3io-Helix

Table 1. Energetics of the concerted a-helix — 3io-helix transition in (Aib)n. For (Ala)n profiles connect a-helix minima to = (-60°,-29°). For (Aib)n profiles...

Zhang L and J Hermans 1994. 3io-Helix versus a-Helix A Molecular Dynamics Studv of Conformational Preferences of Aib and Alanine. Journal of the American Chemical Society 116 11915-11921. 

Variations on the a helix in which the chain is either more loosely or more tightly coiled, with hydrogen bonds to residues n + 5 or n + 3 instead of n + 4 are called the n helix and 3io helix, respectively. The 3io helix has 3 residues per turn and contains 10 atoms between the hydrogen bond donor and acceptor, hence its name. Both the n helix and the 3to helix occur rarely and usually only at the ends of a helices or as single-turn helices. They are not energetically favorable, since the backbone atoms are too tightly packed in the 3io helix and so loosely packed in the n helix that there is a hole through the middle. Only in the a helix are the backbone atoms properly packed to provide a stable structure. 

According to the PDB X-ray crystal structure 1 ao6, human serum albumin contains 69.2% o -helix and 1.7% 3io-helix, the rest being made up of turns and long loops. The amide I ROA couplet centered at 1650 cm-1 (Fig. 4), which is negative at low wavenumber and positive at high,... 

According to the PDB X-ray crystal structure 2cna, jack bean con-canavalin A contains 43.5% /1-strand, 1.7% a-helix, and 1.3% 3io-helix,... 

Fig. 23. Energy contour diagram for single-stranded helical polyglycine. The units of energy are kcal mole-1. The symbols R and L indicate the location of the standard right-and left-handed a-helical conformations, B that of the B helix of myoglobin, cu that of the to-helix, 3io that of the 3io helix, and II that of the polyglycine II structure (Scott and Scheraga, 1966c).

As mentioned above, the Gly-rich domains (GGX) is found to form a helical conformation, 3io-helix (Kummerlen et al., 1996), which serves as a transition between (3-sheets and less rigid protein structures. Hydrogen bonds form between these helices and will interlock molecules to some extent, while it also keeps the molecules aligned (Hayashi et al., 1999). Therefore, the GGX sequence may contribute to both the fiber s tensile strength and extensibility. 

Another member of the M-superfamily, conomarphin also contains 15 residues but is devoid of disulphide bonds and contains a d-amino acid.169 Although the mature toxin has no sequence similarity to other M-superfamily peptides, its signal sequence suggests it is part of the M-superfamily. Despite the lack of disulphide bonds, the peptide still has a well-defined structure characterised by a loop region in the middle of the peptide and a 3io helix at the C-terminus. Mutation of the d-Phe residue and subsequent structural analysis suggests that this residue is important in stabilising its well-defined structure. Conomarphin represents a new family of conotoxins, the biological activity of which remains to be determined.169... 

Interestingly, for these molecules the most common a-helical structural motive is not stable in the gas phase. It converts into a 3io helix for small polypeptides with n<8 upon geometry optimization with DFT methods. Only for n > 8, a conformations start to form in the middle of the helix. However, these helices are energetically less stable than the pure 3io helices [34],... 

Many TM helices are not ideal, straight, and regular, as is illustrated by the seven helices ofrhodopsin (Palczewski et al., 2000) shown in Fig. 1. TM helices exhibit frequent distortions from ideality, including kinks and regions of ir and 3io helix. These distortions can cause the axis of... 

---