Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26

Published: 21 June 2021| Version 1 | DOI: 10.17632/jvkcfwyz47.1
Anna Salerno-Kochan, Andreas Horn, Pritha Ghosh, Chandran Nithin, Anna Kościelniak, Daniela Strauss, Oliver Rossbach, Janusz M. Bujnicki, Monika Gaik, Jan Medenbach, Sebastian Glatt


This dataset includes the models from molecular dynamics simulations described in the article 'Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26'. The initial structure of the Mei-P26-NHL:RNA complex was generated by superimposing the Mei-P26 protein with the Brat-RNA complex (PDB ID: 5EX7) and copying the coordinates of the Brat RNA ligand. The superposition was performed for the 257 Cα atoms (RMSD = 1.343 Å), which matches between the Mei-26-NHL and Brat proteins. The sequence of that RNA was modified to UUUUUUU, UUUUACA, or UUUGUUGU using UCSF Chimera to prepare three starting structures for Mei-P26-NHL:RNA complexes. Molecular dynamics simulations for Mei-P26-NHL:RNA complexes for the three cases were performed using the Amber18 package. Molecular dynamics simulations were run for Brat in complex with UUGUUAA, UUUUACA and UUGUUGU RNAs as controls. Additional control simulation was run for Brat in complex with UUGUUGUUUUUUUU and the starting structure for this simulation was taken from the Brat-RNA complex with PDB ID: 4ZLR. The input structure for the simulation was prepared using tleap in a truncated octahedral box of 10 Å allowance using the TIP3P water model. Simulations were performed using the combination of the Amber ff14sb force field for proteins and the χOL3 force field for RNA. The structure was energy-minimized for 10,000 cycles with restraints, followed by 10,000 cycles without restraints. The minimized structures were subjected to heating, density equilibration and short runs of equilibration. The heating was done from 100 K to 300 K for 500 ps with restraints on the entire structure and the density equilibration was performed for 500 ps, also with restraints on the entire structure. The equilibration of the structures was run for four short rounds. The first three rounds of equilibration were run for 200 ps each with the main chain atoms constrained. The final round of equilibration was performed for 1 µs (10-6 s). The production run was run for 1000 ns. We have used constant pressure periodic boundary conditions (ntb = 2) with isotropic position scaling (ntp = 1) with a pressure relaxation time taup = 2.0 ps for the production run. The particle-mesh Ewald (PME) procedure (45) was used for computing the electrostatic interactions. The cut-off values used for electrostatics and LJ interactions were set as 12 Å. The equilibration steps were run with the NVT ensemble (ntb = 1) while the production run was performed with the NPT ensemble. The minimization was performed using Sander, and the subsequent steps were performed using the CUDA version of PMEMD available in the Amber package (46–48). The simulation trajectories were clustered using the reimplementation of NMRCLUST algorithm available in UCSF Chimera and the representative frames are provided as PDB files in this dataset.



Molecular Dynamics