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

Abstract

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.

Potential Efficacy of β-Amyrin Targeting Mycobacterial Universal Stress Protein by In Vitro and In Silico Approach

“…The PDB structures were assessed by employing different in silico methods ( Table 3 ). The crystal structures of the selected M. tuberculosis H 37 Rv proteins (PDB: 7LD8, 4Q4N, 5XE2, 4LJ1, 1TQ8, 4CHG, 5WZ4, 2JAX, 5SV2, 6L2A) [ 44 ] are provided in Figure S2 .…”

“…After the evaluation of the complete mycobacterial database, 238 proteins were found to belong to the VDA category and 135 proteins had available structural information in the RSCB-PDB databank. In Table 3 , a counteractive study on these proteins led to the determination of 10 proteins, which were Rv1477 , Rv1495 , Rv1566 , Rv2801c , Rv2010 , Rv2623, Rv0554 , Rv1636 , Rv2549c , and Rv2757c [ 44 ]. Rv0554 is an integral part of the menaquinone regulatory operon in Mycobacterium.…”

“…The co-integrative analysis of both these categories showed that there were 10 VDA functional category proteins, having PDB structures that were also present, and these 10 proteins were, therefore, present in both categories. We employed various bioinformatics tools which might empower experimental work to identify the prospective targets of this bacterium and illuminated the efficacy of significant regulators of mycobacterial pathways ( Table S2 ) [ 44 ].…”

MOLECULAR BASIS AND INTEGRATIVE ANALYSIS OF Rv1463 AS PROBABLE CONSERVED ATP-BINDING PROTEIN BY COMPUTATIONAL APPROACH

“…The predicted destability value mostly destabilizing on positioned Aspartate into Alanine -0.583 kcal/mol and Aspartate into Glycine -0.379 kcal/mol. Here, Aspartate into Alanine (ASP175ALA) mutation predicted as the most destabilizing and it will destabilize the protein conformation (see Figure 8) [45][46][47]. As many studies already revealed the importance of ATP binding genes in various biological processes of living organisms, thus this work delivers importance of Rv1463 as different and interesting part for understanding the molecular mechanism of survival of this bacterium.…”

Mechanistic Insight into the Enzymatic Inhibition of β-Amyrin against Mycobacterial Rv1636: In Silico and In Vitro Approaches

“…The Mycobrowser, a Mycobacterial searching browser, was used to obtain the sequence of Universal stress protein Rv1636 from M. tuberculosis . This server is an online database with an extensive library of infectious and non-infectious strains of mycobacterial proteins for extensive genomic and proteomic investigation [ 35 , 36 ].…”