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Structure Based Annotation of Helicobacter pylori Strain 26695 Proteome

The availability of complete genome sequences of H. pylori 26695 has provided a wealth of information enabling us to carry out in silico studies to identify new molecular targets for pharmaceutical treatment. In order to construe the structural and functional information of complete proteome, use of...

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Autores principales: Singh, Swati, Guttula, Praveen Kumar, Guruprasad, Lalitha
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4280198/
https://www.ncbi.nlm.nih.gov/pubmed/25549250
http://dx.doi.org/10.1371/journal.pone.0115020
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author Singh, Swati
Guttula, Praveen Kumar
Guruprasad, Lalitha
author_facet Singh, Swati
Guttula, Praveen Kumar
Guruprasad, Lalitha
author_sort Singh, Swati
collection PubMed
description The availability of complete genome sequences of H. pylori 26695 has provided a wealth of information enabling us to carry out in silico studies to identify new molecular targets for pharmaceutical treatment. In order to construe the structural and functional information of complete proteome, use of computational methods are more relevant since these methods are reliable and provide a solution to the time consuming and expensive experimental methods. Out of 1590 predicted protein coding genes in H. pylori, experimentally determined structures are available for only 145 proteins in the PDB. In the absence of experimental structures, computational studies on the three dimensional (3D) structural organization would help in deciphering the protein fold, structure and active site. Functional annotation of each protein was carried out based on structural fold and binding site based ligand association. Most of these proteins are uncharacterized in this proteome and through our annotation pipeline we were able to annotate most of them. We could assign structural folds to 464 uncharacterized proteins from an initial list of 557 sequences. Of the 1195 known structural folds present in the SCOP database, 411 (34% of all known folds) are observed in the whole H. pylori 26695 proteome, with greater inclination for domains belonging to α/β class (36.63%). Top folds include P-loop containing nucleoside triphosphate hydrolases (22.6%), TIM barrel (16.7%), transmembrane helix hairpin (16.05%), alpha-alpha superhelix (11.1%) and S-adenosyl-L-methionine-dependent methyltransferases (10.7%).
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spelling pubmed-42801982015-01-07 Structure Based Annotation of Helicobacter pylori Strain 26695 Proteome Singh, Swati Guttula, Praveen Kumar Guruprasad, Lalitha PLoS One Research Article The availability of complete genome sequences of H. pylori 26695 has provided a wealth of information enabling us to carry out in silico studies to identify new molecular targets for pharmaceutical treatment. In order to construe the structural and functional information of complete proteome, use of computational methods are more relevant since these methods are reliable and provide a solution to the time consuming and expensive experimental methods. Out of 1590 predicted protein coding genes in H. pylori, experimentally determined structures are available for only 145 proteins in the PDB. In the absence of experimental structures, computational studies on the three dimensional (3D) structural organization would help in deciphering the protein fold, structure and active site. Functional annotation of each protein was carried out based on structural fold and binding site based ligand association. Most of these proteins are uncharacterized in this proteome and through our annotation pipeline we were able to annotate most of them. We could assign structural folds to 464 uncharacterized proteins from an initial list of 557 sequences. Of the 1195 known structural folds present in the SCOP database, 411 (34% of all known folds) are observed in the whole H. pylori 26695 proteome, with greater inclination for domains belonging to α/β class (36.63%). Top folds include P-loop containing nucleoside triphosphate hydrolases (22.6%), TIM barrel (16.7%), transmembrane helix hairpin (16.05%), alpha-alpha superhelix (11.1%) and S-adenosyl-L-methionine-dependent methyltransferases (10.7%). Public Library of Science 2014-12-30 /pmc/articles/PMC4280198/ /pubmed/25549250 http://dx.doi.org/10.1371/journal.pone.0115020 Text en © 2014 Singh et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Singh, Swati
Guttula, Praveen Kumar
Guruprasad, Lalitha
Structure Based Annotation of Helicobacter pylori Strain 26695 Proteome
title Structure Based Annotation of Helicobacter pylori Strain 26695 Proteome
title_full Structure Based Annotation of Helicobacter pylori Strain 26695 Proteome
title_fullStr Structure Based Annotation of Helicobacter pylori Strain 26695 Proteome
title_full_unstemmed Structure Based Annotation of Helicobacter pylori Strain 26695 Proteome
title_short Structure Based Annotation of Helicobacter pylori Strain 26695 Proteome
title_sort structure based annotation of helicobacter pylori strain 26695 proteome
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4280198/
https://www.ncbi.nlm.nih.gov/pubmed/25549250
http://dx.doi.org/10.1371/journal.pone.0115020
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