Four-fold helix

In TMA, the ratio of the unit cell dimensions a/b is almost 2/1, yet the interchain distance is close to that of ATAI and even closer to both TEA polymorphs (cf. Table II). The true conformation of TMA, although nominally a four-fold helix (cf. Fig. 

Natta and co-workers (35) have shown by careful x-ray investigation that crystalline polyaldehydes are isotactic polymers crystallizing in a four-fold helix with an identity period of 4.8 A. (Figure 4). 

The net has eubie symmetry in its highest space group, basically meaning that viewed from the x, y or z direction this net will look the same. Two views of this net are shown in Figure 5.3. As we shall see in Chapter 6 some other nets give very similar views if seen from certain directions, but are easily discerned from the srs net by rotating the view. Also note that the four-fold helix is a common theme in nets containing three-connected nodes. 

It is not possible to give a straight answer as to why this is so, but both the symmetry of the net (The connectors in eta are all of equal length, but of two different types, those within a four-fold helix and those connecting the helices. In srs there is only one type) and the possibilities of interpenetration have to be considered. (A majority of the srs structures are interpenetrated.)... 

Secondary structural predictions about NPAs, and direct biophysical measurements, have demonstrated that the NPAs are rich in a-helix, with no p-structure either predicted from secondary structure prediction algorithms, or detected by circular dichroism (Kennedy et al, 1995b). In this they are the antithesis of the similarly sized cLBPs and lipocalins. The predictions are that each individual NPA unit protein will fold into four main regions of helix, and it has been speculated that the tertiary structure is as a four-bundle helix protein, similar to other invertebrate carrier proteins (Sheriff et al., 1987). 

Figure 19.1 (a) View of the 24-subunit structure of human H-chain ferritin (rHuHF) viewed down the four-fold symmetry axis, (b) The subunit of rHuHF, with the short E-helix at the top of the four-helix bundle, (c) rHuHF viewed down the three-fold symmetry axis. (From Lewin et al., 2005. Copyright with permission from The Royal Society of Chemistry, 2005.)... 

Since the primary structure of a peptide determines the global fold of any protein, the amino acid sequence of a heme protein not only provides the ligands, but also establishes the heme environmental factors such as solvent and ion accessibility and local dielectric. The prevalent secondary structure element found in heme protein architectures is the a-helix however, it should be noted that p-sheet heme proteins are also known, such as the nitrophorin from Rhodnius prolixus (71) and flavocytochrome cellobiose dehydrogenase from Phanerochaete chrys-osporium (72). However, for the purpose of this review, we focus on the structures of cytochromes 6562 (73) and c (74) shown in Fig. 2, which are four-a-helix bundle protein architectures and lend themselves as resource structures for the development of de novo designs. 

Finally, three groups have reported the preparation of artificial enzymes with catalytic activity. Stewart and co-workers [73] incorporated a catalytic triad from the serine proteases into a designed four a-helix protein (80). In their design, they incorporated one of the amino acids involved in the catalytic function at the N-terminal side of the a-helices that are linked together by their C-terminal position (Fig. 29). The authors proposed that the oxyanion hole and the hydrophobic binding pocket are created by the three-dimensional structure formed by the folding of 80. Compared to the spontaneous reaction, impressive... 

Molluscan hemocyanins. Two FUs from moUuscan hemocyanins were resolved, the oxy-form of O. dofleini He FU g (Figure 5b) and the deoxy-form of R. thomasiana He (Figure 5c ). Each FU consists of two domains. The N-terminal domain II carries the active site with a four alpha-helix bundle folding motif with two copper atoms. The C-terminal domain III replaces topologically the domain I in arthropod subunits and looks like a squeezed beta-barrel. Although the Rapana structure is not resolved as well as the Octopus FU, two different conformations can be deduced. In the oxy FU of Octopus hemocyanin, domain III covers the entrance to the active site completely while in the deoxy-form this domain is shifted a few degrees so that the channel to the active site becomes completely uncovered. 

The basic conformational motif of these molecules appears to be the two-fold helix, maintained by intra-chain 05 H03, familiar from cellulose. Electron diffraction studies on single crystals of mannan I revealed an antiparallel arrangement in an orthorhombic unit cell containing four equivalent mannoses. The polymer chain adopted a two-fold helix with (jo=-81°, F = -161° jy 79°) and 161°. In addition to the intra-chain 05 H03 hydrogen... 

A) The protein coat of horse spleen apoferritin deduced from x-ray diffraction of crystals of the protein.The outer surface of the protein coat shows the arrangement of the 24 ellipsoidal polypeptide subunits. N refers to the N-terminus of each polypeptide and E to the E-helix (see B). Note the channels that form at the four-fold axes where the E-helices interact, and at the threefold axes near the N-termini of the subunits. (B) A ribbon model of a subunit showing the packing of the four main alpha-helices (A, B, C, and D), the connecting L-loop and the E-helix. 

Table 17.2. a Compilation of database-retrieved hexapeptides related to the peptide YLQTYH (residues 13 -18) of barnase. For each peptide a folding score is calculated as the product of fold pattern weight and similarity index. The cumulative scores for the four fold types are given at the bottom. The hexapeptide YLQTYH is the C-terminal end of an early formed helix [37] in barnase and adopts the secondary structure hhhhhn in the crystal [67]... 

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