Motifs repetitive

Figure 4.11 Schematic diagram of the structure of the ribonuclease inhibitor. The molecule, which is built up by repetitive P-loop-a motifs, resembles a horseshoe with a 17-stranded parallel p sheet on the inside and 16 a helices on the outside. The P sheet is light red, a helices are blue, and loops that are part of the p-loop-(x motifs are orange. (Adapted from B. Kobe et al.. Nature 366 7S1-756,...

Coacervation occurs in tropoelastin solutions and is a precursor event in the assembly of elastin nanofibrils [42]. This phenomenon is thought to be mainly due to the interaction between hydro-phobic domains of tropoelastin. In scanning electron microscopy (SEM) picmres, nanofibril stmc-tures are visible in coacervate solutions of elastin-based peptides [37,43]. Indeed, Wright et al. [44] describe the self-association characteristics of multidomain proteins containing near-identical peptide repeat motifs. They suggest that this form of self-assembly occurs via specific intermolecular association, based on the repetition of identical or near-identical amino acid sequences. This specificity is consistent with the principle that ordered molecular assembhes are usually more stable than disordered ones, and with the idea that native-like interactions may be generally more favorable than nonnative ones in protein aggregates. 

Bisoffi, M., Marti, S. and Betschart, B. (1996) Repetitive peptide motifs in the cuticlin of Ascaris suum. Mokcubr and Biochemical Parasitobgy 80, 55-64. 

Silk proteins (spidroins in spiders and fibroins in Lepidoptera insects) are assembled into well-defined nanofibrillar architectures (Craig and Riekel, 2002 Eby et al., 1999 Inoue et al., 2000b, 2001 Li et al., 1994 Putthanarat et al, 2000 Vollrath et al., 1996). Spidroins and fibroins are largely constructed from two chemically distinct repetitive motifs or blocks (Table I), an insoluble crystalline block and a soluble less-crystalline block (Craig, 2003 Fedic et al., 2002 Hayashi and Lewis, 2000 Hayashi et al., 1999). The crystalline blocks are composed of short side-chained amino acids in highly repetitive sequences that give rise to /1-sheet structures. 

Helical heptad repeat sequences have been reported to be well behaved although they are difficult to characterize by NMR spectroscopy due to spectral overlap. The motifs that have been shown to have native-like properties, and are not highly repetitive, have cores composed of aromatic amino acid side chains of, for example, phenylalanine and tryptophan. In four-helix bundle motifs [1, 2], the /1/la-motif BBAl [5] and the /1-sheet protein Betanova [9], the formation of the folded structure appears to be strongly dependent on such residues although the energetics have not been calculated by substitution studies. As a tentative rule, therefore, the probability of success in the design of a new protein is probably much higher if residues are included that can form aromatic clusters in the core (Fig. 5). 

In addition to the DCTAE/DDTAV motifs, a highly conserved repetitive strand turn motif rich in aromatic amino acids (the QW motif) occurs in all OSCs and SCs and is repeated four to eight times (Table 3). These repeats are likely to be important for protein structure and stability and also for catalytic activity [55, 62-64]. The aromatic amino acids of the QW motif have been proposed to constitute sites of negative point charge that may interact with the intermediate cations during the cyclisation process [62]. 

Unlike crystalline subsystems, one cannot understand the structure of an amorphous particle from a knowledge of the spatial organization of a small group of its constituent atoms. The reason is that the atoms are not arranged in a regular, periodic array which would enable one to define the whole space occupied by the particle by simple translational repetitions of a basic structural motif of atoms. The spatial organization of the ions comprising the amorphous material in bone mineral is, at present, completely unknown. 

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. 

Hancock, J.M. and Armstrong, J.S. (1994) SIMPLE34 an improved and enhanced implementation for VAX and SUN computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences. Cabios 10, 67-70. 

Kieliszewski, M.J. Lamport, D.T.A. (1994). Extensin repetitive motifs, functional sites, post-translational codes and phytogeny. Plant J. 5, 157-172. 

Fibrous protein sequences are often characterized by the presence of simple repetitive motifs. Some are exact in length and/or sequence, but others are only approximate and display considerable variation. Some motifs contain residues that are absolutely conserved in some positions, whereas in others it is only the sequence character that is maintained over the repeat length. In many fibrous proteins the repeats occur contiguously, whereas in others they are found widely separated in the sequence. The varieties of sequence repeat that have been observed are typed and catalogued here by Parry (Chapter 2). Each motif forms a discrete element of structure in many instances, these are arranged helically with respect to one another. In many cases an elongate structure is formed, and this can lead naturally to molecular aggregation and the formation of functional filaments. 

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