Secondary-structural motifs

The parallel /3-sheet is also the secondary structural motif of the pathogenic form of ataxin-3, a 42-kDa peptide expressed in the brain (Bevivino and Loll 2001). The peptide becomes harmful when the number of glutamine residues near its C-terminus... 

The ROA spectra of hen lysozyme [3, 35] and bovine P-lactoglobulin [3] are shown in Fig. 7.5. These spectra contain marker bands for the secondary structural motifs discussed above showing that this information is retained... 

The Rev protein of HIV-1 facilitates the nuclear export of incompletely spliced viral mRNAs and plays, therefore, an important role in the production of viral structural proteins. Rev specifically binds to a responsive element which folds into a stem-internal loop-stem secondary structure, the Rev-binding element (RBE) located into the rev gene. In vitro selection has been used to determine interactions between Rev and the RBE. RNA motifs which could bind Rev up to ten-fold better than the wild-type sequence have been isolated either from an RNA library constituted of partly randomized RBE (Bartel et al., 1991) or from completely random sequence pools, based on the RBE secondary structure (Giver et al., 1993 Tuerk and MacDougal-Waugh, 1993). Novel RNA sequences and secondary structural motifs have been selected. In particular, a wild-type G G pair is frequently replaced by an A A or even by a C A pair which are isosteric (Giver etal., 1993). 

The original design of our bistable RNA molecules did not make use of the algorithm cited above. Our empirical approach was based on two common secondary structure motifs which we set in competition with each other [30] for this purpose a GNRA- and UNCG-hairpin appeared suitable (Figure 1.1.3). 

To verify experimentally that the catalytic activity was caused by this secondary structure motif, we prepared a 53-nucleotide truncated version of one clone, which contained a condensed version of the motif near the 5 end. The activity of this oligoribonucleotide was found to be unchanged compared with that of the parent sequence. Next, we rationally increased the thermodynamic stability by eliminating unpaired bases from the helices, increasing the GC content of the helices, and replacing loops 1 and 2 with the stabilizing tetraloop sequences UUCG. The... 

Coherent transport of vibrational energy is further limited by vibrational energy relaxation. Experiments on the amide I band of different peptides (NMA, apamin, scyllatoxin BPTI, and the cyclic pentapeptide) revealed a vibrational relaxation rate of approximately Ti = 1.2 ps, which is essentially independent of the particular peptide (30,53). A similar value has recently been reported for myoglobin at room temperature, with only a weak dependence of the relaxation rate on temperature down to cryogenic temperatures (140). In other words, vibrational relaxation of the amide I mode reflects an intrinsic property of the peptide group itself rather than a specific characteristic of the primary or secondary structural motifs of the... 

Milton Hearn (Monash University) described his work to design novel affinity ligands that are capable of recognizing secondary structure motifs of proteins. Such ligands could speed the introduction of new tag sequences for use in fusion constructs. 

In sulfothermophile transcripts, the 16S-23S rRNA spacers are short compared with those of other archaea and bacteria they lack tRNAs and, although they contribute to the processing stems of the 16S and 23S rRNAs, the stems are truncated and, at least for Tp. tenax, a single, bifurcated processing stem is generated for the two rRNAs [82], However, despite differences between the organization and structure of the sulfothermophile rRNA transcripts and those of the other archaea, secondary structural motifs can be discerned in the 16S rRNA leader sequences and in the 16S-23S rRNA spacer regions which are common and exclusive to the archaea [108],... 

Transcripts from open reading frames and 16S-23S rRNA operons tend to terminate inefficiently at interspaced stretches of (T)-rich sequences. No common secondary structural motifs are associated with the terminator regions. 

The amphipathic a helix, defined as an a helix with opposing polar and nonpolar faces oriented along its long axis, is a common secondary structural motif in biologically active peptides and proteins. The discovery of this structural motif was made by studying space-filling models of... 

Koch-Nolte F, Petersen D, Balasubramanian S efal. (1996) Mouse cell membrane proteins Rt6-1 and Rt6-2 are arginine protein mono(ADPribosyl)transferases and share secondary structure motifs with ADP-ribosylating bacterial toxins. In J. Biol. Chem. 271 7686-93... 

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