Model building by comparison at CASP3: Using expert knowledge and computer automation

Bates, Paul A.; Sternberg, Michael J. E.

doi:10.1002/(sici)1097-0134(1999)37:3+<47::aid-prot7>3.0.co;2-f

Cited by 149 publications

(71 citation statements)

References 24 publications

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“…All the selected sequences were indicated to have lectin domains. Models were built for this set of sorted sequences using various structure prediction tools for further selection on the basis of the ability of the sequence to fold into a reasonably complete β-prism (Rost 1996;Bates and Sternberg 1999;Bates et al 2001;Contreras-Moreira and Bates 2002). The sequences for which models could not be predicted or the model did not yield either of the β-prism folds lay in the twilight zone of similarity (~15-30%).…”

Section: Methodsmentioning

confidence: 99%

Multiplicity of carbohydrate-binding sites in β-prism fold lectins: occurrence and possible evolutionary implications

et al. 2007

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The beta-prism II fold lectins of known structure, all from monocots, invariably have three carbohydrate-binding sites in each subunit/domain. Until recently, beta-prism I fold lectins of known structure were all from dicots and they exhibited one carbohydrate-binding site per subunit/domain. However, the recently determined structure of the beta-prism fold I lectin from banana, a monocot, has two very similar carbohydrate-binding sites. This prompted a detailed analysis of all the sequences appropriate for two-lectin folds and which carry one or more relevant carbohydrate-binding motifs. The very recent observation of a beta-prism I fold lectin, griffthsin, with three binding sites in each domain further confirmed the need for such an analysis. The analysis demonstrates substantial diversity in the number of binding sites unrelated to the taxonomical position of the plant source. However, the number of binding sites and the symmetry within the sequence exhibit reasonable correlation. The distribution of the two families of beta-prism fold lectins among plants and the number of binding sites in them, appear to suggest that both of them arose through successive gene duplication, fusion and divergent evolution of the same primitive carbohydrate-binding motif involving a Greek key. Analysis with sequences in individual Greek keys as independent units lends further support to this conclusion.It would seem that the preponderance of three carbohydrate-binding sites per domain in monocot lectins, particularly those with the beta-prism II fold, is related to the role of plant lectins in defence.

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Section: Methodsmentioning

confidence: 99%

Multiplicity of carbohydrate-binding sites in β-prism fold lectins: occurrence and possible evolutionary implications

et al. 2007

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“…The secondary structure was predicted using the MNPredict Program [26] and the tertiary structure model was calculated at 3D-Jigsaw [27][28][29] server. Fig.…”

Section: Theoretical Structural Calculationsmentioning

confidence: 99%

Conformational stability of recombinant manganese superoxide dismutase from the filamentous fungus Trichoderma reesei

Chambergo¹,

Valencia²,

Ferreira-Junior³

et al. 2012

International Journal of Biological Macromolecules

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Superoxide dismutases (SODs; EC 1.15.1.1) are part of the antioxidant system of aerobic organisms and are used as a defense against oxidative injury caused by reactive oxygen species (ROS). The cloning and sequencing of the 788-bp genomic DNA from Trichoderma reesei strain QM9414 (anamorph of Hypocrea jecorina) revealed an open reading frame encoding a protein of 212 amino acid residues, with 65-90% similarity to manganese superoxide dismutase from other filamentous fungi. The TrMnSOD was purified and shown to be stable from 20 to 90°C for 1h at pH from 8 to 11.5, while maintaining its biological activity.

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“…Three-dimensional structures of Hemolin proteins from P. xylostella, H. cunea and G. mellonella were predicted by 3D-JIGSAW (http://www.bmm.icnet. uk/~3djigsaw/) (Bates et al, 2001;Bates and Sternberg, 1999;Contreras-Moreira and Bates, 2002).…”

Section: Analysis Of Pxhemolin Cdna and Deduced Amino Acid Sequencesmentioning

confidence: 99%

Cloning and expression pattern of a hemolin homologue from the diamondback moth, Plutella xylostella

Kim

et al. 2010

Genes Genom

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Hemolin has been known to play a key role in insect innate immunity. In an attempt to examine expression pattern of the Hemolin gene in the diamondback moth, Plutellea xylostella, the full-length cDNA of Hemolin was cloned using 5'-RACE PCR technique. The cDNA contained a 5' untranslated region of 48 nucleotides and a 3' untranslated region of 198 nucleotides, including a stop codon (TAA) and a poly (A) tail. It consists of 1,401 bp with an open reading frame of 1,245 bp, encoding 414 amino acids. The deduced amino acid sequence of PxHemolin has relatively low identities (35−42%) to various insect Hemolins. However, it has high three-dimensional structural similarity to Hemolin. Interestingly, analysis of spatial expression pattern of PxHemolin shows that it was highly expressed in the Malpighian tubule and the silk gland although it was also detected in fat body and gut. Furthermore, PxHemolin mRNA was highly induced 3 hr after immune-challenging with lipopolysaccharide and was gradually up-regulated after laminarin treatment. These data suggest that PxHemolin may play a role in innate immune responses although it remains to further elucidate the precise biological R. J. Kim and Y. H. Jo are equally contributed to this work. functions in P. xylostella.

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Model building by comparison at CASP3: Using expert knowledge and computer automation

Cited by 149 publications

References 24 publications

Multiplicity of carbohydrate-binding sites in β-prism fold lectins: occurrence and possible evolutionary implications

Multiplicity of carbohydrate-binding sites in β-prism fold lectins: occurrence and possible evolutionary implications

Conformational stability of recombinant manganese superoxide dismutase from the filamentous fungus Trichoderma reesei

Cloning and expression pattern of a hemolin homologue from the diamondback moth, Plutella xylostella

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