P-sheets antiparallel

Figure 2.5 Schematic illustrations of antiparallel (3 sheets. Beta sheets are the second major element of secondary structure in proteins. The (3 strands are either all antiparallel as in this figure or all parallel or mixed as illustrated in following figures, (a) The extended conformation of a (3 strand. Side chains are shown as purple circles. The orientation of the (3 strand is at right angles to those of (b) and (c). A p strand is schematically illustrated as an arrow, from N to C terminus, (bj Schematic illustration of the hydrogen bond pattern in an antiparallel p sheet. Main-chain NH and O atoms within a p sheet are hydrogen bonded to each other.

Figure 2.15 The Greek key motif is found in antiparallel p sheets when four adjacent p strands are arranged in the pattern shown as a topology diagram in (a). The motif occurs in many p sheets and is exemplified here by the enzyme Staphylococcus nuclease (b). The four p strands that form this motif are colored red and blue.

On the basis of simple considerations of connected motifs, Michael Leviff and Cyrus Chothia of the MRC Laboratory of Molecular Biology derived a taxonomy of protein structures and have classified domain structures into three main groups a domains, p domains, and a/p domains. In ct structures the core is built up exclusively from a helices (see Figure 2.9) in p structures the core comprises antiparallel p sheets and are usually two P sheets packed... 

The p-a-P motif, which consists of two parallel p strands joined by an a helix, occurs in almost all structures that have a parallel p sheet. Four antiparallel p strands that are arranged in a specific way comprise the Greek key motif, which is frequently found in structures with antiparallel p sheets. 

Polypeptide chains are folded into one or several discrete units, domains, which are the fundamental functional and three-dimensional structural units. The cores of domains are built up from combinations of small motifs of secondary structure, such as a-loop-a, P-loop-p, or p-a-p motifs. Domains are classified into three main structural groups a structures, where the core is built up exclusively from a helices p structures, which comprise antiparallel p sheets and a/p structures, where combinations of p-a-P motifs form a predominantly parallel p sheet surrounded by a helices. 

We saw in Chapter 2 that the Greek key motif provides a simple way to connect antiparallel p strands that are on opposite sides of a barrel structure. We will now look at how this motif is incorporated into some of the simple antiparallel P-barrel structures and show that an antiparallel P sheet of eight strands can be built up only by hairpin and/or Greek key motifs, if the connections do not cross between the two ends of the p sheet. 

Figure 5.10 Idealized diagrams of the Greek key motif. This motif is formed when one of the connections of four antiparallel fi strands is not a hairpin connection. The motif occurs when strand number n is connected to strand + 3 (a) or - 3 (b) instead of -r 1 or - 1 in an eight-stranded antiparallel P sheet or barrel. The two different possible connections give two different hands of the Greek key motif. In all protein structures known so far only the hand shown in (a) has been observed.

Figure 6.4 Schematic diagram of the structure of the enzyme barnase which is foided into a five stranded antiparallel p sheet (blue) and two a helices (red).

The setpin fold comprises a compact body of three antiparallel p sheets, A, B and C, which ate partly coveted by a helices (Figure 6.22). In the structure of the uncleaved form of ovalbumin, which can be regarded as the canonical structure of the serpins, sheet A has five strands. The flexible loop starts at the end of strand number 5 of p sheet A (plS in Figure 6.22), then... 

Figure 6,22 Schematic diagram of the structure of ovalbumin which illustrates the serpin fold. The structure is built up of a compact body of three antiparallel p sheets,...

Dimerization of pairs of Cro monomers depends primarily on interactions between p strand 3 from each subunit (Figure 8.4). These strands, which are at the carboxy end of the chains, are aligned in an antiparallel fashion and hydrogen bonded to each other so that the three-stranded p sheets of the monomers form a six-stranded antiparallel p sheet in the dimer (Figure 8.5). 

Figure 8.S The three P strands of each subunit in lambda Cro are aligned in the dimer so that a six-stranded antiparallel p sheet is formed as shown in this topology diagram. The P strands are colored as in Figure 8.4.

The two homologous repeats, each of 88 amino acids, at both ends of the TBP DNA-binding domain form two stmcturally very similar motifs. The two motifs each comprise an antiparallel p sheet of five strands and two helices (Figure 9.4). These two motifs are joined together by a short loop to make a 10-stranded p sheet which forms a saddle-shaped molecule. The loops that connect p strands 2 and 3 of each motif can be visualized as the stirmps of this molecular saddle. The underside of the saddle forms a concave surface built up by the central eight strands of the p sheet (see Figure 9.4a). Side chains from this side of the P sheet, as well as residues from the stirrups, form the DNA-binding site. No a helices are involved in the interaction area, in contrast to the situation in most other eucaryotic transcription factors (see below). 

Figure 9.17 Schematic diagram illustrating the tetrameric stmcture of the pS3 oligomerization domain. The four subunits have different colors. Each subunit has a simple structure comprising a p strand and an a helix joined by a one-residue turn. The tetramer is built up from a pair of dimers (yellow-blue and red-green). Within each dimer the p strands form a two-stranded antiparallel p sheet which provides most of the subunit interactions. The two dimers are held together by interactions between the four a helices, which are packed in a different way from a four-helix bundle. (Adapted from P.D. Jeffrey et al.. Science 267 1498-1502, 1995.)...

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. 

Figure 17.3 The polypeptide chain of lysozyme fiom hacteiiophage T4 folds into two domains. The N-terminal domain is of the a + P type, built up from two a helices (red) and a four-stranded antiparallel P sheet (green). The C-terminal domain comprises seven short a helices (brown and blue) in a rather irregular arrangement. (The last half of this domain is colored blue for clarity.)...

The immunoglobulin fold is best described as two antiparallel p sheets packed tightly against each other 304... 

One model proposed to explain why specific mixtures form fibrils is a lateral arrangement of strands in an antiparallel p-sheet (Fig. 19). This permits favourable contacts between both hydrophobic and oppositely charged side chains. 

Figure 5-7. A p-turn that links two segments of antiparallel p sheet. The dotted line indicates the hydrogen bond between the first and fourth amino acids of the four-residue segment Ala-Gly-Asp-Ser.

Figure 39-13. A schematic representation of the three-dimensional structure of Cro protein and its binding to DNA by its helix-turn-helix motif. The Cro monomer consists of three antiparallel p sheets (P1-P3) and three a-helices (a,-a3).The helix-turn-helix motif is formed because the aj and U2 helices are held at about 90 degrees to each other by a turn offour amino acids. The helix of Cro is the DNA recognition surface (shaded). Two monomers associate through the antiparallel P3 sheets to form a dimer that has a twofold axis of symmetry (right). A Cro dimer binds to DNA through its helices, each of which contacts about 5 bp on the same surface of the major groove. The distance between comparable points on the two DNA a-helices is 34 A, which is the distance required for one complete turn of the double helix. (Courtesy of B Mathews.)...

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