Extended Backbones

The linear peptide that is closest to being fully extended in the solid state is the racemate DLLeu-Gly-Gly (Goswami et a/., 1977), in which the (f) and ij/ angles deviate from ISC by less than 15°. The molecule is a zwitterion with terminal and COO groups, as is usually found in unprotected 

A classic parallel pleated sheet structure is exhibited in the crystal by Gly-LPhe-Gly, as shown in Fig. 26 (Marsh and Glusker, 1961), where NH 0=C hydrogen bonds are formed between the adjacent molecules. The phenylalanine side-chain group is extended away from the polar moieties of the peptide chain. An example of an antiparallel pleated sheet is shown by the LAla-LAla-LAla molecules (Fig. 27) (Fawcett et al, 1975). 

Peptides such as BrAc-LPhe-LPhe-OEt (Wei et aL, 1972) and Ac-LPhe-LTyr-OH (Stenkamp and Jensen, 1973) assume a Z shape for the backbone. 

A number of dipeptides, such as Gly-Trp (Pasternak, 1956), Gly-Asp (Pasternak et al, 1954), Gly-Tyr (Smits and Wiebenga, 1953), Gly-Leu (Pattabhi et ai, 1974), and Ala-Gly (Koch and Germain, 1970), have a twist of 90° about the N—C bond, resulting in a T shape for the molecule, with the bulky side group, if present, directed away from the COO terminus. Pivalyl-LSer-NHMe has a similar conformation (Aubry et ai, 1976). 

In addition to the conformations already described, there are several examples of extended peptides with a very pronounced V shape, such as Boc-Gly-LAla-OH (Gadret et a/., 1977) and LThr-LPhe-ONb (Mallikarjunan et ai, 1969). 

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At this stage, it is clear that ribosomal protein synthesis will not allow the incorporation of D-amino acids or those that are too bulky, and that only a-ami-no and a-hydroxy acids can be introduced those with extended backbones such as y-amino acids cannot be introduced in this manner. Also, in spite of the development of improved suppressor tRNAs, the incorporation of small, highly polar amino acids remains difficult. 

Problems do, however, occur during cyclization with all-L- or all-D-residues (see Section 6.8.1.3.1). Cyclodimerization can be triggered by an extended backbone conformation of the linear precursor, and C-terminal epimerization derived from slow amide bond formation. These lead to dimers or epimerized side products. 73,241 Cyclization of such tetrapeptides are successful only in a few exceptional cases.1169,73 To overcome this problem, protection of the backbone amide with Boc has been proposed since this approach favors the c/s-amide bond configuration which induces one or more suitable conformations for cyclization. 69 As a consequence, the cyclization yield of c[-Ala-]4 242 improved from 1 to 27% 69 (see also the use of Al-Hmb protection in Section 6.8.1.3.1). 

The structures of the two stereoregular polymers assuming an imaginary planar, fully extended backbone are given in Scheme 13.6. In this representation all methyl groups in the isotactic polymer lie on the same side of the backbone plane, while in the syndiotactic polymer they alternate. 

The linker between helix and strand (H-L3-E) has one major sub-cluster. The first residue is mostly Gly and the second is hydrophobic with significant population of Ala residues, liie side chain of the centi linker residue points outwards but the carbonyl oxygen of L2 points inside the space between the packed helices (Figure 7), nu g this different from those observed in H-L3-H or E-L3-E linkers. The linker E-L3-H that links strands and helices has two major clusters and descriptions of backbone conformations are listed in Table n. The third linker residue L3 of the first sub-cluster has x, of g conformation. For the second sub-cluster, L2 has main chain conformation and g side chain conformationand L3 has extended backbone conformation and g side chain conformation. 

Karle, I. L., Karle, J., Mastropaolo, D., Camerman, A., and Camerman, N. [Leu ]enkephalin four cocrystallizing conformers with extended backbone that form an antiparallel / sheet. Acta Cryst. B39, 625-637 (1983). 

Figure 8.42. The sequential assignment process illustrated for the 300 ms NOESY spectrum of gramicidin-S 8.17 in DMSO, starting from the a-proton of proline. Inter-residue uH-NH NOES are often stronger than the intra-residue NOEs in an extended backbone conformation.

To determine the minimum requirements for binding to NPY receptors, we prepared a series of small peptides containing elements of the N- and C-terminal regions of NPY. Analysis of the NPY model suggested that peptides containing 4—5 residues, in an extended backbone conformation, bridged the distance between Tyr-1 and Tyr-36 (approximately 14 A). 

Dendronized polymers Distinguishing features o Extended backbone o Defined surface o Loadable interior o Monodisperse diameter o Highly dense and responsive thickness o Large number of end-groups (chargeable) o Resistant against collapse... 

I.L. Karle, J. Karle, D. Mastropaolo, A. Camerman, N. Camerman, [Leuslenkephalin four cocrystallizing conformers with extended backbones that form an antipaiallel [beta]-sheet, Acta CrystaUogr. B39 (1983) 625-637. 

In conclusion, the extended backbone is regularly coiled by rotation around the axis and translation parallel to the axis of the elementary structure of the helix. The elements are composed of a planar amide group and a tetrahedral carbon. The shape of the coil is that of the thread of a screw each turn comprises 3.6 amino acids. The residues are separated from each other by a distance of approximately 1.5 A. The i helix is held together by hydrogen bonds, van der Waals forces, and hydrophobic forces, and each amide group is bonded to the third amide group from it on the chain. 

The studies now reported show that chloromethyl ketone polypeptide inhibitors bind in an antiparallel jS-pIeated sheet fashion to a length of extended backbone, Ser-125—Leu-126—Gly-127 in subtilisin, and Ser-214— Trp 215—Gly 216 in y-chymotrypsin. In each case there are the same geometric relationships of the pleated sheet to the active serine, and glycine residues are involved in j3-pleated sheet hydrogen bonding in both (see Figure 2). In the case of y-chymotrypsin these deductions were made from... 

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