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ISSN 2063-5346
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Investigating the Interaction between PITRM1 and Sulfiredoxin at the Cysteine-Rich Oxidation Prone Region: A Molecular Modelling and Dynamics Study

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Carlton Ranjith Wilson Alphonse , Rajaratnam Rajesh Kannan, Nandhagopal Soundrapandiyan
» doi: 10.48047/ecb/2023.12.si4.975

Abstract

This study aimed to investigate the interaction between PITRM1 and sulfiredoxin at the oxidation prone region in the presence of ATP using a combination of protein modelling, docking, and molecular dynamics (MD) simulation techniques. The three-dimensional structures of PITRM1 and sulfiredoxin were modelled using the SWISS-MODEL server, and their quality was assessed using the Ramachandran plot generated by PROCHECK. The PITRM1-sulfiredoxin complex was generated through protein-protein docking using ClusPro, and the best-docked complex was selected based on the lowest energy score. Additionally, ATP was docked with the selected complex to investigate its binding mode. MD simulation was performed on the selected complex using GROMACS with the CHARMM36 force field. The stability of the complex was analysed by calculating the root mean square deviation (RMSD) and root mean square fluctuation (RMSF) of the complex, and the protein-protein interaction energy and hydrogen bonding were also examined using GROMACS tools.The results showed that the modelled structures of PITRM1 and sulfiredoxin were of high quality and suitable for further analysis. The protein-protein docking analysis identified specific binding modes between PITRM1 and sulfiredoxin, with the Cysteine rich oxidation prone region being a major focus. ATP docking revealed its interaction with the PITRM1-sulfiredoxin complex. The MD simulation of the complex demonstrated its stability over a 100 ns simulation period, as indicated by the low average RMSD and RMSF values. The analysis of hydrogen bonding and minimum distance measurements suggested strong binding interactions between PITRM1, sulfiredoxin, and ATP. Specifically, the presence of multiple hydrogen bonds within the interface of PITRM1 and sulfiredoxin indicated a crucial role in stabilizing the complex.In conclusion, this study provides valuable insights into the interaction between PITRM1 and sulfiredoxin at the Cysteine rich oxidation prone region in the presence of ATP. The findings suggest that sulfiredoxin plays a protective role in maintaining the activity of PITRM1 and preventing its oxidation-induced inactivation. This study contributes to a better understanding of the molecular mechanisms underlying the interaction between PITRM1 and sulfiredoxin and may have implications for the development of therapeutic strategies targeting Alzheimer's disease.

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