pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination

Lobley, Anna; Sadowski, Michael I.; Jones, David T.

doi:10.1093/bioinformatics/btp302

Cited by 275 publications

(210 citation statements)

References 42 publications

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“…The secondary structure of genes specific to S. haematobium were predicted using PSIPRED 51 . For each orphan protein of S. haematobium, we attempted to search for homologs with known three-dimensional structures using pGenTHREADER (foldlib database; 17 June 2011) 52 .…”

Section: Methodsmentioning

confidence: 99%

Whole-genome sequence of Schistosoma haematobium

et al. 2012

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Schistosomiasis is a neglected tropical disease caused by blood flukes (genus Schistosoma; schistosomes) and affecting 200 million people worldwide 1 . No vaccines are available, and treatment relies on one drug, praziquantel 2 . Schistosoma haematobium has come into the spotlight as a major cause of urogenital disease, as an agent linked to bladder cancer 1,3 and as a predisposing factor for HIV/AIDS 4,5 . The parasite is transmitted to humans from freshwater snails 1 . Worms dwell in blood vessels and release eggs that become embedded in the bladder wall to elicit chronic immune-mediated disease 6 and induce squamous cell carcinoma 7 . Here we sequenced the 385-Mb genome of S. haematobium using Illumina-based technology at 74-fold coverage and compared it to sequences from related parasites 8,9 . We included genome annotation based on function, gene ontology, networking and pathway mapping. This genome now provides an unprecedented resource for many fundamental research areas and shows great promise for the design of new disease interventions.

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Section: Methodsmentioning

confidence: 99%

Whole-genome sequence of Schistosoma haematobium

et al. 2012

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“…All three of them have complete crystal structures except for gliadin protein. Thus, we opted for fold based GenTHREADER (Rapid Fold Recognition) software [42] for template identification for wheat gliadin.…”

Section: Fold Based Template Identificationmentioning

confidence: 99%

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2017

RJLBPCS

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Introduction: Gliadin intake causes celiac disease in selected population of Homo sapiens. Short motifs in α/β gliadin wheat protein were behind this food related disorder. Materials and Methods: Fold based template selection software GenTHREADER was considered for template selection and Modeller software was used for modelling wheat gliadin. T-Coffee software was used for the sequence alignment. Finally, antigenic region was identified. Results: Through in silico based study, we identified a novel motif 'HNxxH' in α/β gliadin wheat gliadin in C-terminal region which shows striking resemblance with the helical zinc binding motif 'HExxH' of metalloproteases.Interestingly, this short segment of gliadin is reported to be both an antigen and toxin which aligns well with the zinc binding site of the metalloproteases. Sequence analysis reports a spatial arrangement of the first two histidine residues from predicted motif of gliadin very much similar to the arrangement exhibited by the histidine residues in the selected metalloproteases like Astacin, Matrix metalloproteases and Predicted metal-dependent hydrolase. Additionally, glutamic acid, glycine and histidine from 2 nd , 8 th and 11 th position were substituted by asparagine, isoleucine and glutamine, respectively in this domain. Conclusion: A wet lab based analysis could certainly confirm the evolutionary relatedness of both gliadin and metalloproteases from sequential, structural and immunological perspective.

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“…The crystal structure with higher resolution of 1.2 Å (4NYQ [3]) was downloaded from Protein Data Bank (www.rcsb.org) [12]. We performed fold based search to identify potential distal structural homologs of CMP using pGENTHREADER [13] and pDOMTHREADER [13]. pGenTHREADER, is a new protein fold recognition method that is both fast and reliable.…”

Section: A) Identification Of Distant Homologous Through Fold Based Mmentioning

confidence: 99%

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2017

RJLBPCS

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Objective:The cockroach milk protein (CMP) is found in the mid-gut of a Pacific Beetle Viviparous cockroach in liquid state. This becomes crystals due to the ingestion by embryos in the midgut.The main aim of this study is to identify distant homologs of the CMP from sequence and structure perspective. Methods:In this study we carried Fold based approaches like pDomTHREADER and pGenTHREADER to identify distant homologs. Multiple sequence alignment (MSA) was performed to identify sequence identity between homologous proteins. PRINTS, PRODOM and PROSITE were used for protein domain analysis.Structural superimposition of CMP with Bacterial Outer Membrane Lipoprotein (Blc) of E. coli and Apolipoprotein D (ApoD) of Homo sapiens were carried out using Chimera. Finally, the domain mobility was studied using iMODs online server. Results: Based on the fold based method, CMP is closely related to Blcprotein (E.Coli). From alignment perspective, CMP and ApoD exhibits higher sequence similarity compared to Blc and Lazarillo (Schistocerca americana). Furthermore, protein domain of ApoD was identified to be of lipocalin family as per the PROSITE database search. From structural perspective, both CMP and ApoD superimposes well with each other. Furthermore, CMP shows lesser domain mobility compared to Blc and ApoD protein due to the presence of proline residues. This data reveals significant evolution of proteins during speciation. Conclusion: Significant structural similarities were observed between CMP and ApoD. The sequential and structural aspects of cockroach milk protein holds further scope for comparative analysis between lipocalin families based on different adaptation or protein modifications.

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pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination

Cited by 275 publications

References 42 publications

Whole-genome sequence of Schistosoma haematobium

Whole-genome sequence of Schistosoma haematobium

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