Conformations antiparallel-chain pleated sheet

The frequencies obtained for different conformations of globular proteins in HjO and DjO solution are internally consistent, in general agreement with corresponding values of fibrous proteins and with the limited data available in the literature concerning deuterated proteins in D2O solution. Dissolution in aqueous environment by itself does not noticeably alter the amide I frequencies. A tentative set of characteristic frequencies and interaction constants was obtained for the amide I modes of N-deuterated proteins. These modes were easily observed in DjO solution and showed sufficient variations in frequency to permit a distinction between the a-helical, the antiparallel-chain pleated sheet, and the solvated random configurations of globular proteins (Table 10.10). 

The influence of chain length and side-chain modifications of ACTH-derived peptides on active avoidance behaviour in rats will be discussed. H-Met(02)-Glu-His--Phe-D-Lys-Phe-OH (Org 2766) emerged from these studies as an orally active peptide with an increased potency and selectivity of action. Physico-chemical data (from the literature) on the reference peptide ACTH--(4-10) did not point to a preferred conformation in solution, whereas in the crystalline state an antiparallel 3-pleated sheet structure was found. At the receptor site we suggested an a-helical conformation in which the Phe and Met residues are close together. Additional support for this suggestion came from the behavioural activity of [des-Tyr", Met ]enkephalin and of cyclo--(-Phe-Met-cAhx-), eAhx merely serving as a spacer. 

The (3-strand sequences are stretched out conformations of these polypeptide sections and are typically stabilized by inter-strand hydrogen bonds between keto (C = 0) oxygens and peptide bond NHs, the strands being arrayed in an antiparallel fashion. This type of secondary structure is favoured by amino acid residues with small R groups (such as Gly, Ala and Ser) that minimize steric overlap between chains. Thus a well-known protein having this type of secondary structure is silk fibroin that has a high proportion of repeated sequences involving Gly, Ala and Ser and an extensive antiparallel (3-pleated sheet structure. The macroscopic properties of silk fibroin (flexibility but lack of stretchability) reflect this type of secondary structure at the molecular level. 

All the ferrichromes whose conformations have been studied are des-scribedin Fig. 1. This structural model is based on the X-ray crystallographic study of ferrichrome A by Zalkin et al. (27, 28) and in most respects, it is confirmed by PMR solution studies (29, 30). The structure exhibited by the model in Fig. 1 is globular with the three substituted ornithyl side chains embracing the metal ion in octahedral coordination while the cyclohexapeptide backbone assumes a distorted antiparallel /3-pleated sheet structure. 

FIGURE 4-7 The /8 conformation of polypeptide chains. These top and side views reveal the R groups extending out from the /3 sheet and emphasize the pleated shape described by the planes of the peptide bonds. (An alternative name for this structure is /3-pleated sheet.) Hydrogen-bond cross-links between adjacent chains are also shown, (a) Antiparallel /3 sheet, in which the amino-terminal to carboxyl-terminal orientation of adjacent chains (arrows) is inverse, (b) Parallel f) sheet. 

Linear chains of proteins have conformation angles of ( ) = -120° and j/ = 120°. Such chains may orient in a parallel or an antiparallel manner, and the hydrogen bond angles are close to 160°, with lengths of about 2-3 A (Fig. 9.2.5). Such intermolecular hydrogen bond chains lead to 3-pleated sheets, which are extremely insoluble in water and do not swell. They are favored when R is small (e.g.,HorCH3). 

The secondary structure covers the spatially arranged conformations produced by hydrogen bonding between peptide bonds such as helix sequences and pleated sheet structures. Here, the tendency toward helix formation for the same amino acid residues in poly(a-amino acids) and proteins is mostly, but not always, of the same magnitude (Table 30-1). The peptide chains in the pleated sheet structure are mainly arranged antiparallel. Segments in the coil conformation are generally not included in the secondary structure. 

The secondary structure describes the overall conformation or shape of the protein molecule. Typical types of secondary structure are helices (cf Sections 4.2 and 4.6) and pleated sheets (j5 structures). Secondary structure results from main-chain hydrogen-bonded interactions. In pleated sheets, the a-amino acid chains can be arranged parallel or antiparallel to each other, with the antiparallel structure being thermodynamically more stable. a-Amino acids that yield helical homopolymers usually (but not inevitably) form helical sequences in proteins and polypeptides. The random coil that results from the rupture or lack of stabilizing hydrogens is not considered a secondary structure. Segments of a-helix, pleated sheet, and random coil are possible in the same molecule. 

Pleated sheet conformation with three polypeptide chains running in opposite (antiparallel) directions. Hydrogen bonding between chains Is indicated by dashed lines. 

From WAXS and SAED data of both ProNectin F lyophilized powder and sprayed fibrils, the current model indicates that ProNectin F crystallizes into a chain folded pleated sheet of beta strands (Anderson et a/. 1994). The strands are oriented antiparallel. The beta strands are not fully extended, but have a more compressed crankshaft conformation. This conformation agrees with the predicted conformation of unoriented silk fibroin protein, the Silk I structure (Lotz and Keith 1971). The crystal dimension in the c direction (along the peptide backbone) is consistent with a theoretical length of 11.6 nm for nine SEP blocks (54 amino acids) in this conformation. This predicts that the width of the ProNectin F tile is controlled at least in part by the number of amino acids in the silklike block domains. 

Poly(L-tyrosine), which adopts the antiparallel pleated sheet conformation in water at low ionization, has also been studied by far ultraviolet c.d. It was suggested that lower molecular weight polymers possessed only a few polypeptide chains folded into long open-chain / -structures, whereas a higher molecular weight polymer took up a more compact shape, in which the /S-sheet had folded over on to itself into a double-layer. This could be regarded as the first prototype of tertiary structure observed in a -forming homopolymer. 

The lack of a center of symmetry in the monomer repeat imit structure of PA6 imparts a directionality to the PA6 chains. Consequently, PA6 can form the a-crystalline, planar hydrogen bonded sheet structure only between antiparallel chains. Parallel chains, on the other hand, form a 7-crystalline, pleated sheet structure in which the chains assume a twisted helix conformation to permit lull H-bonding. Due to these symmetry and entropic restrictions, PA6 is somewhat less crystalline and less ordered, usually containing a mixture of a and 7-crystalline forms in the injection molded parts. As a consequence of these crystallinity and morphology differences, PA6 is intrinsically more ductile than PA66, since it is easier to deform a less ordered polymer phase. 

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