Motif molecular

Meiselbach H, Sticht H, Enz R (2006) Structural analysis of the protein phosphatase 1 docking motif molecular description of binding specificities identifies interacting proteins. Chem Biol 13 49-59... 

He, B. and Wilson, E.A. (2003) Electrostatic modulation in steroid receptor recruitment of LXXLL and FXXLF motifs. Molecular and Cellular Biology, 23, 2135-2150. 

Rdblovd, K., Spackova, N., Stefl, R., Csaszar, K., Kofea, J., Leontis, N. B., Sponer, J. (2003). Non-Watson-Crick base pairing and hydration in RNA motifs Molecular dynamics of 5S rRNA Loop E. Biophysical Journal, 84, 3564. 

Oiengo C A and W R Taylor 1993. A Local Alignment Method for Protein Structure Motifs. ]ourr Molecular Biology 233 488-497. 

On the basis of simple considerations of connected motifs, Michael Leviff and Cyrus Chothia of the MRC Laboratory of Molecular Biology derived a taxonomy of protein structures and have classified domain structures into three main groups a domains, p domains, and a/p domains. In ct structures the core is built up exclusively from a helices (see Figure 2.9) in p structures the core comprises antiparallel p sheets and are usually two P sheets packed... 

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). 

Molecular biology studies have identified a loop containing 20-25 amino acid residues between S5 and S6 (or Ml and M2, Fig. 2) forming the pore. The G(Y/F) G motif located in the pore represents the K+-selectivity signature, which is common to all K+ channels. The external entry to the channel pore and its adjacent residues constitute binding sites for toxins and blockers. The internal vestibule of the pore and the adjacent residues in S5 and S6 contribute to binding sites for compounds such as 4-aminopyiidine and quinidine. The S4-S5 linker lies close to the permeation pathway and is required for... 

Whether the chemical repeating motif is a simple disaccharide or up to a complex octasaccharide, the molecular morphologies of branched polysaccharides are quite intriguing. The structure of welan (43) is a pleasant surprise. Others... 

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. 

In light of the importance of the / -turn motif in peptide and protein recognition, and the design and synthesis of bioactive small molecules, / -turn mimetics has attracted considerable attention. Seebach and coworkers have shown recently that low molecular weight open-chain / - and y-peptides designed to promote turn formation can be used as templates for mimicking the a-peptide hormone somatostatin. 

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