Functional, structural and epitopic prediction of hypothetical proteins of Mycobacterium tuberculosis H37Rv: An in silico approach for prioritizing the targets

Gazi, Md. Amran; Kibria, Mohammad Golam; Mahfuz, Mustafa; Islam, Md. Rezaul; Ghosh, Prakash; Afsar, Nure Alam; Khan, Mukhtar A.; Ahmed, Tahmeed

doi:10.1016/j.gene.2016.06.057

Cited by 19 publications

(16 citation statements)

References 111 publications

(101 reference statements)

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“…Specific domains could be identified using one, two, three, four, or five of the above-stated tools and therefore, different confidence levels were assigned (e.g., 20, 40, 60, 80, and 100%). In our previous studies, published elsewhere, we only considered the proteins with 100% confidence [10,42]. However, in the current study, HPs having 60% or above confidence level have been considered to gain the greater coverage.…”

Section: Analysis Of Hps From C Jejuni Genomementioning

confidence: 99%

“…Several contemporary bioinformatics tools, for instance, CDART, SMART, Pfam, INTERPROSCAN, MOTIF, SU-PERFAMILY, and SVMProt have been well established to specify the functions of many bacterial HPs [9][10][11]. Besides, the exploration of protein-protein interaction (PPI) for instance, using STRING database [12], is crucial for comprehending the aspect of biological network.…”

Section: Introductionmentioning

confidence: 99%

“…Functional prediction of HPs by using in silico approaches has been successfully applied for various bacteria and parasites [10,16,17]. In the present study, we have chosen C. jejuni as a template to explore the functions of HPs from its genome with a higher accuracy using well-optimized bioinformatics tools.…”

Section: Introductionmentioning

confidence: 99%

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Questing functions and structures of hypothetical proteins from Campylobacter jejuni: a computer-aided approach

et al. 2020

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Campylobacter jejuni (C. jejuni) is considered to be one of the most frequent causes of bacterial gastroenteritis globally, especially in young children. The genome of C. jejuni contains many proteins with unknown functions termed as hypothetical proteins (HPs). These proteins might have essential biological role to show the full spectrum of this bacterium. Hence, our study aimed to determine the functions of HPs, pertaining to the genome of C. jejuni. An in-silico work flow integrating various tools were performed for functional assignment, three-dimensional structure determination, domain architecture predictors, subcellular localization, physicochemical characterization, and protein–protein interactions (PPIs). Sequences of 267 HPs of C. jejuni were analyzed and successfully attributed the function of 49 HPs with higher confidence. Here, we found proteins with enzymatic activity, transporters, binding and regulatory proteins as well as proteins with biotechnological interest. Assessment of the performance of various tools used in this analysis revealed an accuracy of 95% using receiver operating characteristic (ROC) curve analysis. Functional and structural predictions and the results from ROC analyses provided the validity of in-silico tools used in the present study. The approach used for this analysis leads us to assign the function of unknown proteins and relate them with the functions that have already been described in previous literature.

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Section: Analysis Of Hps From C Jejuni Genomementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Questing functions and structures of hypothetical proteins from Campylobacter jejuni: a computer-aided approach

et al. 2020

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“…To predict the cellular function of a protein it is important to get information about its sub-cellular localization i.e. a protein can be present in outer membrane, inner membrane, periplasm, extracellular space or in cytoplasm [ 16 ]. Sub-cellular localization of viral proteins were predicted using Virus-PLoc [ 17 ] online server tool [ 18 ], TMHMM [ 19 , 20 ] and HMMTOP [ 21 , 22 ].…”

Section: Main Textmentioning

confidence: 99%

“…For precise function annotation, various tools like SVMport, ProtNet [ 25 , 26 ], Pfam, Motif [ 27 , 28 ], CDART [ 24 , 29 ], CATH [ 30 , 31 ], SMART [ 32 , 33 ], Superfamily [ 34 , 35 ] and InterProscan [ 27 , 36 ] were used that classified all 38 proteins of HAdV into families and subfamilies on the basis of their sequence, structure and function [ 16 , 37 ]. DISULFIND [ 38 ] server was used to evaluate occurrence of disulfide bonds between cysteine residues [ 39 ].…”

