P-sheets parallel

Figure 2.6 Parallel p sheet, (a) Schematic diagram showing the hydrogen bond pattern in a parallel p sheet, (b) Ball-and-stlck version of (a). The same color scheme is used as in Figure 2.5c. (c) Schematic diagram illustrating the pleat of a parallel p sheet.

This motif is called a beta-alpha-beta motif (Figure 2.17) and is found as part of almost every protein structure that has a parallel p sheet. For example, the molecule shown in Figure 2.10b, triosephosphate isomerase, is entirely built up by repeated combinations of this motif, where two successive motifs share one p strand. Alternatively, it can be regarded as being built up from four consecutive p-a-p-a motifs. 

Figure 2.17 Two adjacent parallel p strands are usually connected by an a helix from the C-termlnus of strand 1 to the N-termlnus of strand 2. Most protein structures that contain parallel p sheets are built up from combinations of such p-a-P motifs. Beta strands are red, and a helices are yellow. Arrows represent P strands, and cylinders represent helices, (a) Schematic diagram of the path of the main chain, (b) Topological diagrams of the P-a-P motif.

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. 

The packing interactions between a helices and p strands are dominated by the residues Val (V), He (I), and Leu (L), which have branched hydrophobic side chains. This is reflected in the amino acid composition these three amino acids comprise approximately 40% of the residues of the P strands in parallel P sheets. The important role that these residues play in packing a helices against P sheets is particularly obvious in a/P-barrel structures, as shown in Table 4.1. 

Figure 4.2 A p-a-p motif is a right-handed structure. Two such motifs can be joined into a four-stranded parallel p sheet in two different ways. They can be aligned with the a helices either on the same side of the p sheet (a) or on opposite sides (b). In case (a) the last p strand of motif I (red) is adjacent to the first p strand of motif 2 (blue), giving the strand order 1 2 3 4. The motifs are aligned in this way in barrel structures (see Figure 4.1a) and in the horseshoe fold (see Figure 4.11). In case (b) the first p strands of both motifs are adjacent, giving the strand order 4 3 12. Open twisted sheets (see Figure 4.1b) contain at least one motif alignment of this kind. In both cases the motifs ate joined by an ct helix (green).

Each repeat forms a right-handed P-loop-a structure similar to those found in the two other classes of a/p structures described earlier. Sequential p-loop-a repeats are joined together in a similar way to those in the a/P-bar-rel stmctures. The P strands form a parallel p sheet, and all the a helices are on one side of the P sheet. However, the P strands do not form a closed barrel instead they form a curved open stmcture that resembles a horseshoe with a helices on the outside and a p sheet forming the inside wall of the horseshoe (Figure 4.11). One side of the P sheet faces the a helices and participates in a hydrophobic core between the a helices and the P sheet the other side of the P sheet is exposed to solvent, a characteristic other a/p structures do not have. 

Figure 4.11 Schematic diagram of the structure of the ribonuclease inhibitor. The molecule, which is built up by repetitive P-loop-a motifs, resembles a horseshoe with a 17-stranded parallel p sheet on the inside and 16 a helices on the outside. The P sheet is light red, a helices are blue, and loops that are part of the p-loop-(x motifs are orange. (Adapted from B. Kobe et al.. Nature 366 7S1-756,...

Figure S.28 Schematic diagrams of the two-sheet P helix. Three complete coils of the helix are shown in (a). The two parallel P sheets ate colored gieen and red, the loop regions that connect the P strands ate yellow, (b) Each stmctuial unit Is composed of 18 residues forming a P-loop-P-loop structure. Each loop region contains six residues of sequence Gly-Gly-X-Gly-X-Asp where X is any residue. Calcium Ions are bound to both loop regions. (Adapted from F. Jumak et al., Ciirr. Opin. Struct. Biol. 4 802-806, 1994.)...

In these p-helix structures the polypeptide chain is coiled into a wide helix, formed by p strands separated by loop regions. In the simplest form, the two-sheet p helix, each turn of the helix comprises two p strands and two loop regions (Figure 5.28). This structural unit is repeated three times in extracellular bacterial proteinases to form a right-handed coiled structure which comprises two adjacent three-stranded parallel p sheets with a hydrophobic core in between. 

