Parallel /3-pleated sheets

The two peptides form a symmetrical dimer stabilized by four hydrogen bonds (red dashes) and hydrophobic contacts. The two monomers form a four-stranded, anti-parallel pleated sheet. 

Fig. 2.28 X-ray crystal structures of parallel sheet-forming and all-un//fce-/F -peptides 116 and 117 [10, 191]. Views along the parallel amide planes and crystal packing diagram show the parallel pleated sheet arrangement (view perpendicular to the amide planes).

Arnott, S., Dover, S. D., and Elliott, A. (1967). Structure of / -poly-L-alanine Refined atomic co-ordinates for an anti-parallel /(-pleated sheet./. Mol. Biol. 30, 201-208. 

In a further exploration of the relationship between dye structure and wet fastness on silk, four novel monoazo J acid derivatives (3.169 X = Xx to X4), including 3.168 (X = X2) made from 2-aminobenzophenone, were synthesised. Silk was dyed at pH 4 and 85 °C and the dyeings tested for fastness to washing, perspiration and dry cleaning. The highest allround fastness was shown by the 4 aminobenzophenone derivative (X = X4), a structure that resembles the anti-parallel pleated sheet arrangement of polypeptide chains in silk [183]. 

Figure 11.4 Pleated sheets of fibrous proteins. Parallel pleated sheets are composed of polypeptide chains which all have their N-terminal amino acid at the same end whereas anti-parallel pleated sheets involve polypeptide chains which are alternately reversed in direction. Both forms of sheet show a high degree of hydrogen bonding between the chains.

Figure 4.11 Ramachandran plot showing permissible conformational regions. aR and aL indicate positions of the right- and left-handed a helices /3A and /3P indicate the positions of the anti-parallel and parallel pleated sheet structures, respectively. C indicates collagen.

Hair keratin has historically been associated with the a-helical structure. For that reason, it is termed a-keratin. And indeed the basic keratin polypeptides are a-helical except for their N- and C-terminal domains. These are believed to be involved in head-to-tail condensation to form keratin polymers. When hair keratin is stretched, the resulting secondary structure is the parallel pleated sheet (see Chapter 4). Stretched keratin is referred to as /3-keratin to emphasize its secondary structure. 

Fig. 19.15a-d. Distribution of out-of-plane (0) and in-plane (y) angles for N-H- -0=C hydrogen bonds in a a-helices, b / -turns (crosses) and 310-helices (dots), c parallel and d anti-parallel -pleated sheets [596]... 

P structure is the structure where the polypeptide chain is elongated. The structure can be the type where all the molecular chain run in the same direction and form a parallel pleated sheet or the type where the molecular chain run in the alternate direction and form anti parallel chain pleated sheet. In the case of P-structure, there are three important features, namely the period that is repeating period of the polypeptide chain, the spacing of the molecular chain in the sheet and the distance between the sheets [76]. 

There are two ways in which proteins chains can form the pleated sheet structure. One is with the chains running in the same direction i.e. the -COOH or NH2 ends of the polypeptide chains lying all at the top or all at the bottom of the sheet. This is called parallel pleated-sheet structure. In another type, known as antiparallel p-pleated sheet structure, the polypeptide chains alternate in such a way that the -COOH end of the one polypeptide is next to the -NH2 end of the other i.e., polypeptide chains run in opposite directions. 

Efforts to obtain characteristic CD spectra of antiparallel and parallel / -pleated sheet conformations have utilized the vacuum ultraviolet and drawn on infrared spectra to substantiate the two different states. It was found by Balcerski et al. [78] that films of Boc-(l Ala)7-OMe formed antiparallel )3-pleated sheets and films of Boc-... 

Figure 24. A, Stereo pair plot of poIy-L-alanine in the antiparallel -pleated sheet conformation of Pauling and Corey [47]. Sheet is tilted 10°. Stereo pairs arranged for cross-eye viewing. B, Stereo pair plots of poly-L-alanine in the parallel -pleated sheet conformation of Pauling and Corey [47]. Stereo pairs are arranged for cross-eye viewing.

Figure 33. Stereo pair plots of the Gramicidin A transmembrane channel. It is a single-stranded, left-handed j8-helix with approximately six residues per turn. A, Side view. Two molecules are hydrogen-bonded head to head (amino end to amino end) by means of six hydrogen bonds. The intermolecular hydrogen bonds have the pattern of an antiparallel -pleated sheet (see Figure 24A), whereas the intramolecular hydrogen bonding pattern is a parallel -pleated sheet (see Figure 24B). B, Channel view of a monomer. Reproduced, with permission from [96].