Section: Main Textmentioning

confidence: 99%

Structural and functional annotation of hypothetical proteins of human adenovirus: prioritizing the novel drug targets

et al. 2017

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ObjectiveHuman adenoviruses are small double stranded DNA viruses that provoke vast array of human diseases. Next generation sequencing techniques increase genomic data of HAdV rapidly, which increase their serotypes. The complete genome sequence of human adenovirus shows that it contains large amount of proteins with unknown cellular or biochemical function, known as hypothetical proteins. Hence, it is indispensable to functionally and structurally annotate these proteins to get better understanding of the novel drug targets. The purpose was the characterization of 38 randomly retrieved hypothetical proteins through determination of their physiochemical properties, subcellular localization, function, structure and ligand binding sites using various sequence and structure based bioinformatics tools.ResultsFunction of six hypothetical proteins P03269, P03261, P03263, Q83127, Q1L4D7 and I6LEV1 were predicted confidently and then used further for structure analysis. We found that these proteins may act as DNA terminal protein, DNA polymerase, DNA binding protein, adenovirus E3 region protein CR1 and adenoviral protein L1. Functional and structural annotation leading to detection of binding sites by means of docking analysis can indicate potential target for therapeutics to defeat adenoviral infection.Electronic supplementary materialThe online version of this article (10.1186/s13104-017-2992-z) contains supplementary material, which is available to authorized users.

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Domain‐wise differentiation of Mycobacterium tuberculosis H₃₇Rv hypothetical proteins: A roadmap to discover bacterial survival potentials

Beg

Hejazi

Thakur

et al. 2021

Biotech and App Biochem

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Proteomic information revealed approximately 3,923 proteins in Mycobacterium tuberculosis H 37 Rv genome of which around ∼25% of proteins are hypothetical proteins (HPs). The present work comprises computational approaches to identify and characterize the HPs of M. tuberculosis that symbolize the putative target for rationale development of a drug or antituberculosis strategy. Proteins were primarily classified based on motif and domain information, which were further analyzed for the presence of virulence factors (VFs), determination of localization, and signal peptide/enzymatic cleavage sites. 863 HPs were found, and 599 HPs were finalized based on motifs, that is, GTP (525), Trx (47), SAM (14), PE-PGRS (5), and CBD (8). 80 HPs contain virulence factor (VF), 24 HPs localized in membrane region, and 4 HPs contain signal peptide/enzymatic cleavage sites. The overall parametric study finalizes four HPs Rv0679c, Rv0906, Rv3627c, and Rv3811 that also comprise GTPase domain. Structure prediction, structure-based function prediction, molecular docking and mutation analysis of selected proteins were done. Docking studies revealed that GTP and GTPase inhibitor (mac0182344) were docked with all four proteins with high affinities. In silico point mutation studies showed that substitution of aspartate with glycine within a GTPase motif showed the largest decrease in stability and pH differentiation also affects protein's stability. This analysis thus fixes a roadmap in the direction of finding potential target of this bacterium for drug development and enlightens the efficacy of GTP as a major regulator of Mycobacterial cellular pathways.

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Functional, structural and epitopic prediction of hypothetical proteins of Mycobacterium tuberculosis H37Rv: An in silico approach for prioritizing the targets

Cited by 19 publications

References 111 publications

Questing functions and structures of hypothetical proteins from Campylobacter jejuni: a computer-aided approach

Questing functions and structures of hypothetical proteins from Campylobacter jejuni: a computer-aided approach

Structural and functional annotation of hypothetical proteins of human adenovirus: prioritizing the novel drug targets

Domain‐wise differentiation of Mycobacterium tuberculosis H₃₇Rv hypothetical proteins: A roadmap to discover bacterial survival potentials

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Functional, structural and epitopic prediction of hypothetical proteins of Mycobacterium tuberculosis H37Rv: An in silico approach for prioritizing the targets

Cited by 19 publications

References 111 publications

Questing functions and structures of hypothetical proteins from Campylobacter jejuni: a computer-aided approach

Questing functions and structures of hypothetical proteins from Campylobacter jejuni: a computer-aided approach

Structural and functional annotation of hypothetical proteins of human adenovirus: prioritizing the novel drug targets

Domain‐wise differentiation of Mycobacterium tuberculosis H37Rv hypothetical proteins: A roadmap to discover bacterial survival potentials

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Domain‐wise differentiation of Mycobacterium tuberculosis H₃₇Rv hypothetical proteins: A roadmap to discover bacterial survival potentials