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The Febs Journal (1)
Jorda, Julien (2)
Kajava, Andrey V. (1)
Uversky, Vladimir N. (1)
Xue, Bin (1)
Yeates, Todd O. (1)
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Protein tandem repeats: the more perfect the less structured
Uversky, Vladimir N.
Kajava, Andrey V.
The Febs Journal
We analysed structural properties of protein regions containing arrays of perfect and nearly perfect tandem repeats. Naturally occurring proteins with perfect repeats are practically absent among the proteins with known 3D structures. The great majority of such regions in the Protein DataBank (PDB) are found in the de novo designed proteins. The abundance of natural structured proteins with tandem repeats is inversely correlated with the repeat perfection: the chance to find natural structured proteins in PDB increases with a decrease in the level of repeat perfection. Prediction of intrinsic disorder within the tandem repeats in the SwissProt proteins supports the conclusion that the level of repeat perfection correlates with their tendency to be unstructured. This correlation is valid across the various species and subcellular localizations, although the level of disordered tandem repeats varies significantly between these datasets. On average, in prokaryotes, tandem repeats of cytoplasmic proteins were predicted to be the most structured, whereas in eukaryotes, the most structured portion of the repeats was found in the membrane proteins. Our study supports the hypothesis that in general, the repeat perfection is a sign of recent evolutionary events rather than of exceptional structural and (or) functional importance of the repeat residues.
bioinformatics; disordered conformation; evolution; sequence analysis; protein structure
Widespread Disulfide Bonding in Proteins from Thermophilic Archaea
Yeates, Todd O.
Disulfide bonds are generally not used to stabilize proteins in the cytosolic compartments of bacteria or eukaryotic cells, owing to the chemically reducing nature of those environments. In contrast, certain thermophilic archaea use disulfide bonding as a major mechanism for protein stabilization. Here, we provide a current survey of completely sequenced genomes, applying computational methods to estimate the use of disulfide bonding across the Archaea. Microbes belonging to the Crenarchaeal branch, which are essentially all hyperthermophilic, are universally rich in disulfide bonding while lesser degrees of disulfide bonding are found among the thermophilic Euryarchaea, excluding those that are methanogenic. The results help clarify which parts of the archaeal lineage are likely to yield more examples and additional specific data on protein disulfide bonding, as increasing genomic sequencing efforts are brought to bear.
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