When a system of interest is a mixture of two states that have each been characterized spectroscopically, then it is possible to calculate the fraction of each state within the mixture. As an example, let the system of interest be a protein comprised of a-helix and parallel -pleated sheet and let the observable be the molar ellipticity at a specified wavelength, [0]obs- Taking the characteristic molar ellipticities at the specified wavelength to be [0] and [0] p for the a-helix and the parallel 8-pleated sheet, respectively, the observed molar ellipticity may be expressed in terms of the mole fractions Xi of each of the conformations, i.e.,... 

A structure such as the six-stranded coenzyme binding domain in the dehydrogenases would be disrupted by insertions or deletions of amino acids (see Fig. 7 for elaboration). Hence, sequence comparisons of parallel pleated sheet regions are particularly reliable. Structural methods of alignment of sheet areas have been discussed in Section II. The corresponding amino acid comparisons are made in Table IV. For tbe purpose of this chapter, the present LDH numbering scheme (4) will be used as the generalized reference system. 

Fia. 7. A parallel pleated sheet (a) with hydrophobic residues pointing up and hydrophilic residues pointing down. If a deletion should occur in one strand it will cause a disruption in the physical properties of the protein (b), making the event of such a deletion within a sheet most improbable. 

SI, 9II, and /Sill are the three pleated sheet regions of the catalytic domain schematically illustrated in Fig. 10. The individual strands of these sheets are numbered sequentially from the amino terminal, dk. .. 0F are the strands of the parallel pleated sheet region in the coenzyme binding domain schematically illustrated in Fig. 5. The helices are labeled al. . . a4 in the catalytic domain and oA. . . E in the coenzyme binding domain. Ill. . . R17 are reverse bends defined according to Venkatachalam 117). 

There are three hydrophobic regions in this domain. One is involved in the subunit interaction and is discussed in Section II,C,3,c. The other two are important for the folding of this domain since they form hydro-phobic cores between the helices and the parallel pleated sheet (116). Table V lists the residues involved. The importance of these hydrophobic cores for the proper folding is realized from the fact that almost all residues in LDH and GAPDH which are structurally equivalent to those of LADH listed in Table V are also hydrophobic. 

Core N1 is formed by residues from aA, aB, aC, and the strands of the parallel pleated sheet. Core N2 is formed by residues from aCD, aE, and the strands. 

The unique folding of the nucleotide binding domain creates a specific crevice for binding of a dinucleotide molecule. The coenzyme is bound in the central region of the carboxyl end of the parallel pleated sheet. Residues from fiA, ySB, ySD, aB, aE and the loops connecting fiA with oB and j8D with oE are involved in this binding. The middle strand pA is shorter at the carboxyl end than its neighboring strands y3B and )8D. Furthermore, the loop which connects /8A with oB turns to the left... 

Fig. 10. Parallel pleated sheet area in dogfish M< LDH ternary complex. There is a twist of about 100° between the extreme edges of the strand.

Both serine 195 and histidine 57 are required for the activity of chymotrypsin therefore, they must be close to each other in the active site. The determination of the three-dimensional structure of the enzyme by X-ray crystallography provides evidence that the active-site residues do indeed have a close spatial relationship. The folding of the chymotrypsin backbone, mostly in an anti parallel pleated-sheet array, positions the essential residues around an active-site pocket (Eigure 7.13). Only a few residues are directly involved in the active site, but the whole molecule is necessary to provide the correct three-dimensional arrangement for those critical residues. 

Figure 26. Intermolecular hydrogen bonding in Gly-LPhe-Gly exhibiting a parallel pleated sheet arrangement (Marsh and Glusker, 1961).

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). 

Hydrogen bonds (a) in a parallel -pleated sheet structure, in which all the polypeptide chains are oriented in the same direction, and (b) in an antiparallel fi-pleated sheet, in which adjacent polypeptide chains run in opposite directions. For color key, see Fig. 22.7. 

With respect to point (vii) above, the descriptions of the structures of newly-solved proteins invariably include accounts of the domains which make up the whole molecule. For example, in the structure of S-rhodanese, determined to 2.5 A resolution by Ploegman et two globular domains are reported. These are similar even though there is no sequence homology. The core of each domain is a five-stranded parallel pleated sheet flanked by two a-helices on one side and three on the other. The authors comment that this type of architecture has been found in other proteins e.g. flavodoxin and the dehydrogenases) although a detailed comparison indicated that the similarity did not extend beyond the pleated sheet. The active site of the enzyme lies in a pocket between the two domains. 

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