P„ helix

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.)...

Parallel p-helix domains have a novel fold... 

In the first edition of this book this chapter was entitled "Antiparallel Beta Structures" but we have had to change this because an entirely unexpected structure, the p helix, was discovered in 1993. The p helix, which is not related to the numerous antiparallel p structures discussed so far, was first seen in the bacterial enzyme pectate lyase, the stmcture of which was determined by the group of Frances Jurnak at the University of California, Riverside. Subsequently several other protein structures have been found to contain p helices, including extracellular bacterial proteinases and the bacteriophage P22 tailspike protein. 

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. 

The basic structural unit of these two-sheet p helix structures contains 18 amino acids, three in each p strand and six in each loop. A specific amino acid sequence pattern identifies this unit namely a double repeat of a nine-residue consensus sequence Gly-Gly-X-Gly-X-Asp-X-U-X where X is any amino acid and U is large, hydrophobic and frequently leucine. The first six residues form the loop and the last three form a p strand with the side chain of U involved in the hydrophobic packing of the two p sheets. The loops are stabilized by calcium ions which bind to the Asp residue (Figure S.28). This sequence pattern can be used to search for possible two-sheet p structures in databases of amino acid sequences of proteins of unknown structure. 

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... 

The number of helical turns in these structures is larger than those found so far in two-sheet p helices. The pectate lyase p helix consists of seven complete turns and is 34 A long and 17-27 A in diameter (Figure 5.30) while the p-helix part of the bacteriophage P22 tailspike protein has 13 complete turns. Both these proteins have other stmctural elements in addition to the P-helix moiety. The complete tailspike protein contains three intertwined, identical subunits each with the three-sheet p helix and is about 200 A long and 60 A wide. Six of these trimers are attached to each phage at the base of the icosahedral capsid. 

Figure S.29 Schematic diagrams of the three-sheet P helix, (a) The three sheets of parallel P strands are colored green, blue and yellow. Seven complete colls are shown In this diagram but the number of colls varies in different stmctures. Two of the P sheets (blue and yellow) are parallel to each other and are perpendicular to the third (green).

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 5.30 Schematic diagrams of the structure of the enzyme pectate lyase C, which has a three-sheet parallel P-helix topology.

Figure 14.8 Proposed model of p sheet helix of the fibrous form of transthyretin. The repeating unit of the P helix comprises 24 P strands with an average twist of 15° between each strand giving a complete turn of 360°. Four transthyretin polypeptide chains contribute to the repeat unit and are shown here in different colors. (Adapted from C. Blake and L. Serpell, Structure 4 989-998, 1996.)...

The temperature measurements in range from —40 to 23 °C revealed the presence of conformational equilibrium between conformers of the opposite helicity (M- and P-helix). The barrier of 13 kcal/mol of the chemical exchange was estimated. It was shown that peripheral stereocenters control the absolute sense of helicity in the foldamers studied.103... 

To quantitatively characterize the PM populations using chiroptical characteristics, it may be useful to use the gabs values of 16 at each temperature with reference to the regression curve of these gabs values in 17, which is assumed to adopt a purely P 73-helical structure, instead of the Ae value. The analysis is based on the assumption that the weak temperature dependence of the ymax for 17 is due to a minute modification in the screw pitch of the P helix, rather than any formation of the M-helical motif. 

Figure 4.13 (a) Temperature dependence of dissymmetry ratios of poly ( S )-3,7-dimethy locty 1-3-methylbutylsilane (16) (three different Mw samples) and poly (5) -3,7-dimethyloctyl-2-methyl-propylsilane (17) (a purely P helix) in isooctane, (b) Temperature dependence of P and M populations of 16 in isooctane by reference to the regression curve of gabs values in 17. 

Contrarily, /7-21 shows an unclear double well potential curve with minima at dihedral angles of about P 1600 and M 200°. The P helix is much more stable compared to the corresponding M by about 2.3 kcal per repeat unit. The barrier heights of the respective M and P are about 3.9 and 1.4 kcal per... 

M-helix with ordered p-helix with disordered... 

The carbonic anhydrase (Cam) in M. thermophila cells is elevated several fold when the energy source is shifted to acetate, suggesting a role for this enzyme in the acetate-fermentation pathway. It is proposed that Cam functions outside the cell membrane to convert CO2 to a charged species (reaction A4) thereby facilitating removal of product from the cytoplasm. Cam is the prototype of a new class (y) of carbonic anhydrases, independently evolved from the other two classes (a and P). The crystal structure of Cam reveals a novel left-handed parallel P-helix fold (Kisker et al. 1996). Apart from the histidines ligating zinc, the activesite residues of Cam have no recognizable analogs in the active sites of the a- and P-classes. Kinetic analyses establish that the enzyme has a zinc-hydroxide mechanism similar to that of Cab (Alber et al. 1999). 

A single P strand can also be wound into a cylinder with the hydrogen bonds running parallel to the helix axis. A right-handed parallel P helix of this type has been found in the bacterial enzyme pectate lyase.121122 The polypeptide chains of the 353-residue protein contain seven complete turns of about 22... 

Antifreeze proteins, that are 3-4 times as effective as those in fish, have been isolated from some insects and other arthropods.1 11 0 They help beetle larvae to overwinter. The insect proteins have a parallel P helix structure resembling that in Fig. 2-17 and stabilized by S — S bridges.0 Some plants also synthesize antifreeze proteins.11 1 One of these, isolated from carrots, is a member of the leucine-rich-repeat family ... 

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