Repeating motifs

Associated chemical units become systematically arranged in Ihe crystal structure, which is constructed from a single motif that develops repetitively. The resulting three-dimensional array is called the space lattice of the crystal. The lattice or framework is defined by three directions and by ihe distance along those directions where the motif repeats itself. Because the units within the structure adhere lo a strict arrangement, the external facial planes of a crysial represent the limiting surfaces of that growth and are an external expression of its internal atomic order. Crystals are formed, therefore, where constituent atoms or ions are free to combine in constant chemical proportions and arc an expression of the environmental conditions that promote their formation. 

Line helices (chordal helices) are composed of dimensionless points. A chordal helix is uniform if all points are equivalent such a helix will have a circular cross-section and could be inscribed on a right circular cylinder. A nonuniform chordal helix is regular if it contains motifs repeated in a definite pattern and irregular if the motifs are not so repeated. For our purposes, chordal helices are useful mathematical abstractions. 

The notion fractal means an object possessing a complex structure the form of elements of which repeats on all levels of measurement—from macroscopic to microscopic. Fractal is defined as a geometrical figure consisting of identical motif repeating itself on an ever-reduced scale [1,2]. 

The simplest two-dimensional space group is represented in four variations in Figure 8-29. This space group does not impose any restrictions on the parameters a, b, and y. The equal motifs repeated by the translations may occur in the following four different versions (strafing from the upper left and clockwise) they may be completely separated from one another they may consist of disconnected parts they may intersect each other and finally, they may fill the entire plane without gaps and overlaps. Of course, such variations are possible for any of the more complicated two-dimensional space groups as well. 

Vibrational dispersion is, for vibrations of the same type, the variation of the relative phase of atomic displacements with their frequency. Although it is a well known effect in molecular spectroscopy it is not usually presented as such. Rather there is an emphasis on treating each vibration individually and the deep similarities between vibrations of the same type are often obscured. Dispersion in molecules is normally seen in its discrete form and the effect of continuous dispersion is only observed in the spectroscopy of polymers ( 10.1.1.1). The connection between the discrete and continuous forms is most easily seen by considering the vibrations of molecules composed of simple chemical motifs repeated several-fold. We have chosen to demonstrate this with the highest frequency vibrations in benzene, the stretches of the six C-H repeat units. 

This motif is called a beta-alpha-beta motif (Figure 2.17) and is found as part of almost every protein structure that has a parallel p sheet. For example, the molecule shown in Figure 2.10b, triosephosphate isomerase, is entirely built up by repeated combinations of this motif, where two successive motifs share one p strand. Alternatively, it can be regarded as being built up from four consecutive p-a-p-a motifs. 

Leucine residues 2, 5, 7, 12, 20, and 24 of the motif are invariant in both type A and type B repeats of the ribonuclease inhibitor. An examination of more than 500 tandem repeats from 68 different proteins has shown that residues 20 and 24 can be other hydrophobic residues, whereas the remaining four leucine residues are present in all repeats. On the basis of the crystal structure of the ribonuclease inhibitor and the important structural role of these leucine residues, it has been possible to construct plausible structural models of several other proteins with leucine-rich motifs, such as the extracellular domains of the thyrotropin and gonadotropin receptors. 

The horseshoe structure is formed by homologous repeats of leucine-rich motifs, each of which forms a p-loop-a unit. The units are linked together such that the p strands form an open curved p sheet, like a horseshoe, with the a helices on the outside of the p sheet and the inside exposed to solvent. The invariant leucine residues of these motifs form the major part of the hydrophobic region between the a helices and the p sheet. 

The two homologous repeats, each of 88 amino acids, at both ends of the TBP DNA-binding domain form two stmcturally very similar motifs. The two motifs each comprise an antiparallel p sheet of five strands and two helices (Figure 9.4). These two motifs are joined together by a short loop to make a 10-stranded p sheet which forms a saddle-shaped molecule. The loops that connect p strands 2 and 3 of each motif can be visualized as the stirmps of this molecular saddle. The underside of the saddle forms a concave surface built up by the central eight strands of the p sheet (see Figure 9.4a). Side chains from this side of the P sheet, as well as residues from the stirrups, form the DNA-binding site. No a helices are involved in the interaction area, in contrast to the situation in most other eucaryotic transcription factors (see below). 

Chain metasilicates Si03 formed by comersharing of Si04 tetrahedra arc particularly prevalent in nature and many important minerals have this basic structural unit (cf, polyphosphates, p, 528), Despite the apparent simplieily of their structure motif and stoichiometry considerable structural diversity is encountered because of the differing conformations that can be adopted by the linked tetrahedra. As a result, the repeat distance along the c -axis can be (1). 

The ankyrin repeat motif is one of the most common protein-protein interaction domains. Ankyrin repeats are modules of about 33 amino acids repeated in tandem. They are found in a large number of proteins with diverse cellular functions such as transcriptional regulators, signal transducers, cell-cycle regulators, and cytoskeletal proteins. 

Several nonconventional cadherins that contain cadherin repeats have been described but they have specific features not found in the classical cadherins [1]. The cadherin Flamingo, originally detected in Drosophila, contains seven transmembrane segments and in this respect resembles G protein-coupled receptors. The extracellular domain of Flamingo and its mammalian homologs is composed of cadherin repeats as well as EGF-like and laminin motifs. The seven transmembrane span cadherins have a role in homotypic cell interactions and in the establishment of cell polarity. The FAT-related cadherins are characterized by a large number of cadherin repeats (34 in FAT and 27 in dachsous). Their cytoplasmic domains can bind to catenins. T- (=truncated-)cadherin differs from other cadherins in that it has no transmembrane domain but is attached to the cell membrane via a glycosylpho-sphatidylinositol anchor. 

Peifer M, Berg S, Reynolds AB (1994) A repeating amino acid motif shared by proteins with diverse cellular roles. Cell 76 789-791... 

An essential step of NR action is the interaction of these receptors with the specific DNA sequence HREs. Indeed, HREs position the receptors, and the transcriptional complexes recruited by them, close to the target genes. HREs are bipartite elements that are composed of two hexameric core half-site motifs. These consensus nucleotide sequences form direct, indirect, or inverted repeats, which consist of two half-sites separated... 

Signaling by PKC is terminated by concentrations of its ligands dropping to basal levels (i.e., Ca2+ and diacylglycerol) and by dephosphorylation of the three processing sites. Dephosphorylation is controlled, in part, by a recently discovered hydrophobic phosphorylation motif phosphatase. This phosphatase, PHLPP (for PH domain Leucine-rich repeat Protein Phosphatase) dephosphorylates conventional and novel PKC isozymes, initiating their downregulation. 

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