A more complex p helix is present in pectate lyase and the bacteriophage P22 tailspike protein. In these p helices each turn of the helix contains three short p strands, each with three to five residues, connected by loop regions. The p helix therefore comprises three parallel p sheets roughly arranged as the three sides of a prism. However, the cross-section of the p helix is not quite triangular because of the arrangement of the p sheets. Two of the sheets are... 

In addition to the antiparallel p-structures, there is a novel fold called the P helix. In the p-helix structures the polypeptide chain is folded into a wide helix with two or three p strands for each turn. The p strands align to form either two or three parallel p sheets with a core between the sheets completely filled with side chains. 

Figure 11.13 Schematic diagram of the three-dimensional structure of subtilisin viewed down the central parallel p sheet. The N-terminal region that contains the a/p stmcture is blue.

Lyim and co-workers carried out smdies of the Ap(io 35) peptide - derived from residues 10-35 of the p-amyloid responsible for Alzheimer s disease - which forms fibrils composed of parallel p-sheets [62]. The peptide was compared to its C-terminal PEG-derivatised analogue. TEM experiments showed that both formed fibrils [63] (Fig. 21) but the uranyl acetate stain was not found inside the peptide-PEG fibrils, indicating that PEG was at the outer edge of the fibril. 

Fig. 2 (a) Antiparallel and (b) parallel P-sheet structures of two peptide chains connected by hydrogen bonds... 

Interacting P sheets can be arranged either to form a parallel P sheet, in which the adjacent segments of the... 

The crystal structure of one LRR protein, the RNAse inhibitor, has revealed that leucine-rich repeats correspond to p-a structural units. This units are arranged for a parallel p-sheet with one surface exposed to solvent so that the protein acquires an unusual non-globular shape, which may be responsible for proteinbinding functions [57]. 

Figure 1. The three-dimensional structure of PelC. A. A schematic diagram illustrating the major secondary structural features of the PelC polypeptide backbone. The three parallel p sheets are represented by arrows in light, medium and dark gray.

FIGURE 4.7 Structure of the dimeric complex between FGF2 and FGF receptor 1. The Ig-like domains 2 and 3 of the two FGF receptor 1 molecules are composed of parallel p sheets and they are shown in medium and light gray, respectively. The two FGF2 molecules are composed of a bundle of p sheets that are shown in dark gray. PDB id 1CVS. (Plotnikov, A. N. et al., Cell, 98, 641, 1999.)... 

Figure 22 Schematic representation of proposed models for the fibril formation in the cases of pH 3.3 and 7.5. (A) hCT monomers in solution (B) a homogeneous association to form the a-helical bundle (micelle) (C) a homogeneous nucleation process to form the P-sheet and heterogeneous association process (D) a heterogeneous fibrillation process to grow a large fibril, a-helix, antiparallel p-sheet, and parallel p-sheet forms are shown by a box, drawn by dark grey and grey, respectively. From Ref. 163 with permission.

Fig. 4.12(a). An outline structure of a protein (here the enzyme phospholipase A2), showing a-helical runs of amino acids as cylinders (A-E) and anti-parallel P-sheet runs as heavy black arrows. Disulfide cross-links are shown (the enzyme is extracellular), and runs of no a/p secondary structure appear as thin lines. The structure is relatively immobile, and binds calcium in a constrained loop. (Reproduced with permission from Professor J. Drenth.)... 

The effect of formalin-treatment on the structural properties of RNase A was examined using circular dichroism (CD) spectropolarimetry. A brief introduction to CD spectropolarimetry is provided in Section 15.15.2 for those readers unfamiliar with this biophysical method. The secondary structure of RNase A consists of one long four-stranded anti-parallel p-sheet and three short a-helixes,44 which places RNase A in the a + p structural class of proteins. The effect of a 9-day incubation of RNase A (6.5mg/mL) in 10% formalin on the protein secondary structure was examined with CD spectropolarimetry in the far-UV region (170-240nm) as shown in Figure 15.6a. The resulting... 

Figure 4.8 Super-secondary structures found in proteins (a) P-a-P motifs (b) anti-parallel P-sheets connected by hairpin loops (c) a-a motifs. (From Voet and Voet, 2004. Reproduced with permission from John Wiley Sons., Inc.)...

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