Computational analysis of hypothetical proteins from Mycobacterium orygis identifies proteins with therapeutic and diagnostic potentials

Abstract

The genome of Mycobacterium orygis encodes 3767 proteins that includes 442 functionally uncharacterized proteins, known as hypothetical proteins (HPs). These functionally unknown proteins may play significant biological role in bacterium's survivability, virulence etc., hence functional annotation of these HPs with bioinformatics techniques might shed light on these aspects. So, the present study aimed to assign functions to those HPs in M. orygis genome. With the help of an extensive in silico workflow involving several bioinformatic tools, physicochemical characteristics, protein-protein interaction, sub-cellular localization, functional classification, and antigenicity of the HPs were analyzed. Out of 4039 genes and 3767 encoded proteins, 422 were annotated as “hypothetical protein, unknown function” in NCBI database. Out of 422 HPs, the FASTA sequences of 400 proteins, available in the NCBI database, were extracted. Preliminarily 400 proteins were screened for presence of conserved domain by different bioinformatic tools and 32 shortlisted proteins were further analyzed. The analysis revealed that these proteins may be involved in enzymatic, toxin-antitoxin system, cellular and other processes. Virulence and antigenicity of the complete set of HPs were also predicted. Based on antigenicity scores and sub-cellular localization, four proteins were selected for secondary and tertiary structure modelling. Molecular docking and MD-simulation of four proteins with TLR1 showed stable binding. B-cell and T-cell epitopes were identified for two proteins (QOY47331.1 and QOY49361.1) with highest antigenicity scores. The result of the present study may facilitate better understanding of virulence, pathogenesis and therapeutic target. The information about the structures of the HPs with highest antigenicity score could aid in structure-based inhibitor design and devising novel diagnostic assays.