Pleated sheets, protein conformations

Fig. 2. Protein secondary stmcture (a) the right-handed a-helix, stabilized by intrasegmental hydrogen-bonding between the backbone CO of residue i and the NH of residue t + 4 along the polypeptide chain. Each turn of the helix requires 3.6 residues. Translation along the hehcal axis is 0.15 nm per residue, or 0.54 nm per turn and (b) the -pleated sheet where the polypeptide is in an extended conformation and backbone hydrogen-bonding occurs between residues on adjacent strands. Here, the backbone CO and NH atoms are in the plane of the page and the amino acid side chains extend from C ...

Chothia, C. Conformation of twisted p-pleated sheets in proteins. /. Mol. Biol. 75 295-302, 1973. 

Klunk, W. E., Pettegrew, J. W., and Abraham, D.J. (1989). Quantitative evaluation of Congo red binding to amyloid-like proteins with a beta-pleated sheet conformation. J. Histochem. Cytochem. 37, 1273-1281. 

In the last one and one-half decades many studies have been made on the ORD and CD of ribosomal proteins. Early studies (McPhie and Grat-zer, 1966 Sarkar et al., 1967 Cotter and Gratzer, 1969) were made on a mixture of proteins, and the general conclusion was that both in the ribosome and in the isolated state (usually after acetic acid and urea extraction) the protein moiety contained approximately 25% a helix together with some -pleated sheet and random-coil conformation. 

To illustrate protein conformations in a clear (but extremely simplified) way, Richardson diagrams are often used. In these diagrams, a-helices are symbolized by red cylinders or spirals and strands of pleated sheets by green arrows. Less structured areas of the chain, including the p-turns, are shown as sections of gray tubing. 

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. 

FIGURE 10.3 A beta arrangement or pleated sheet conformation of proteins. 

In an early inaccurate model for the structure of biological membranes, a phospholipid bilayer was coated on both sides by protein in an unfolded or jS-pleated sheet conformation. This model reflected the prevailing view of membrane structure from about 1940 until the early 1970s. 

Fig. 30. Schematic representation of vertical cross section of nacre showing alternating layers of mineralizing matrix (hexagons) and carrier protein (pleated sheet conformation). The CaC03 has been omitted for graphical reasons...

The key role exercised by aspartic acid in MM is probably taken over by serine in the carrier protein. Conformation of the CP under ideal conditions involves only 0-pleated sheets but, depending on the primary structure, a-conformations will occur. The ratio of glycine alanine serine largely determines which types of cross- 3-struc-tures are developed. 

Two of the most common secondary structures found in proteins are helical and pleated-sheet conformations, shown in the diagram above. One might compare the helical structure of a protein, for example, with the spiral-shaped cord found on many home telephones. These structures form when atoms, ions, or other chemical species in one part of the protein s primary structure are attracted to other atoms, ions, or chemical species with opposite electrical charges in another part of the structure. 

Secondary protein structures are the local regular and random conformations assumed by sections of the peptide chains found in the structures of peptides and proteins. The main regular conformations found in the secondary structures of proteins are the a-helix, the fl-pleated sheet and the triple helix (Figure 1.8). These and other random conformations are believed to be mainly due to intramolecular hydrogen bonding between different sections of the peptide chain. 

Alternatively, a protein might have a pleated sheet conformation, more common with sequences of amino acid units with small R groups on the a-carbon (see Figure 3-lb). Thus, the secondary structure for a given protein depends in large part upon the tendency of the R groups to attract or repel each other along the chain. In other words, the secondary structure is dependent upon the primary structure. 

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... 

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. 

A schematic comparison of the levels of protein stmcture. Primary stmcture is the covalently bonded stmcture, including the amino acid sequence and any disulfide bridges. Secondary structure refers to the areas of a helix, pleated sheet, or random coil. Tertiary stmcture refers to the overall conformation of the molecule. Quaternary structure refers to the association of two or more peptide chains in the active protein. 

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