Helix parallel

Theoretical calculations indicate that the CD of parallel and antiparallel (3-sheets are quite similar. This conclusion is supported by the CD spectrum of pelC,[1011021 a protein that has a parallel (3-helix motif, 1031 and therefore is more than 30% parallel (3-sheet with no antiparallel (3-sheet. Moreover, the parallel (3-sheet has a rather small degree of twist. The band positions and relative amplitudes in the CD spectrum of this protein resemble those for poly(Lys) in the (3-sheet form, which is an antiparallel sheet that is expected to be only slightly twisted because of the linear side chains. 

The first structures of this kind were reported in 1993 pectate lyase G from Erwinia chrysanthemi (Yoder et al, 1993) and alkaline protease from Pseudomonas aeruginosa (Baumann et al, 1993). Based on consideration of these crystal structures, the term parallel //-helix was introduced for a fold containing three //-strands per coil, and parallel //-roll for a fold with two //-strands per coil (Baumann etal, 1993 Yoder andjurnak, 1995 Yoder et al., 1993). The epithet parallel was intended to emphasize the distinction between these folds and the previously observed helical structure of the antibiotic gramicidin which contains both l- and D-amino acids and... 

Fig. 10, taken from the exceptional review of Sitming, illustrates some recently obtained insights into the effect of protein structure of the L-subunit on herbicide action. Fig. 10 (A) shows how Qb is situated in the binding site ofthe L-subunit ofwild-typeRp. viridis. The figure includes transmembrane helices D and E and the membrane-parallel helix de. Here His 190 and His230 in the L-subunit of Rp. viridis and the corresponding His215 and His272 in D1 are the known ligands to Qb and the Fe-atom. Ubiquinone Qb in the bacterial RC fills the entire pocket formed by helices D and E and the de loop. Hydrogen bonds are...

The y-crystalline form of i-PP has been studied through best fitting of X-ray diffraction powder profile [9, 10]. A novel crystal architecture was found where layers of parallel helixes two chain wide (bilayers) present a chain axis orientation with a tilt of 80° with respect to the one of the adjacent bilayers. This packing can explain several experimental results and is consistent with the model proposed for the interface between parent and daughter lamellae in branching a-form of i-PP [11, 12]. 

Kerr ID. Sankararamakrishnan R. Smart OS, et al. Parallel helix bundles and ion channels molecular modeling via simulated annealing and restrained molecular dyanamics. Biophys J 1994 67 1501-1515. 

A Simple model for a parallel helix lattice protein... 

Parallel Day 1 South-facing slope is heated—single helix 2 Upslope flow on both heated slopes—double helix... 

The hairpin motif is a simple and frequently used way to connect two antiparallel p strands, since the connected ends of the p strands are close together at the same edge of the p sheet. How are parallel p strands connected If two adjacent strands are consecutive in the amino acid sequence, the two ends that must be joined are at opposite edges of the p sheet. The polypeptide chain must cross the p sheet from one edge to the other and connect the next p strand close to the point where the first p strand started. Such CTossover connections are frequently made by a helices. The polypeptide chain must turn twice using loop regions, and the motif that is formed is thus a p strand followed by a loop, an a helix, another loop, and, finally, the second p strand. 

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. 

Figure 3.S Schematic diagram of packing side chains In the hydrophobic core of colled-coll structures according to the "knobs In holes" model. The positions of the side chains along the surface of the cylindrical a helix Is pro-jected onto a plane parallel with the heUcal axis for both a helices of the coiled-coil. (a) Projected positions of side chains in helix 1. (b) Projected positions of side chains in helix 2. (c) Superposition of (a) and (b) using the relative orientation of the helices In the coiled-coil structure. The side-chain positions of the first helix, the "knobs," superimpose between the side-chain positions In the second helix, the "holes." The green shading outlines a d-resldue (leucine) from helix 1 surrounded by four side chains from helix 2, and the brown shading outlines an a-resldue (usually hydrophobic) from helix 1 surrounded by four side chains from helix 2.

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).

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 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... 

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).

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