Protein structure 3-pleated sheet

Long, thin, resilient proteins (such as hair) typically contain elongated, elastic a-helical protein molecules. Other proteins (such as silk) that form sheets or plates typically contain protein molecules having the beta pleated-sheet structure. Proteins without a structural function in the body (such as hemoglobin) typically have a globular structure. 

The p-pleated sheet structure occurs in fibrous as well as globular proteins and is formed by intermolecular hydrogen bonds between a carboxyl group oxygen of one amino acid and an amine hydrogen of an adjacent polypeptide chain. Parallel p-pleated sheets form when the adjacent polypeptide chains are oriented in one direction (from N-terminal to C-terminal end or vice versa). Antiparallel p-pleated... 

Silk is produced from the spun threads from silkworms (the larvae of the moth Bombyx mori and related species). The main protein in silk, fibroin, consists of antiparallel pleated sheet structures arranged one on top of the other in numerous layers (1). Since the amino acid side chains in pleated sheets point either straight up or straight down (see p. 68), only compact side chains fit between the layers. In fact, more than 80% of fibroin consists of glycine, alanine, and serine, the three amino acids with the shortest side chains. A typical repetitive amino acid sequence is (Gly-Ala-Gly-Ala-Gly-Ser). The individual pleated sheet layers in fibroin are found to lie alternately 0.35 nm and 0.57 nm apart. In the first case, only glycine residues (R = H) are opposed to one another. The slightly greater distance of 0.57 nm results from repulsion forces between the side chains of alanine and serine residues (2). 

The fact that a denatured protein can spontaneously return to its native conformation was demonstrated for the first time with ribonuclease, a digestive enzyme (see p. 266) consisting of 124 amino acids. In the native form (top right), there are extensive pleated sheet structures and three a helices. The eight cysteine residues of the protein are forming four disulfide bonds. Residues His-12, Lys-41 and His-119 (pink) are particularly important for catalysis. Together with additional amino acids, they form the enzyme s active center. 

The p pleated sheet structure occurs commonly in insoluble structural proteins and only to a limited extent in soluble proteins. It is characterised by hydrogen-bonding between polypeptide chains lying side by side, as illustrated in Fig. 5.A3b. 

What kind of bonding stabilizes helical and /3-pleated-sheet secondary protein structures ... 

Figure 3-1. a. Alpha-helix structure for a polypeptide or protein b. Pleated sheet structures, depicting parallel (1) and antiparallel (2) variants (Elias 1997, reprinted courtesy ofWiley-VCH.). 

Be familiar with the various secondary structures of proteins and their dimensions the a helix, /3 turns, pleated sheet structures, and collagen and what dictates the assumption of such... 

Figure 4.8 Parallel and antiparallel pleated sheet structures. Dotted lines indicate hydrogen bonds. (Reproduced with permission from Bezkorovainy A. Basic Protein Chemistry. Springfield, IL Thomas, p. 114, 1970.)...

Ramachandran plots serve to answer the question of why the a-helical or the pleated sheet structures have the properties that they do however, the plots do not serve to predict whether a given polypeptide chain will assume the a-helical, the pleated sheet, or a random conformation. Anfinsen and his colleagues have proposed that it is the amino acid composition and sequence in a given peptide chain that determine the conformation the chain assumes. Ideally, we should be able to look at an amino acid sequence of a protein and then... 

Hydrophobic interactions are formed when two or more hydrophobic groups (for example, side chains of valine, leucine, phenylalanine, and so on) in an aqueous environment find themselves sufficiently close to exclude water molecules from their vicinity. These interactions are primarily a result of entropy effects and are believed to be of major importance in the maintenance of the tertiary structures of proteins. Scheraga and coworkers have also proposed that hydrophobic interactions may be involved in the stabilization of the a helix and the pleated sheet structures. 

The tertiary structure of a protein is its complete three-dimensional conformation. Think of the secondary structure as a spatial pattern in a local region of the molecule. Parts of the protein may have the a-helical structure, while other parts may have the pleated-sheet structure, and still other parts may be random coils. The tertiary structure includes all the secondary structure and all the kinks and folds in between. The tertiary structure of a typical globular protein is represented in Figure 24-17. 

Many proteins can be made to clump into fibrous amyloid deposits like those seen in Alzheimer s disease, Creutzfeldt-Jakob disease (the human counterpart of mad cow disease), and other serious ailments. To help prove this point, a natural enzyme to convert to amyloid fibrils—insoluble protein aggregates with a /3-pleated sheet structure—simply by maintaining protein for some time in the unfolded state. Until now, scientists have generally believed that only specific proteins such as amyloid /3-protein and prions are capable of being converted into amyloid fibrils.11 A variety of spectroscopic techniques have been used to confirm the gradual development of amyloid fibrils and to verify the fibrils predominant /3-pleated sheet structure. In the partially unfolded intermediates that form under denaturing conditions, hydrophobic amino acid residues and polypeptide backbone normally buried inside fully folded structures become exposed. Further work is needed to confirm and advance these findings. 

Figure II-2 Major elements of secondary structure of proteins. Left, the a-helix right, representation of the antiparallel pleated sheet structures for polypeptides. (After Pauling, L., and R. B. Corey (1951). Proc Natl Acad Sci USA 37 729).

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. 

Recent investigations using circular dichroism have suggested that protein stability was closely related to specific elements of secondary structure with a-heUcal structures remaining unchanged-whereas P-pleated sheet structures were affected by the addition of methanol. Hence, the relatively high content of a-heUcal strac-tural elements and low content of P-sheet of PST-01 (see Table 4.4) was seen as... 

For comparative purposes, the stability of a protein needs to be referred to specific standard conditions this is usually 25 °C and aqueous solution, and is denoted by the symbols A G25 and A G ,z0 respectively. In order to determine the values of A G° parameters, observations must be made of some intrinsic parameter that changes when the protein unfolds. This can be UV absorption, fluorescence, optical rotary dispersion (ORD) or circular dichroism (CD) (Sect. 7.1), the latter being particularly useful since it can be used to establish when the unfolding process is complete. This is because the CD spectra of fully unfolded proteins are very similar to one another, and very different from those of native proteins which contain a-helices and /3-pleated sheet structures (Figure 5-12). 

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. 

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