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Thomas J Santangelo, L'ubomíra Cubonová, Katherine M Skinner, John N Reeve
Thermococcus kodakarensis (formerly Thermococcus kodakaraensis) strains have been constructed with synthetic and natural DNA sequences, predicted to function as archaeal transcription terminators, identically positioned between a constitutive promoter and a beta-glycosidase-encoding reporter gene (TK1761). Expression of the reporter gene was almost fully inhibited by the upstream presence of 5'-TTTTTTTT (T(8)) and was reduced >70% by archaeal intergenic sequences that contained oligo(T) sequences. An archaeal intergenic sequence (t(mcrA)) that conforms to the bacterial intrinsic terminator motif reduced TK1761 expression approximately 90%, but this required only the oligo(T) trail sequence and not the inverted-repeat and loop region...
November 2009: Journal of Bacteriology
David Zanuy, Buyong Ma, Ruth Nussinov
Experimentally, short peptides have been shown to form amyloids similar to those of their parent proteins. Consequently, they present useful systems for studies of amyloid conformation. Here we simulate extensively the NFGAIL peptide, derived from the human islet amyloid polypeptide (residues 22-27). We simulate different possible strand/sheet organizations, from dimers to nonamers. Our simulations indicate that the most stable conformation is an antiparallel strand orientation within the sheets and parallel between sheets...
March 2003: Biophysical Journal
Buyong Ma, Ruth Nussinov
The aggregation observed in protein conformational diseases is the outcome of significant new beta-sheet structure not present in the native state. Peptide model systems have been useful in studies of fibril aggregate formation. Experimentally, it was found that a short peptide AGAAAAGA is one of the most highly amyloidogenic peptides. This peptide corresponds to the Syrian hamster prion protein (ShPrP) residues 113-120. The peptide was observed to be conserved in all species for which the PrP sequence has been determined...
October 2002: Protein Science: a Publication of the Protein Society
S Heidmann, C Schindewolf, G Stumpf, H Domdey
Various signal motifs have been reported to be essential for proper mRNA 3'-end formation in the yeast Saccharomyces cerevisiae. However, none of these motifs has been shown to be sufficient to direct 3'-end processing and/or transcription termination. Therefore, several structural motifs have to act in concert for efficient 3'-end formation. In the region upstream of the three polyadenylation sites of the yeast gene for alcohol dehydrogenase I (ADH1), we have identified a hitherto unknown signal sequence contained within the octamer AAAAAAAA...
July 1994: Molecular and Cellular Biology
K Morimoto, A Ohkubo, A Kawai
The mRNA-encoding G protein of the attenuated HEP-Flury strain of rabies virus was sequenced by the cDNA cloning technique. The G-mRNA was composed of 2059 nucleotides, with the coding region located from the 28th to 1602nd nucleotide, and was capable of encoding a polypeptide of 524 amino acids. Although the coding region was highly homologous (90% or more) to that of ERA and PV strains, the 3' noncoding region of the HEP virus G-mRNA was longer than that reported for other strains by some 400 nucleotides...
December 1989: Virology
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