Comparative analysis of coiled-coil prediction methods

Gruber, Markus; Söding, Johannes; Lupas, Andrei N.

doi:10.1016/j.jsb.2006.03.009

Cited by 151 publications

(125 citation statements)

References 21 publications

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“…Often the highest scores were at the N terminus as expected, but this domain was spuriously predicted elsewhere in the protein as well. For example, a typical false positive was found in the polyglutamate repeat in the LRR of Hero, which cannot physically form a coiledcoil (Ernst et al 2002;Gruber et al 2006). We do not attempt to distinguish between regular coiled-coils and the leucine zipper subclass, but note that many leucine zippers reported in the R-gene literature were not predicted to be coiled-coils, even though a requisite pattern of leucine residues was present.…”

Section: Resultsmentioning

confidence: 99%

The Fractionated Orthology of Bs2 and Rx/Gpa2 Supports Shared Synteny of Disease Resistance in the Solanaceae

et al. 2009

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Comparative genomics provides a powerful tool for the identification of genes that encode traits shared between crop plants and model organisms. Pathogen resistance conferred by plant R genes of the nucleotide-binding-leucine-rich-repeat (NB-LRR) class is one such trait with great agricultural importance that occupies a critical position in understanding fundamental processes of pathogen detection and coevolution. The proposed rapid rearrangement of R genes in genome evolution would make comparative approaches tenuous. Here, we test the hypothesis that orthology is predictive of R-gene genomic location in the Solanaceae using the pepper R gene Bs2. Homologs of Bs2 were compared in terms of sequence and gene and protein architecture. Comparative mapping demonstrated that Bs2 shared macrosynteny with R genes that best fit criteria determined to be its orthologs. Analysis of the genomic sequence encompassing solanaceous R genes revealed the magnitude of transposon insertions and local duplications that resulted in the expansion of the Bs2 intron to 27 kb and the frequently detected duplications of the 59-end of R genes. However, these duplications did not impact protein expression or function in transient assays. Taken together, our results support a conservation of synteny for NB-LRR genes and further show that their distribution in the genome has been consistent with global rearrangements.

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Section: Resultsmentioning

confidence: 99%

The Fractionated Orthology of Bs2 and Rx/Gpa2 Supports Shared Synteny of Disease Resistance in the Solanaceae

et al. 2009

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“…2). The highest propensity to form a coiled coil was calculated (using the program PCOILS [5]) for the region from residue 24 to 69, followed by the region from residue 87 to 107 (Fig. 2).…”

Section: Methods (I) Cloning Expression and Purification Of Proteinsmentioning

confidence: 99%

Evidence for an Elongated Dimeric Structure of Heparin-Binding Hemagglutinin from Mycobacterium tuberculosis

et al. 2008

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Heparin-binding hemagglutinin (HBHA) is a virulence factor of tuberculosis which is responsible for extrapulmonary dissemination of this disease. A thorough biochemical characterization of HBHA has provided experimental evidence of a coiled-coil nature of HBHA. These data, together with the low-resolution structures of a full-length form and a truncated form of HBHA obtained by small-angle X-ray scattering, have unambiguously indicated that HBHA has a dimeric structure with an elongated shape.

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“…HHalign reported a weak similarity (E50.015) between a short region of P4 within its coiledcoil domain (aa 316-348 in RBLV P4) and the last two helices of the DnaK peptide-binding domain. Thus, the suggested similarity between P4 and DnaK is probably not authentic, as it is not statistically significant and occurs within the coiled-coil region, which is known to provoke spurious hits in similarity searches with unrelated helical proteins (Ferron et al, 2006;Gruber et al, 2006).…”

Section: Comparison With Previous Studiesmentioning

confidence: 99%

Experimental and bioinformatic evidence that raspberry leaf blotch emaravirus P4 is a movement protein of the 30K superfamily

Chen

Karlin

et al. 2013

Journal of General Virology

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Emaravirus is a recently described genus of negative-strand RNA plant viruses. Emaravirus P4 protein localizes to plasmodesmata, suggesting that it could be a viral movement protein (MP). In the current study, we showed that the P4 protein of raspberry leaf blotch emaravirus (RLBV) rescued the cell-to-cell movement of a defective potato virus X (PVX) that had a deletion mutation in the triple gene block 1 movement-associated protein. This demonstrated that RLBV P4 is a functional MP. Sequence analyses revealed that P4 is a distant member of the 30K superfamily of MPs. All MPs of this family contain two highly conserved regions predicted to form b-strands, namely b1 and b2. We explored by alanine mutagenesis the role of two residues of P4 (Ile106 and Asp127) located in each of these strands. We also made the equivalent substitutions in the 29K MP of tobacco rattle virus, another member of the 30K superfamily. All substitutions abolished the ability to complement PVX movement, except for the I106A substitution in the b1 region of P4. This region has been shown to mediate membrane association of 30K MPs; our results show that it is possible to make non-conservative substitutions of a well-conserved aliphatic residue within b1 without preventing the membrane association or movement function of P4.

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Comparative analysis of coiled-coil prediction methods

Cited by 151 publications

References 21 publications

The Fractionated Orthology of Bs2 and Rx/Gpa2 Supports Shared Synteny of Disease Resistance in the Solanaceae

The Fractionated Orthology of Bs2 and Rx/Gpa2 Supports Shared Synteny of Disease Resistance in the Solanaceae

Evidence for an Elongated Dimeric Structure of Heparin-Binding Hemagglutinin from Mycobacterium tuberculosis

Experimental and bioinformatic evidence that raspberry leaf blotch emaravirus P4 is a movement protein of the 30K superfamily

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