Peptide antiparallel chain

Figure 11. (a) The chemical structure of a 24-membered macrocyclic molecule composed of alternating D- and L-amino acids, cyclo(Gln-(D-Leu-Trp)4-D-Leu 7. (b)A self-assembled tubular structure spanned across the bilayer lipid membrane. Flat ring-shaped units in the antiparallel configuration stack to form a tubular structure through extensive inter subunit hydrogen bonding and peptide side chain-lipid interactions. ... 

The main spectroscopic observation that required explanation was the 60-cm splitting in the infrared-active amide 1 (mainly CO s) modes of antiparallel-chain pleated sheet (APPS) polypeptides. Miyazawa (1960a) proposed that such splittings must be a consequence of the interactions between similar oscillators within the repeat unit of the structure, namely, the four peptide groups in the present case. He showed by a perturbation treatment that the frequencies for the four possible coupled modes would depend on the relative phases of the vibrations and the magnitudes of the interactions between peptide groups according to the relation... 

Fig. 10.5. (a) A schematic representation of the vibrational modes of the parallel-chain pleated sheet the arrows represent the components of the transition moments of peptide groups in the plane of the paper. The plus and minus signs represent the components of the transition moments perpendicular to the plane of the paper, the former pointing upward, and the latter pointing downward, (b) A schematic representation of the vibrational modes of the antiparallel-chain pleated sheet (Miyazawa, 1960c). (From Schellman and Schellman, 1964.)... 

In an antiparallel j3-pleated sheet, neighboring sections of a polypeptide chain run in opposite (antiparallel) directions, and the C = 0 group of each peptide bond is hydrogen-bonded to the N — H group of a peptide bond in a section of the neighboring antiparallel chain. 

Despite these successes serious side reactions can result from the action of alkali on cysteine or cystine-containing peptides. Open-chain unsymmetrical cystine derivatives [92, 103, 166] and some cyclic molecules including oxytocin [153] and calcitonin [24, 25] are known to undergo rapid base-catalyzed disulphide interchange yielding symmetrical disulphides or mixtures of polymer and parallel and antiparallel dimers [107, 153]. Furthermore the possibility of /3-elimination of trityl, benzhydryl, and benzyl mercaptide ion from the corresponding peptide bound cysteine residue is known [154] the extent of... 

The major stmctural feature of the HAz chain (blue in Figure 5.20) is a hairpin loop of two a helices packed together. The second a helix is 50 amino acids long and reaches back 76 A toward the membrane. At the bottom of the stem there is a i sheet of five antiparallel strands. The central i strand is from HAi, and this is flanked on both sides by hairpin loops from HAz. About 20 residues at the amino terminal end of HAz are associated with the activity by which the vims penetrates the host cell membrane to initiate infection. This region, which is quite hydrophobic, is called the fusion peptide. 

Fig. 2.27 The two types of extended /1-peptide strands with conformation requirements around the C(a)-C(/1) bonds. (A) Parallel and antiparallel polar sheets with antiperiplanar conformations around the C(a)-C fl) bond are promoted by unlike-fi -ami-no acids with alkyl side-chains. Antiperiplanar side-chains at C(a) and C(/3) occupy positions approximately perpendicular to the amide planes. (B) Extended strands formed by alternating +)-sc and (-)-sc conformations...

Fig. 2.30 Comparison of antiparallel hairpin structures in / -peptides 120-122. (A) / -Pep-tides 120, 121 with a 12-membered R/S dini-pecotic (Nip or/ -HPro) turn segment (gray color). Summary of backbone-backbone and side-chain-side-chain NOEs collected in CD2CI2 and X-ray crystal structure of 121 (stereo-view) [154, 193], The intramolecular H-bond N" 0 distances are shown. The angles (N-H -O) are 170.8° (inner H-bond) and 1 72.3 ° (outer H-bond). (B) jS-Peptide 122 with...

While conformation II (Fig. 2.34) of Uke-y -amino acids is found in the 2.614-helical structure, conformation I, which similarly does not suffer from sy -pen-tane interaction, should be an appropriate alternative for the construction of sheet-like structures. However, sheet-like arrangement have not been reported so far for y-peptides composed of acyclic y " -amino acid residues. Nevertheless, other conformational biases (such as a,/9-unsaturation, cyclization between C(a) and C(y)) have been introduced into the y-amino acid backbone to restrict rotation around ethylene bonds and to promote extended conformation with formation of sheets in model peptides. Examples of such short chain y-peptides forming antiparallel (e.g. 152 [208]) and parallel (e.g. 153-155 [205, 208]) sheet-hke structures are shown in Fig. 2.38. 

Fig. 2 (a) Antiparallel and (b) parallel P-sheet structures of two peptide chains connected by hydrogen bonds... 

Fig. 5. Comparison of ab initio, DFT/BPW91/6-31G -computed IR and VCD spectra over the amide I, II, and III regions for model peptides (of the generic sequence Ac-Alaw-NHCH3). These are designed to reproduce the major structural features of an o -helix (top left, n— 6, in which the center residue is fully H-bonded), a 3i helix (PLP Il-like, top right, n— 4), and an antiparallel /1-sheet (n= 2, 3 strands, central residue fully H-bonded) in planar (bottom left) and twisted (bottom right) conformations. The computations also encompass all the other vibrations in these molecules, but those from the CH3 side chains were shifted by H/D exchange (CH3) to reduce interference with the amide modes.

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