Molecular dynamics simulations of RNA Pol I closed complex in WT and with modifications to DNA base pairs -27 and -28

The starting structure for the modelling was cryo-EM based structure of S. cerevisiae pre-initiation complex, showing Pol I, RRN3 and CF bound on a rDNA promoter at 2.90 Å resolution. This structure (‘RNA Polymerase I closed conformation 2’; accession code: 6RQL) was downloaded from the PDB database and prepared using the Protein Preparation Workflow of Maestro with default settings. This included filling in missing sidechains, optimizing hydrogen bonds and protonation using PROPKA at pH 7.4, deleting water molecules >5Å from the heteroatoms and a short energy minimization using OPLS4 force field. The initial structures for the complexes with DNA mutations were constructed from this pre-processed structure by manually mutating the base pairs at position -28 or -27 of the rDNA promoter from C·G to A·T (tDNA·ntDNA) and from A·T to C·G, respectively. MD simulations (3*80 ns/system) were conducted with Desmond using default parameters from Schrödinger Suite version 2024-1 on the CSC (IT Center for Science, Finland) supercomputer Puhti.