Helix class

HhH2 Helix-hairpin-helix class 2 (Poll family) motifs E(MFP)AB 0(0) 4(4) 1BGX... 

The cell illustrated opposite, a rod, has a structure divided by membrane discs into which the 7-helix receptor rhodopsin is integrated (see p. 224). In contrast to other receptors in the 7-helix class (see p. 384), rhodopsin is a light-sensitive chromoprotein. Its protein part, opsin, contains the aldehyde retinal (see p. 364)—an isoprenoid which is bound to the e-amino group of a lysine residue as an aldimine. 

Muscle, whose structure and function are discussed in Chapter 19, develops in response to four members of the myoD family. These include myoD, myogenin, myf5, and MRF4.417-419 All are muscle-specific transcription factors of the basic helix -loop -helix class. An unusual aspect of muscle development is formation of multinucleate myotubes (muscle fibers p. 1096)420 Apoptosis plays an important role in muscle development and can present significant complications in damaged cardiac muscle.421 Defects in several developmental control genes are responsible for congenital heart diseases.422... 

Correlation of Lipid Association xoith Amphipathic Helix Class... 

Homeo box A common sequence element of about 180 base pairs that is found in homeotic genes. It codes for a sequence-specific DNA-binding element of the helix-loop-helix class. 

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. 

Antiparallel tt-helix proteins are structures heavily dominated by a-helices. The simplest way to pack helices is in an antiparallel manner, and most of the proteins in this class consist of bundles of antiparallel helices. Many of these exhibit a slight (15°) left-handed twist of the helix bundle. Figure 6.29 shows a representative sample of antiparallel a-helix proteins. Many of these are regular, uniform structures, but in a few cases (uteroglobin, for example) one of the helices is tilted away from the bundle. Tobacco mosaic virus protein has small, highly... 

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. 

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