Unraveling the M1R Protein of Monkeypox Virus: An Integrated Structural Bioinformatics, Immunological Profiling, and Molecular Dynamics Simulation Approach
Deep in silico Analysis of Monkeypox M1R Protein
Abstract
Background: Monkeypox virus (MPXV) is a zoonotic pathogen that influences humans as well as animalsposing a significant public health concern due to its emergence and circulation. The structural dynamics and features of several MPXV proteins, including M1R, have not been completely studied.
Methods: This experiment focuses on the prediction and analysis of the secondary and tertiary constructs for the M1R protein. Briefly, its amino acid sequence was collected from the UniProt database. A wide range of in silico approaches were employed, including ProtParam, SOPMA, PSIPRED, CD Search, GalaxyTMB, Robetta, I-TASSER, and GROMACS, in order to explore the physicochemical properties, structural features, and functional insights of the M1R protein. The tertiary structure models were evaluated to detect the most reliable solution, which was then used for Immunoinformatics analyses such as MHC I/II and B-cell epitope prediction using the IEDB and Ellipro tools, respectively. Epitopes from the M1R protein were evaluated based on antigenicity, affinity of binding, along solubility. Furthermore, active sites were forecast by the CASTp v3.0 tool.
Results: Physicochemical calculations indicate that M1R had favorable thermostability and hydrophilic features. Structural analyses suggested that M1R is a lipid membrane protein component of DNA viruses, suggesting it as a robust antigenic target. Immunogenicity analyses indicated it as a potentially suitable target for immunogenic protein design. As well, molecular dynamics simulations (MDS) were carried out for 100-ns using an all-atom forcefield. Analysis of various molecular dynamics parameters of M1R throughout the MDS trajectory, including RMSD, RMSF, radius of gyration (Rg), and solvent accessible surface area (SASA), indicated good stability of the M1R and unveiled important molecular dynamics characteristics such as the flexibility of certain protein regions.
Conclusion: Multiple epitopes were detected in our experiment, with 12 B-cell epitopes identified using the Robetta model and 6 B-cell epitopes predicted by the Galaxy model, alongside 3 MHC-I and 3 MHC-II epitopes, which scored favorably. Results of the present computational analysis provide clues to unleash the potential of M1R as an immunotherapy target for the development of antiviral solutions against MPXV in the future.
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| Issue | Vol 8, No 4 (2025) | |
| Section | Original Article | |
| DOI | https://doi.org/10.18502/igj.v8i4.20099 | |
| Keywords | ||
| Monkeypox Structural Immunology Molecular mechanics Molecular dynamic simulation M1R protein | ||
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