Turns of helix

Fig. 1. The two principal elements of secondary stmcture in proteins, (a) The a-helix stabilized by hydrogen bonds between the backbone of residue i and i + 4. There are 3.6 residues per turn of helix and an axial translation of 150 pm per residue. represents the carbon connected to the amino acid side chain, R. (b) The P sheet showing the hydrogen bonding pattern between neighboring extended -strands. Successive residues along the chain point...

The answer is quite clear. His 64, which is part of the catalytic triad, is in the first turn of helix Ob (Figure 11.13). This helix would be on the other side of the P sheet, far removed from the active site if the motif P2-o.b-P3 were right-handed. Therefore, to produce a proper catalytic triad of Asp 32, His 64, and Ser 221, helix Ob must be on the same side of the p sheet as Ser 221 consequently, the motif has evolved to be left-handed. 

Strong localized, nucleus e.g., two or three turns of helix... 

Two types of crosslinking domains exist in tropoelastin those rich in alanine (KA) and those rich in proline (KP). Within the KA domains, lysine residues are typically found in clusters of two or three amino acids, separated by two or three alanine residues. These regions are proposed to be Q-helical with 3.6 residues per turn of helix, which has the effect of positioning two lysine sidechains on the same side of the helix, although there is no direct structural evidence (Brown-Augsburger et al., 1995 Sandberg et al, 1971), and facilitating the formation of desmosine crosslinks. Desmosine crosslinks are formed by the condensation of two allysine... 

Two short pathways that link the a-helical and /3-hairpin macrostates without making use of microstates with an instantaneous temperature above 488K are shown in Fig.5.1. The path shown in Fig.5.1 (upper) involves the unwinding of both ends of the helix, leaving approximately one turn of helix in the middle of the molecule. This turn then serves as a nucleation point for the formation of the /3-turn, which is stabilized by hydrophobic interactions between the side chains of Y45 and F52. The native hydrogen bonds nearest to the turn then form, after which the remainder of the native hairpin structure forms. This pathway is similar to previously proposed mechanisms for the folding of the G-peptide /3-hairpin from a coil state, which emphasize the formation of hydrophobic contacts before hydrogen bond formation [17,18, 140-143] and the persistence of the /3-turn even in the unfolded state [143]. 

The bases are nearly perpendicular to the helix axis, and adjacent bases are separated by 3.4 A. The helical structure repeats every 34 A, so there are 10 bases (= 34 A per repeat/3.4 A per base) per turn of helix. There is a rotation of 36 degrees per base (360 degrees per full tum/10 bases per turn). 

Figure 31.18. Higher-Order Chromatin Structure. A proposed model for chromatin arranged in a helical array consisting of six nucleosomes per turn of helix. The DNA double helix (shown in red) is wound around each histone octamer (shown in blue). [After J. T. Finch and A. Klug. Proc. Natl. Acad. Sci. USA 73(1976) 1900.]...

Strongly increased disorder is seen for the C-terminal two turns of helix 3, which also diverge from the helix axis defined by the residues 200-218, and a loop connecting the second P strand with helix... 

Figure 3.4 The right-handed a-helix formed by the polypeptide chain of a protein with 3.6 amino acid residues per turn of helix, (a)...

In an aqueous solution, amylose has a random coil structure with a variable amount of single helical structure composed of six, seven or eight glucose residues per turn of helix (Szejtli et al, 1967). When amylose undergoes retrogradation (precipitation from solution), the molecules associate together to form double hehces that further associate to give the precipitate. 

A-DNA is normally seen in dehydrated samples of DNA, such as in crystals prepared for X-ray crystallography. Another form of DNA secondary structure is Z-DNA, a left-handed helix, which is believed to occur during DNA transcription. There are 12 base pairs per turn of helix, and unlike the other two forms of DNA, the msyor and minor grooves are nearly identical in width. Figure 20.10 shows the three forms side by side for comparison. 

Compare this with the CD of A-DNA (not shown in the Figure 9.10). A-DNA is 26 A in diameter, has 11 bases per turn of helix, has a helical twist of 33° per base pair, and a pitch of 28°. This DNA shows an intense positive band at 190 nm, a good negative band at 210 nm, and a positive band at 260 nm. 

Except for peptides with many aromatic amino acids, the CD spectra of a-helical polypeptides comprised of more than about 10 amino acid residues are relatively independent of the exact amino acid composition [31]. A minimum of 2-3 turns of helix (7-11 residues) appears to be sufficient to generate a typical spectrum [40]. The CD of p-sheet structure is more variable, probably mainly as a result of different amounts of twisting [40]. P-tums also have highly variable spectra. 

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