Simulations of Sec61 with a substrate-selective inhibitor

Simulation inputs and outputs for manuscript "Signal peptide mimicry primes Sec61 for client-selective inhibition" by Rehan et al. Nature Chemical Biology 19, pages 1054–1062 (2023). DOI: 10.1038/s41589-023-01326-1.

The Sec61 complex, embedded in a lipid bilayer mimicking ER in composition [1–4], was simulated in the presence ("Sec61_KZR8445", 5×1 µs) and absence ("Sec61_noinhibitor", 3×1 µs) of the cotransin KZR-8445 inhibitor. Additionally, a N300A mutant of Sec61α ("Sec61_KZR8445_N300A") was simulated in the presence of KZR-8445 for 1 µs. The replicas are labeled with "R". 

The GROMACS-compatible files include:

• Run input files (.tpr)
• Trajectory with coordinates written every 1 ns (.xtc)
• Energy file (.edr)
• Final coordinates after 1 µs of simulation (.gro)
• Continue points for extending the simulation (.cpt)

Additionally, for each type of simulation (with KZR8445, without KZR8445, N300A mutation), common files are included:

• Index file (.ndx)
• Topology file (.top)

The run parameter file (md.mdp) is common for all systems. The topologies (.itp) referred to by the top files are compressed into the TOP.tar archive.

Additional details on the methodology used in the simulations is described below:

We used the CHARMM36m protein force field [5,6], the CHARMM36 lipid force field [7], the CGenFF force field for the inhibitor with the ligand containing a positive dummy particle describing the bromobenzyl sigma hole [8,9], and CHARMM-specific TIP(S)3P model for water [10,11]. The systems were generated in CHARMM-GUI [12,13], including the protein positioning using PPM 2.0 [14] and the ligand parametrization within CHARMM-GUI [15].

The leap-frog integrator was used with a time step of 2 fs. Buffered Verlet lists were used [16]. The Lennard-Jones forces were switched to zero between 1.0 and a cut-off distance of 1.2 nm. Long-range electrostatic interactions were included by the smooth particle mesh Ewald algorithm [17,18]. Temperatures of the protein (including the inhibitor), the lipids, and the solvent (water and ions) were separately coupled to a Nosé–Hoover thermostat [19,20] with a target temperature of 310 K and a relaxation time of 1 ps. The pressure was maintained at 1 bar with a semi-isotropic Parrinello–Rahman barostat [21]. The target pressure was set to 1 bar, the compressibility to 4.5 × 10^–5 bar^–1 and the relaxation time constant 5 ps. Bonds involving hydrogens were constrained with p-LINCS [22,23].

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