In-silico Structural and Functional Characterisation of Hypothetical Protein WP_020728386.1 from Mycobacterium marinum: A Potential Dioxygenase Involved in Pathogenesis
Masum Billah *
Department of Computer Science and Information Technology, Gazipur Agricultural University, Gazipur, Dhaka, Bangladesh.
Farhana Afrin Vabna
Department of Biotechnology, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh.
*Author to whom correspondence should be addressed.
Abstract
Background: Mycobacterium marinum is ubiquitous in aquatic environment and is mostly spread by coming into contact with fresh and salt water, such as from swimming pools, aquariums, and marine life. It is considered the most serious fish pathogen, known for triggering a variety of symptoms at a time, including uncoordinated swimming, abdominal swelling, weight loss, skin ulceration, the growth of white nodules in the liver, kidney, and spleen in both fresh and marine water fish.
Aims: The objective of this investigation was to assess the intended function of the hypothetical protein WP_020728386.1.
Methodology: It is a computer-based in silico dry lab study utilising various software and manipulating databases. The study is conducted from 2024 to 2025. The projected tertiary structure was assessed using servers such as Swiss Model. The Swiss-Model Interactive Workplace, ProSA-web, PROCHEK, Ramachandran Plot, Z scores, and structural evaluations are used to choose the most suitable materials. To find out homologous proteins, different bioinformatics tools were used for searching sequence similarity.
Results: Fish dwelling in both fresh and saltwater are susceptible to infection from the opportunistic pathogen Mycobacterium marinum. This infection causes morbidity and mortality in fish by causing necrotising granuloma similar to tuberculosis. Additionally, it causes nodular lymphangitis, skin nodules, and ulcers in human as signs of preliminary cutaneous infections that can progress to osteomyelitis, tenosynovitis, and arthritis, leading to serious health hazards. Because of the presence of the extradiol ring cleavage dioxygenase family protein, the protein WP_020728386.1 present in Mycobacterium marinum has an enormous effect on catalysing the incorporation activity of molecular oxygen atoms into substrates, resulting in ring cleavage in aromatics. But the target hypothetical protein hasn't been completely revealed yet. As a result, an in-silico method was developed in this study to record the structure and function of the unidentified protein WP_020728386.1. The tertiary structure of the matrix protein was assessed employing the Ramachandran plot by the PROCHECK program. It can be said a valid model as 91.0% residues were found in the most favoured region. The result of the quantitative analysis was also favourable with having a Z-score of -7.65. Further, this study has identified an important domain extradiol dioxygenase which can be helpful in developing new drug targets for both human and fish species. The analysis of physicochemical parameters, functional annotation, predicted active site of ligand binding, Ramachandran plot analysis, as well as overall fundamental features of the hypothetical protein provides an insight into the studied protein that it might be a very functional and potential protein possessing a crucial role.
Conclusions: As a result of this research, the overall understanding of pathogenesis and pathophysiology will increase, and researchers will be able to concentrate on the protein complex, which might assist in the development of effective treatment drugs and vaccines against Mycobacterium marinum infections.
Keywords: Mycobacterium marinum, in-silico, functional annotation, homology modeling, Ramachandran plot