Structure Based Annotation of Helicobacter pylori Strain 26695 Proteome

Abstract

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%).

Métodos de modelagem da estrutura tridimensional de proteínas: Um guia teórico e prático

“…Outros estudos utilizam abordagens mistas que unem a modelagem por homologia, threading e ab initio. Singh et al (2014), por exemplo, empregaram estes métodos com o objetivo de realizar a anotação baseada em estrutura de genes de Helicobacter pylori, para isto os autores utilizaram as plataformas I-TASSER (servidor que realiza um misto de threading e ab initio), (ZHANG, 2008).…”

An informatic workflow for the enhanced annotation of excretory/secretory proteins of Haemonchus contortus

“…class, architecture, topology and homology; [27] ) and PDB (Protein Data Bank; https://www.rcsb.org/ ; [28] , [29] ). These structure-based approaches have been shown to enhance the performance of protein annotation for non-model organisms (e.g., [30] , [31] , [32] , [33] ).…”

Prediction of Certain Well-Characterized Domains of Known Functions within the PE and PPE Proteins of Mycobacteria

“…Computational methods may precede the selection of proteins for wet-lab experimental validation of their structure and activity. Structure-based functional annotation of proteins has been more useful than sequence-based comparisons alone [ 36 , 37 ], as the protein fold and conservation of active site residues are determinants of molecular function. Therefore, in the absence of experimental structures, computer-based protein modeling methods may be employed to predict the structure and possible function [ 37 , 38 , 39 ].…”