Peptides sheets

Aggeli, A., Nyrkova, I.A., Bell, M., Harding, R., Carrick, L., McLeish, T.C.M., Semenov, A.N., and Boden, N. "Hierarchical self-assembly of chiral rod-like molecules as a model for peptide-sheet tapes, ribbons, bris and bers". Proc. Nat. Acad. Sci. U.S.A. 98,11857-11862 (2001). Attri, A.K., Lewis, M.S., and Korn, E.D. "The formation of actin oligomers studied by analytical ultracentrifugation". ]. Biol. Chem. 266, 6815-6824 (1991). 

As illustrated in Fig. 44.6 the traditional sheet stmctures are relatively linear segments attached by a flexible loop, and held together by some intermolecular forces. In peptide sheets, these forces are complementary hydrogen bonds. For strands with directionality, such as that provided by the peptide bond, ester linkages, or asymetric monomer stmctures, the strands can be assembled in a parallel, antiparallel, or mixed fashion. Strands containing symmetrical stmctures such as ureas, guanadines, or alkynes will be called nondir-ectional. 

Fossey SA, Nemethy G, Gibson KD, Scheraga HA Conformational energy studies of beta-sheets of model silk fibroin peptides. Sheets of poly (Ala-Gly] chains. Biopolymers, 31,1529-1541,1991. 

The primary structure of a peptide is its ammo acid sequence We also speak of the secondary structure of a peptide that is the conformational relationship of nearest neighbor ammo acids with respect to each other On the basis of X ray crystallographic studies and careful examination of molecular models Linus Pauling and Robert B Corey of the California Institute of Technology showed that certain peptide conformations were more stable than others Two arrangements the a helix and the (5 sheet, stand out as... 

Secondary structure (Section 27 19) The conformation with respect to nearest neighbor ammo acids m a peptide or pro tern The a helix and the pleated 3 sheet are examples of protein secondary structures... 

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. 

Figure 13.26 Schematic diagram of the SH2 domain from the Src tyrosine kinase with bound peptide. The SH2 domain (blue) comprises a central p sheet surrounded by two a helices. Three positively charged residues (green) are involved in binding the phosphotyrosine moiety of the bound peptide (red). (Adapted from G. Waksman et al.. Cell 72 779-790, 1993.)...

The Src SH2 domain typifies a large number of those characterized to date. The pTyr fits into a pocket on the opposite side of the central sheet to the pY-r3 pocket (Figure 13.27a). All known SH2 domains bind pTyr in essentially the same way, but some have a different pattern of contacts for the residues that follow. For example, in the Grb2 SH2 domain, a tryptophan side chain from the small sheet fills the pY-r3 pocket, and the bound peptide takes a different course, with important interactions to an asparagine at pY-r2. Screens of peptide libraries have detected the importance of this asparagine. The SH2 domain from PFC-yl contacts five mainly hydrophobic residues that follow pTyr. 

Class 1 and class II MHC molecules bind peptide antigens and present them at the cell surface for interaction with receptors on T cells. The extracellular portion of these molecules consists of a peptide-binding domain formed by two helical regions on top of an eight-stranded antiparallel p sheet, separated from the membrane by two lower domains with immunoglobulin folds. These domains are differently disposed between the two protein subunits in class I and class II molecules. 

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. 

Pleated p sheet (Section 27.19) Type of protein secondary structure characterized by hydrogen bonds between NH and C=0 groups of adjacent parallel peptide chains. The individual chains are in an extended zigzag conformation. 

Parallel /3-sheets tend to be more regular than antiparallel /3-sheets. The range of (f) and i/t angles for the peptide bonds in parallel sheets is much smaller than that for antiparallel sheets. Parallel sheets are typically large structures those composed of less than five strands are rare. Antiparallel sheets, however, may consist of as few as two strands. Parallel sheets characteristically distribute... 

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