Class of helix

Ellis, H. M., Spann, D. R., and Posakony, J. W. (1990). extramacrochaetae, a negative regulator of sensory organ development in Drosophila, defines a new class of helix-loop-helix proteins. Cell 61 27-38. 

The boundary between star and amphiverse helices is formed by the radial helices (11), in which one set of alternate bonds converge at the helix axis. The rectangular helices (12), where 0=90° and u/t =2/1, separate the star and ring helices and represent one class of helix where alternate bonds are parallel. The step helices (13) (ya or yb = 180°) separate the ring and amphiverse helices and have one set of parallel alternate bonds. Many of these figures are also shown on the conformational map in Fig. 24 for the quadrant where the two conformation angles have the same sign. 

Molecular Interactions. Various polysaccharides readily associate with other substances, including bile acids and cholesterol, proteins, small organic molecules, inorganic salts, and ions. Anionic polysaccharides form salts and chelate complexes with cations some neutral polysaccharides form complexes with inorganic salts and some interactions are stmcture specific. Starch amylose and the linear branches of amylopectin form inclusion complexes with several classes of polar molecules, including fatty acids, glycerides, alcohols, esters, ketones, and iodine/iodide. The absorbed molecule occupies the cavity of the amylose helix, which has the capacity to expand somewhat to accommodate larger molecules. The starch—Hpid complex is important in food systems. Whether similar inclusion complexes can form with any of the dietary fiber components is not known. 

In the next class of a/p structures there are a helices on both sides of the p sheet. This has at least three important consequences. First, a closed barrel cannot be formed unless the p strands completely enclose the a helices on one side of the p sheet. Such structures have never been found and are very unlikely to occur, since a large number of p strands would be required to enclose even a single a helix. Instead, the p strands are arranged into an open twisted p sheet such as that shown in Figure 4.1b. 

Like other hormones in this class of cytokines, GH has a four-helix bundle structure as described in Chapter 3 (see Figures 3.7 and 13.18). Two of the a helices, A and D, are long (around 30 residues) and the other two are about 10 residues shorter. Similar to other four-helix bundle structures, the internal core of the bundle is made up almost exclusively of hydrophobic residues. The topology of the bundle is up-up-down-down with two cross-over connections from one end of the bundle to the other, linking helix A with B and helix C with D (see Figure 13.18). Two short additional helices are in the first cross-over connection and a further one in the loop connecting helices C and D. 

For each fold one searches for the best alignment of the target sequence that would be compatible with the fold the core should comprise hydrophobic residues and polar residues should be on the outside, predicted helical and strand regions should be aligned to corresponding secondary structure elements in the fold, and so on. In order to match a sequence alignment to a fold, Eisenberg developed a rapid method called the 3D profile method. The environment of each residue position in the known 3D structure is characterized on the basis of three properties (1) the area of the side chain that is buried by other protein atoms, (2) the fraction of side chain area that is covered by polar atoms, and (3) the secondary stmcture, which is classified in three states helix, sheet, and coil. The residue positions are rather arbitrarily divided into six classes by properties 1 and 2, which in combination with property 3 yields 18 environmental classes. This classification of environments enables a protein structure to be coded by a sequence in an 18-letter alphabet, in which each letter represents the environmental class of a residue position. 

Inward Rectifier Potassium Channels or Kir Channels are a class of potassium channels generated by tetra-meiic arrangement of one-pore/two-transmembrane helix (1P/2TM) protein subunits, often associated with additional beta-subunits. Kir channels modulate cell excitability, being involved in repolarization of action potentials (see Fig. 1), setting the resting potential (see Fig. 1) of the cell, and contributing to potassium homeostasis. 

A peptoid pentamer of five poro-substituted (S)-N-(l-phenylethyl)glycine monomers, which exhibits the characteristic a-helix-like CD spectrum described above, was further analyzed by 2D-NMR [42]. Although this pentamer has a dynamic structure and adopts a family of conformations in methanol solution, 50-60% of the population exists as a right-handed helical conformer, containing all cis-amide bonds (in agreement with modeling studies [3]), with about three residues per turn and a pitch of 6 A. Minor families of conformational isomers arise from cis/trans-amide bond isomerization. Since many peptoid sequences with chiral aromatic side chains share similar CD characteristics with this helical pentamer, the type of CD spectrum described above can be considered to be indicative of the formation of this class of peptoid helix in general. 

Three classes of nucleic acid triple helices have been described for oligonucleotides containing only natural units. They differ according to the base sequences and the relative orientation of the phosphate-deoxyribose backbone of the third strand. All the three classes involve Hoogsteen or reverse Hoogsteen-like hydrogen bonding interaction between the triple helix form-... 

The remaining major classes of water-soluble lipid transporter proteins (other than the polyproteins of nematodes see below) come from plants and helminths. Plants possess very small (approximately 9 kDa) helix-rich, fatty-acid-binding proteins, the structures of some of which are known (Lerche and Poulsen, 1998). A recently described class comes from cestodes these are also very small (approximately 8 kDa), presumably intracellular, and helix-rich, and bind anthelmintic drugs in addition to fatty acids (Janssen and Barrett, 1995 Barrett et al., 1997). The only helix-rich small (approximately 14 kDa) lipid transporter from vertebrates is the acetyl-CoA-binding protein (Kragelund et al., 1993). 

Kennedy, M.W., Garside, L.H., Goodrick, L.E., McDermott, L., Brass, A., Price, N.C., Kelly, S.M., Cooper, A. and Bradley, J.E. (1997) The Ov20 protein of the parasitic nematode Onchocerca volvulus. A structurally novel class of small helix-rich retinol-binding protein. Journal of Biological Chemistry 272, 29442-29448. 

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... 

These AChE forms differ in solubility and mode of membrane attachment rather than in catalytic activity. One class of molecular forms exists as homomeric assemblies of catalytic subunits that appear as monomers, dimers or tetramers (Fig. 11-7). These forms also differ in hydrophobicity, and their amphiphilic character arises from either exposure of an amphipathic helix or post-translational addition of a glycophospholipid on the carboxyl-terminal amino acid. The glycophospholipid allows the enzyme to be tethered on the external surface of the cell membrane. 

The final class of iron proteins that we consider here are a family that contain a carboxylate-bridged diiron centre. They carry out a variety of functions, which have the common link that they react with dioxygen as part of their functional processes. The dimetallic centre is incorporated into a four-helix bundle domain (see Figure 3.9a), which seems to represent... 

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