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.
Mehmet Murat Yaşar (Fri,) studied this question.