Peptide backbone bond

Fig. 9.10. Ligation of two protein fragments by trans-splicing interns a) on the DNA level, the two fragments can be encoded in separate ORFs and are flanked by either a 3 -extension encoding the N-intein (N-fragment) or 5 -extension encoding the C-intein (C-fragment). b) Following transcription and translation, the intein domains dimerize and c) excise themselves, fusing the N- and C-fragment by a peptide backbone bond.

Figure 1.11 Newman projections involving the N—C , bond and C ,—C(0) bond of the a-helix to demonstrate the consequences of highly regular dihedral angles

Figure 1.20 Stereo-defined structures of /3-sheets, (a) Three stranded parallel /3-sheet structure showing hydrogen bonding relationship between parallel p-strands. The N—H donor of each peptide link is able to form a hydrogen bond with the C=0 acceptor of a peptide link in a parallel /3-strand. Shading is used to demonstrate pleating and emphasise amino acid residue side-chain orientations with respect to the sheet and with respect to each other. Peptide backbone bonds are colour coded in the same way as Figs. 1.6 1.8. Arrows define N to C chain directions (b) three stranded antiparallel /3-sheet structure as for (a) except that hydrogen bonding occurs between peptide links in neighbouring antiparallel /3-strands.

Fig. 3. (a) Chemical stmcture of a synthetic cycHc peptide composed of an alternating sequence of D- and L-amino acids. The side chains of the amino acids have been chosen such that the peripheral functional groups of the dat rings are hydrophobic and allow insertion into Hpid bilayers, (b) Proposed stmcture of a self-assembled transmembrane pore comprised of hydrogen bonded cycHc peptides. The channel is stabilized by hydrogen bonds between the peptide backbones of the individual molecules. These synthetic pores have been demonstrated to form ion channels in Hpid bilayers (71). 

Peptide bond resonance has several important consequences. First, it restricts free rotation around the peptide bond and leaves the peptide backbone with only two degrees of freedom per amino acid group rotation around... 

Why should the cores of most globular and membrane proteins consist almost entirely of a-helices and /3-sheets The reason is that the highly polar N—H and C=0 moieties of the peptide backbone must be neutralized in the hydrophobic core of the protein. The extensively H-bonded nature of a-helices and /3-sheets is ideal for this purpose, and these structures effectively stabilize the polar groups of the peptide backbone in the protein core. 

Alternatively, rigidification of the y-peptide backbone to avoid H-bonds between nearest neighbors can be achieved by the introduction of an a,y9-unsaturation into the backbone of each y-amino acid constituent (vinylogous peptides) ]208, 209]. Recent ab-initio calculations suggested that the a,/9-unsaturated y-peptide backbone might support the formation of helices with large 19- and 22-membered H-bonded pseudocycles ]221]. 

Optimal pre-organization of the y-peptide backbone towards the formation of open-chain turn-like motifs is promoted by unlike-y " -amino acid residues. This design principle can be rationalized by examination of the two conformers free of syn-pentane interaction (f and II", Fig. 2.34). Tetrapeptide 150 built from homo-chiral unlike-y -amino acid building blocks 128e has been shown by NMR experiments in pyridine to adopt a reverse turn-like structure stabilized by a 14-mem-bered H-bond pseudocycle [202] (Fig. 2.37 A). 

P2j Z = 2 DX = 1.43 R = 0.067 for 1269 intensities. The uracil residue is in the anti (63.4°) disposition. The conformation of the D-ribosyl group is 2T3 (176.8°, 37.5°). The orientation about the exocyclic, C-4 -C-5 bond is t (—174.2°). The phenyl and uracil ringsofthe same molecule lie in almost parallel planes, 120 pm apart. The phenyl group is disordered. The uracil ring is sandwiched by the phenyl rings, and vice versa. The 0-1 and N-a atoms of the peptide backbone are hydrogen-bonded to 0-4 and N-3 of atranslationally related uracil to form cyclic dimers. Such interactions serve as models for nucleic acid-protein interactions. [Coordinate errors H(02 ) x should be —1574, instead of —1474 H(Na)2 z should be —145 instead of— 645.]... 

Insertion of a thioamide (0[CSNH]) bond into a peptide backbone with noncoordinating side chains increases distinctly the coordination ability of the peptide toward Ni11. The thioamide sulfur is a much more potent donor than the carbonyl-O and it is a basic donor for Ni11 ion coordination around physiological pH.1764... 

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