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

Mehmet Murat Yaşar

doi:10.17776/csj.1746888

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

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

References

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Details

Primary Language

English

Subjects

Atomic and Molecular Physics

Journal Section

Research Article

Authors

Mehmet Murat Yaşar ^*
0000-0001-6211-0350
Türkiye

Publication Date

February 27, 2026

Submission Date

July 20, 2025

Acceptance Date

December 8, 2025

Published in Issue

Year 2026 Volume: 47 Number: 1

DOI

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

IZ

https://izlik.org/JA99SZ59DD

Cite

RIS / Bibtex

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