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Investigation of the Effect of Radiation Damage-Induced Phasing Technique on the Communication Between Lysozyme Residues Using Molecular Dynamics Simulation Method

Year 2026, Volume: 47 Issue: 1, 156 - 161, 27.02.2026

Mehmet Murat Yaşar

https://doi.org/10.17776/csj.1746888
https://izlik.org/JA99SZ59DD

Abstract

In this study, it was investigated whether the Radiation-Damage Induced Phasing (RIP) technique, which is employed for phasing in the structure determination of lysozyme—one of the key enzymes—affects the communication states between residues. This research was conducted in-silico, utilizing the GROMACS-2022 simulation program for molecular dynamics simulations. The simulation duration was set to 200 ns, and the output files were subsequently used to perform analyses including Root Mean Square Deviation, Root Mean Square Fluctuation, Radius of Gyration, Betweenness Centrality, and Dynamic Cross-Correlation. According to the analysis results, it was observed that the functionality of 77 amino acids within the communication network of lysozyme decreased after the application of the RIP technique, while that of 49 amino acids increased. This study is novel in terms of analyzing intra-protein communication networks for structures subjected to RIP and is expected to offer a new perspective for new molecules undergoing structure determination processes and treated with the RIP technique.

Keywords

Betweenness Centrality Dynamic Cross Corelation Lisozyme Molecular Dynamic Simulation Radiation-Damage Induced Phasing.

References

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There are 19 citations in total.

Details

Primary Language English
Subjects Atomic and Molecular Physics
Journal Section Research Article
Authors

Mehmet Murat Yaşar 0000-0001-6211-0350

Submission Date July 20, 2025
Acceptance Date December 8, 2025
Publication Date February 27, 2026
DOI https://doi.org/10.17776/csj.1746888
IZ https://izlik.org/JA99SZ59DD
Published in Issue Year 2026 Volume: 47 Issue: 1

Cite

APA Yaşar, M. M. (2026). Investigation of the Effect of Radiation Damage-Induced Phasing Technique on the Communication Between Lysozyme Residues Using Molecular Dynamics Simulation Method. Cumhuriyet Science Journal, 47(1), 156-161. https://doi.org/10.17776/csj.1746888

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