Amino acids left-handed

SCHEME 7.9 Left hand side—the skeleton of a natural amino acid. Right hand side—an artificial ir-conjugated amino acid building block. 

Figure 2-1 S3. The ViewerLite shows an elaborate depiction of hemoglobin on the right-hand side, with the amino acids in a cascade window on the left.

An a helix can in theory be either right-handed or left-handed depending on the screw direction of the chain. A left-handed a helix is not, however, allowed for L-amino acids due to the close approach of the side chains and the CO group. Thus the a helix that is observed in proteins is almost always right-handed. Short regions of left-handed a helices (3-5 residues) occur only occasionally. 

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. 

Consider, for example, the protein shown in Figure 15.7. The bottom left-hand amino acid is valine, which is linked to proline. Suppose for the sake of argument that we wanted to treat this valine quantum-mechanically and the rest of the protein chain according to the methods of molecular mechanics. We would have to draw a QM/MM boundary somewhere between valine and the rest of the protein. The link atoms define the boundary between the QM and the MM regions. A great deal of care has to go into this choice of boundary. The boundary should not give two species whose chemical properties are quite different from those implied by the structural formulae on either side of this boundary. 

Each polytripeptide chain is twisted around a threefold screw axis and exists in a secondary structure, analogous to the left-handed polyproline II-helix, i.e. with transposition of the peptide bond (pitch 8.4 A, 3 amino acids) (Figs. 2,3). 

C) Stereo-view along the helix axis of the left-handed 3,4-helix formed by, 8 -peptide 2 consisting of (S,S)-trans-2-amino-cyclohexanecar-boxylic acid (trans-ACHC) residues in the solid state as determined by X-ray diffraction (adapted from [6, 125]). (D) Top view... 

Figure 33 The cyclo(Adm-Cyst)3 adopts a figure-eight-like helical structure. The chiral amino acid, cystine, configuration determines the helix disposition (rigjit-handed or left-handed helix). Adamantane plays an important role as a ring size controlling agent. Taken from Ref. [163] with permission.

Fig. 9.6 Mirror image behaviour of enantiomeric molecules. The left-handed L-a-amino acid is converted to the right-handed D-a-amino acid by reflection... 

All but one of the 20 amino acids that make up naturally occurring proteins are chiral, and all of them are classified as being left handed (S configuration). 

The SH3 domain consists of approximately 60 amino acid residues and is C-terminal to the unique domain. Its five P strands form a globular structure whose N- and C-termini are in proximity to each other. SH3 domains mediate both intermolecular and intramolecular interactions, targeting short amino acid sequences that consist of specific proline-rich motifs in a left-handed helix - polyproline... 

Because only one repeat is present in the structure and the number of amino acids between repeats is variable, we cannot yet draw conclusions about whether the monomers spiral around each other or whether this will be a left-handed or right-handed spiral. Future studies (Section IV) will hopefully lead to structural information on the repeat-containing N-terminal half of the bacteriophage T4 short tail fiber and the long tail fibers. 

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