DOI: 10.5281/zenodo.10478555
title: Molecular dynamics trajectories for "Biophysical characterisation of lipid and membrane binding of Calcium-sensor Synaptotagmin-1"

description: Syt-1 MD simulation trajectories

Trajectories for the simulation of Synpatotagmin-1 C2 domains C2A and C2B interacting with models of the synaptic vesicle (SV) and plasma membranes.

The biological background and motivation are described in the paper (ADD LINK). Code for the data analysis based on these trajectories can be found at the project GitHub.

Methods

Equilibration of individual C2 domains.   Starting coordinates of C2A (residues 141-263) and C2B (residues 272-418) in the presence of Ca2+ were obtained from PDB ID 5KJ7 chain K. For simulations in the absence of Ca2+, Ca2+ atoms were removed from the structures. Structural models were placed in a box of TIP3p water with 150 mM K+ and Cl- ions at a ratio neutralising the net charge. Structures were relaxed by energy minimization at a maximum force < 1,000 kJ mol−1 nm−1 followed by 500 ps equilibration in the NVT ensemble (i.e. at a constant number of particles (N), volume (V) and temperature (T)) at 300 K, 500 ps in the NPT ensemble (i.e. at a constant number of particles (N), pressure (P) and temperature (T)) at 1 bar pressure restraining all heavy atoms and 10 ns in the NPT ensemble removing all restraints. Simulations were performed using Gromacs version 2020.4 and the CHARMM36m (July 2020) force field. The particle mesh Ewald method was used employing a 10 Å cut-off for calculating long-range electrostatics in the absence of lipids and a 12 Å cut-off in the presence of lipids. The V-rescale modified Berendsen thermostat with separate coupling groups for protein and solvent, and the Berendsen barostat were employed. H-Bonds were constrained using the LINCS algorithm enabling a time step of 2 fs. The final frame of the simulation was used for setting up the protein/membrane simulations.

Equilibration of isolated SV and plasma membrane bilayers.  Lipid bilayer structures were obtained from CHARMM-GUI specifying a box size of 76 Å edge length, 22.5 Å water layer thickness and a concentration of 150 mM K+ and Cl- ions. Membranes were composed of POPC:DOPS:POPE:Cholesterol;PIP2:DAG (CHARMM-GUI identifiers for PIP2 and DAG were POPI25 and POGL, respectively) at a ratio of 38:18:20:20:0:0 per leaflet for the SV membrane model and a ratio of 38:18:20:20:2:2 per leaflet for the plasma membrane model. Relaxation and equilibration at 300 K were performed following the protocol supplied by CHARMM-GUI. Briefly, the protocol consisted of six equilibration simulations, namely 2 x 125 ps NVT, 1 x 125 ps NPT and 3 x 500 ps NPT, gradually releasing the restraints on the lipids. Finally, a 10 ns unrestrained simulation in the NPT ensemble using the Nosé-Hoover thermostat and the Parrinello-Rahman barostat was performed. The last frame of this simulation was used for assembling the protein-lipid system.

Simulation of C2A and C2B membrane interactions. Equilibrated membrane structures were centred in the xy-plane and the equilibrated protein was placed at a 4 Å distance above the plane using vmd. For each protein-membrane combination, three input structures with the C2 domains oriented at an angle of 0°, 30° and 60° between the z-axis and a vector through the main axis of the C2 domain (from the centre of mass of the protein to the centre of mass of residue 172 of C2A and residue 305 of C2B, respectively) with the Ca2+ binding loops facing towards the membrane were generated. Subsequently, energy minimization and a six-step equilibration protocol as described for initial equilibration of the membranes (see above) were performed.  For production in the NPT ensemble the Nosé-Hoover thermostat (300K; 1 ps coupling constant for water and ions; 2.5 ps for protein and lipids) and the Parinello-Rahman barostat (semi-isotropic; 5 ps time constant). Simulations were computed on an Intel Xeon E5-2680v3 processor running CentOS until >1500 ns simulation time were accumulated.