in the third column can be a-helix (H), P-sheet (B) or coil (C) structure that includes turn and undefined structure. Residues predicted in the transmembrane helix configuration (PTM) in the fourth column are labeled with letter NT except for highly probable TMH conformation when letter O is used. Residues with a potential to form transmembrane P-strands are labeled with letter E in the fourth column. The coil (C) conformation from third column is specified as undefined (U) or turn (T) conformation in the fourth column. Fifth to eighth column contain smoothed preferences for a-helix (PH), P-sheet (PB), turn (PT) and undefined (PU) conformation. The columns 9 and 10 contain numerical values for hydrophobic moments calculated in the case of assumed a-helix configuration (MA) and for moments calculated for assumed P-sheet configuration (MB). Last two columns contain PH-PT difference of preferences (H-T) that helps in visual identification of predicted transmembrane helices and PB+MB-2.0 scores that help in prediction of potential membrane-embedded P-strands. 

Isotactic polymers are composed of isotactic macromolecules. In isotactic macromolecules, all the substituents are located on the same side of the macromolecular backbone. An isotactic macromolecule consists of 100% meso chads. PP synthesized by a Ziegler-Natta catalysis is an isotactic polymer (Figure 20.1). Isotactic polymers are usually semicrystalline and often form a helix configuration. 

Clearly, there should be little effect of the secondary structure of the condensed monolayer on the area covered per residue. This area would be about 16 A whether the monolayer is made of units in the pleated sheet or a-helix configuration, or a mixture of both. The P/L... 

D- or L-amino acids, but a given helix must be composed entirely of amino acids of one configuration. a-Helices cannot be formed from a mixed copolymer of D- and L-amino acids. An a-helix composed of D-amino acids is left-handed. 

In addition, Zn2+ was shown to inhibit dopamine uptake in a mutant containing an engineered tridentate zinc site, in which the i-4 site from His3757.60, Met3717.56, was replaced with histidine, whereas the introduction of histidines at the i-2, i-3, and i-5 position did not increase Zn2+ affinity (29). In contrast, histidines at positions i+2, i+3, and i+4 all resulted in potent inhibition of dopamine uptake by Zn2+. The incorporation of these data in a model of secondary structure provides evidence for an a-helical configuration of the extracellular portion of TM7, as well as the absence of well-defined secondary structure between positions 3757.6o and 37 97.64 (Fig. IB), thereby suggesting an approximate boundary between the C-terminal end of the helix and the beginning of EL4 (29). 

Infrared and circular dichroism (CD) measurements (Moss et al., 1976b) are both consistent with a sizable fraction of the tetramer being in the a-helical configuration, —29% a-helix with negligible j3 structure. This is rather similar to the 25% a-helix and —0% /3 structure obtained for the tetramer prepared from acid-extracted histones (D Anna and Isenberg, 1974b). 

Amylose consists of unbranched al 4-linked chains of 200-300 glucose residues. Due the a configuration at C-1, these chains form a helix with 6-8 residues per turn (1). The blue coloring that soluble starch takes on when iodine is added (the iodine-starch reaction ) is caused by the presence of these helices—the iodine atoms form chains inside the amylose helix, and in this largely non-aqueous environment take on a deep blue color. Highly branched polysaccharides turn brown or reddishbrown in the presence of iodine. 

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