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Depository gathering all the relevant data for the work published in the following preprint: β-actin plasticity is modulated by coordinated actions of histidine 73 methylation, nucleotide type, and ions (https://doi.org/10.1101/2022.12.16.520803) This repository contains all molecular dynamics trajectories put to production regarding 12 Actin systems, the associated pdb files, scripts used for visualisation and computing of observables. Below, a short description of the methodology : All atom simulations using the polarizable force field AMOEBA (2018) in combination with the Tinker-HP Software (v1.3 2021). The systems underwent a minimization of 30 000 step using a L-BFGS optimizer. The next equilibration steps were realised using a timestep of 1fs, the RESPA integrator and the berendsen barostat (when relevant) unless stated otherwise. The solvent was then progressively heat up in the NVT ensemble, from 5K to 300K using 10K steps and spending 5ps at each temperature, before undergoing additional 100ps at 300K. The system was then allowed to slowly relax for 3 times 400ps in the NPT ensemble while applying harmonic restraints of 10, 5 and finally 1 kcal/mol/A on the backbone atoms of the protein. Then, all restraints were removed, and we used the montecarlo barostat in combination with the BAOAB-RESPA1 propagator. Three final equilibration steps were performed for 100ps, 200ps and 500 ps by respectively increasing the outer timestep from 1fs to 2fs up to 5fs. egarding the production run, all calculations were performed in the NPT ensemble, using the montecarlo barostat and the BAOAB-RESPA1 propagator with an outer timestep of 5fs, and hydrogen mass repartioning. 1.52 µs long Adaptive sampling simulations were generated on ten monomer systems and two 4-mer systems, resulting in a total of 18.24 µs. The systems contain Actin structures based on pdb files 1nwk,1j6z and 6bno, with water, KCL and MG2+ ions, ATP and ADP nucleotides. Python and TCl files necessary to the reproduction of figures are available in this repository. The definition of weights necessary to unbias simulation are available under the form of txt files. |
