Helix chain, extended

Fig. 2. Protein secondary stmcture (a) the right-handed a-helix, stabilized by intrasegmental hydrogen-bonding between the backbone CO of residue i and the NH of residue t + 4 along the polypeptide chain. Each turn of the helix requires 3.6 residues. Translation along the hehcal axis is 0.15 nm per residue, or 0.54 nm per turn and (b) the -pleated sheet where the polypeptide is in an extended conformation and backbone hydrogen-bonding occurs between residues on adjacent strands. Here, the backbone CO and NH atoms are in the plane of the page and the amino acid side chains extend from C ...

The a helix is represented in Figure 12-18. Each amide group is attached by a hydrogen bond to the third one from it in either direction along the polypeptide chain. There are 3.60 amino-acid residues per turn of the helix. The total rise of the helix per turn—the pitch of the helix—is about 5.38 A, which corresponds to 1.49 A per residue. The amino-acid side chains extend away from the helix axis, as shown in Figure 12-18. 

The folded form of proteins, reported by Astbury, was identified with the a-helix, the extended one described in terms of intermolecularly hydrogen-bonded array of chains was known in the earlier literature as the... 

Figure 34.4. Myosin Structure at High Resolution. The structure of the SI fragment from muscle myosin reveals the presence of a P-loop NTPase domain (shaded in purple). An a helix that extends from this domain is the binding site for the two light chains.

The five residue linker between helices (H-L5-H) divides up in to three major clusters. The main chain torsion preference for the first sub-cluster are mostly Or at the first position and at the second to fifth positions of the linker. It is not clear if the first position is still a helical residue even though the main chain torsion is still helical. There is a strong preference for Gly at this position (about half of observed) and it might act as a heUx breaker rather than participating in the helical conformation. The third and fourth residues are mostly hydrophobic (about half of them). The entering helix is quite short compared to the exiting helix. The extended linker conformation facilitates mostly the aromatic hydrophobs to point inwards in the gap between the packed helices. 

A. The side chains extend outward from the core structure of the helix. 

About half of rhodopsln s mass forms seven a-hellces, which are embedded In the lipid bllayer of rod disks. The remaining polypeptide chains extend Into the aqueous environment of the cytoplasm or the disk Interior, linking the helices. Retinal Is bound as a protonated Schiff base to a lysine amino acid residue In the carboxyl terminal helix. The chromophore is held In a pocket that is nearly parallel to the membrane surface. When light strikes rhodopsln, the 11-cis double bond of the protein-bound retinal Isomerlzes to the trans form, which leads to the separation from the protein opsin. To complete the visual cycle, the all-transretlnal slowly Isomerlzes back to the 11-cis Isomer, which recombines with opsin to reform rhodopsln. However, little Is known about how the Isomerization of retinal In rhodopsln triggers the transduction process (72,73) ... 

The activating effect of the various deletion mutants prior to the C-helix is also interpretable by a review of the crystal structures of the inactive form of the kinase. In this C-helix-out form, the helix itself is unwound a turn compared to the active form, and the amino acid chain connecting the P-loop to the helix is extended.70 Removing a portion of this sequence would result in... 

The problem whether or not a helical structure of amylose is retained in solution is nearly as old as the discovery of the V-amylose helix from X-ray data in 1943 (7 ) and has been the subject of extensive investigation and controversy. (For review see ( )). At present mainly two models are considered the "extended helix chain" 9) and the "randomly coiled pseudohelical chain" (10). According to Senior eind Hamori (9) the amylose chain conformation is characterized by loose, extended helical regions, which are interrupted by short, disordered regions. Hydrogen bonds between 0(2) and 0(3 ) of neighboring residues are... 

And how about experiments on polymer knots The most important and, luckily, also the easiest subject of such experiments is double helical DNA. One nice experiment can de done using DNA with sticky ends - a long double helix with each chain extending at one end by 15 or so unpaired nucleotides beyond the counterpart chain. If the sequences of these extending pieces are complementary to each other, they will stick upon first collision due to the random fluctuations of the double helical coil. Can we then determine the topology of the product ... 

The -Keratin Structure.—Hair and muscle can be reversibly stretched to about 100 per cent elongation. Some authors have expressed doubt as to whether this elongation is to be attributed to the polypeptide chains, but it seems to us that Astbury s contention that it should be is justified. With a fiber-axis length of 1.53 A per residue for the a helix, an extended chain in the 8-keratin structure would be predicted, on this assumption, to have a fiber-axis residue length of about 3.1 A. The principal meridional x-ray reflection of stretched hair, stretched muscle, and other proteins with the S-keratin structure has in fact a spacing reported by Astbury as about 3.32 A, which is presumably the fiber-axis residue length, and would thus correspond to 117 per cent extension of the a helix. That the jS-kera-... 

The secondary protein structure refers to certain short-range periodic or repeating patterns often foimd along protein chains. Secondary structure is maintained by interactions between amino acids that are fairly close together in the linear sequence of the protein chain or adjacent to each other on neighboring chains. The most common of these patterns is called the alpha (a)-helix, shown in Figure 19.9. hi the a-hehx structure, the amino acid chain is wrapped into a tight coil in which the side chains extend outward from the coil. The structure is... 

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