1. ABOUT THE DATASET -------------------- Title: Molecular dynamics simulation data of the S345F mutant PLCg1 protein from the publication - Bunney et al., Biochem J (2025) 482 (20), "Characterisation of an allosteric site in PLCγ enzymes and implications for development of their specific inhibitors" Creator(s): Dr Kyle Le Huray, Dr Antreas Kalli Organisation(s): University of Leeds Rights-holder(s): Copyright 2025 University of Leeds Publication Year: 2025 Description: A repository of molecular dynamics simulation data from the publication "Characterisation of an allosteric site in PLCγ enzymes and implications for development of their specific inhibitors". The simulations model interactions between a cell membrane and the core domains of the S345F mutant of the PLCγ protein. All-atom molecular dynamics simulations were conducted using the CHARMM36 force field in GROMACS (version 2024.4). To generate the mutant in silico, we used the structure and atomic co-ordinates from the end point of previously published all-atom simulations of the PLCγ1 core domains bound to the membrane, with PI(4,5)P2 present in the active site. The rotamers tool of ChimeraX (version 1.9) was used to mutate serine 345 from the previous simulation model to phenylalanine, selecting the rotamer predicted to be the most stable from the rotamer library. The mutated system was relaxed by performing energy minimisation using the steepest descent method and then subjected to equilibration in the NPT ensemble with the protein backbone co-ordinates restrained, for 1 ns with a 1 fs timestep, using the Berendsen thermostat at 323 K, and the semi-isotropic Berendsen barostat at 1 bar. 3 production simulation replicates were conducted each initialized from the equilibrated system, with velocities sampled from a Boltzmann distribution. Production simulations were run for 50 μs with 20 fs timestep, using the velocity-rescaling thermostat (323 K) and semi-isotropic Parrinello–Rahman barostat (1 bar). Further details can be found in the related publication. Cite as: Le Huray & Kalli (2025): Simulation data from the publication "Characterisation of an allosteric site in PLCγ enzymes and implications for development of their specific inhibitors". University of Leeds. [Dataset] [DOI] Related publication: Bunney et al., Biochem J (2025) 482 (20), "Characterisation of an allosteric site in PLCγ enzymes and implications for development of their specific inhibitors", https://doi.org/10.1042/BCJ20253358 Contact: A.Kalli@leeds.ac.uk 2. TERMS OF USE --------------- Copyright 2025 University of Leeds. Unless otherwise stated, this dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/.] 3. PROJECT AND FUNDING INFORMATION ---------------------------------- This dataset was not created in the course of a funded project. 4. CONTENTS ----------- File listing plcg1_S345F_AT_dataset.zip [ md.mutate_simS324F_canonicalS345F_50ns_unrestrained_1.gro md.mutate_simS324F_canonicalS345F_50ns_unrestrained_1.tpr md.mutate_simS324F_canonicalS345F_50ns_unrestrained_1.xtc md.mutate_simS324F_canonicalS345F_50ns_unrestrained_2.gro md.mutate_simS324F_canonicalS345F_50ns_unrestrained_2.tpr md.mutate_simS324F_canonicalS345F_50ns_unrestrained_2.xtc md.mutate_simS324F_canonicalS345F_50ns_unrestrained_3.gro md.mutate_simS324F_canonicalS345F_50ns_unrestrained_3.tpr md.mutate_simS324F_canonicalS345F_50ns_unrestrained_3.xtc ] File Name Conventions Files prefixed with "md." correspond to production simulations. .tpr files are GROMACS binary input run files for a simulation .gro files are the coordinates from the final frame of a simulation .xtc files are the GROMACS simulation trajectories, thinned to 10% of their original size (due to memory limitations) by only writing every 10th frame from the original. 5. METHODS ---------- To model how the S345F mutant interacts with the membrane, all-atom molecular dynamics simulations were conducted using the CHARMM36 force field in GROMACS (version 2024.4). To generate the mutant in silico, we used the structure and atomic co-ordinates from the end point of previously published all-atom simulations of the PLCγ1 core domains bound to the membrane, with PI(4,5)P2 present in the active site. The rotamers tool of ChimeraX (version 1.9) was used to mutate serine 345 from the previous simulation model to phenylalanine, selecting the rotamer predicted to be the most stable from the rotamer library. The mutated system was relaxed by performing energy minimisation using the steepest descent method and then subjected to equilibration in the NPT ensemble with the protein backbone co-ordinates restrained, for 1 ns with a 1 fs timestep, using the Berendsen thermostat at 323 K, and the semi-isotropic Berendsen barostat at 1 bar. 3 production simulation replicates were conducted each initialized from the equilibrated system, with velocities sampled from a Boltzmann distribution. Production simulations were run for 50 ns with 20 fs timestep, using the velocity-rescaling thermostat (323 K) and semi-isotropic Parrinello–Rahman barostat (1 bar).