All-atom molecular dynamics simulations of synaptic vesicle fusion I: a glimpse at the primed Synaptotagmin-SNARE-complexin complex
Rizo, Josep et al. (2022), All-atom molecular dynamics simulations of synaptic vesicle fusion I: a glimpse at the primed Synaptotagmin-SNARE-complexin complex, Dryad, Dataset, https://doi.org/10.5061/dryad.ns1rn8pw6
Synaptic vesicles are primed into a state that is ready for fast neurotransmitter release upon Ca2+-binding to Syt1. This state likely includes trans-SNARE complexes between the vesicle and plasma membranes that are bound to Syt1 and complexins. However, the nature of this state and the steps leading to membrane fusion are unclear, in part because of the difficulty of studying this dynamic process experimentally. To shed light into these questions, we performed all-atom molecular dynamics simulations of systems containing trans-SNARE complexes between two flat bilayers or a vesicle and a flat bilayer with or without fragments of Syt1 and/or complexin-1. Our results need to be interpreted with caution because of the limited simulation times and the absence of key components, but suggest mechanistic features that may control release and help visualize potential states of the primed Syt1-SNARE-complexin-1 complex. In particular, the simulations suggest that SNAREs alone induce formation of extended membrane-membrane contact interfaces that may fuse slowly, and that the primed state contains macromolecular assemblies of trans-SNARE complexes bound to the Syt1 C2B domain and complexin-1 in a spring-loaded configuration that prevents premature membrane merger and formation of extended interfaces but keeps the system ready for fast fusion upon Ca2+ influx.
After energy minimization, all systems were heated to 310 K over the course of a 1 ns MD simulation in the NVT ensemble and equilibrated for 1 ns in the NPT ensemble using isotropic Parrinello-Rahman pressure coupling. NPT production MD simulations were performed for the times indicated in Table 1 for each system using 2 fs steps, isotropic Parrinello-Rahman pressure coupling and a 1.1 nm cutoff for non-bonding interactions. All simulations were performed at 310 K except one simulation with the qscff system, which was performed at 325 K after a 310 K simulation. Nose-Hoover temperature coupling was used separately for three groups: i) protein atoms plus Ca2+ ions if present; ii) lipid atoms; and ii) water and KCL. Periodic boundary conditions were imposed with Particle Mesh Ewald (PME) summation for long-range electrostatics.
These data sets contain files associated with all-atom molecular dynamics simulations of the neurotransmitter release machinery between two flat bilayers or between a flat bilayer and a vesicle. Each directory corresponds to one simulation as described in the reference associated with this deposition and summarized in Table 1 of that reference. The simulations were performed with gromacs. Please refer to the gromacs manual (https://zenodo.org/record/6451567#.YoPaOJPMLOc) for more details.
For each simulation, filenames have a common beginning (e.g. prsg for the simulation in the prsg directory) followed by a few letters that indicate the nature or order of the simulation: nvt for temperature equilibration runs; par for pressure equilibration runs and mdx for production simulations, where x is a number that denotes the order of a particular run within the chain of concatenated simulations. The filename extensions follow the common gromacs nomenclature. Here is a list of the types of files included in the deposition.
Filenamea.sh or Filenameb.sh: text files with the SLURM instructions to run the simulation. These files show which files were used to run the particular simulation.
Filename.top: topology file that includes calls to the force field and to other topology files and/or restraint files
Filename.itp: topology or restraint file
Filename.ndx: index file
Filename.mdp: file containing the molecular dynamics parameters
Filename.log: log file for the simulation
Filename.gro: file with the coordinates and velocities at the end of the simulation
Filename.cpt: checkpoint file containing the final coordinates and velocities with high precision to continue the simulation
Filaname.edr: energy file
Filenamecenterfit.pdb: selected frames that have been aligned with the initial configuration and converted to PDB format.
In addition, each simulation directory contains force field, restraint and/or topology directories. The filename.xtc trajectory files that contain coordinates and velocities of frames saved during the simulations are not included because of their large size, which would render the deposition very expensive. These files are available from Josep Rizo upon reasonable request. This is the contact information:
Name: Josep Rizo
Institution: Department of Biophysics, UT Southwestern Medical Center Dallas
Address: 6001 Forest Park Road, Dallas, TX 75390-8816
National Institute of Neurological Disorders and Stroke, Award: R35 NS097333
Welch Foundation, Award: I-1304
NSF, Award: MCB-2111728
Natural Science Foundation of Shanghai, Award: 19ZR1473600