GENERAL INFORMATION 1. Title of Dataset: Molecular dynamics simulations of the tripartite interface (Syt1_C2B?SNARE?Cpx Complex) corresponding to Figure 4 in https://doi.org/10.1016/j.jmb.2022.167853 2. Author Information A. Principal Investigator Contact Information Name: Axel T. Brunger Institution: Stanford University Address: 318 Campus Dr. E300C, Stanford, CA 94305, USA Email: brunger@stanford.edu B. Associate or Co-investigator Contact Information Name: Jeremy Leitz Institution: Stanford University Address: 318 Campus Drive, Room E300, Stanford, CA 94305-5432 Email: jleitz@stanford.edu C. Alternate Contact Information ? N/A 3. Date of data collection (molecular dynamics simulations): 2022 4. Geographic location of data collection (molecular dynamics simulations): Stanford, CA, USA 5. Information about funding sources that supported the collection of the data (molecular dynamics simulations): NIH R01MH063105 to Axel T. Brunger HHMI to Axel T. Brunger SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: None 2. Links to publications that cite or use the data: None 3. Links to other publicly accessible locations of the data: None 4. Links/relationships to ancillary data sets: None 5. Was data derived from another source? No 6. Recommended citation for this dataset: None DATA & FILE OVERVIEW 1. File List: Directories: Five molecular dynamics simulations of the tripartite Syt1 C2B-SNARE-Cpx complex, each simulation differs by the random number seed: tripartite_1/ tripartite_2/ tripartite_3/ tripartite_4/ tripartite_5/ Each of these directories contains the following subdirectories: 1_build/ 2_relax/ 3_heat1/ 4_heat2/ 5_prun/ The 1_build/ subdirectories contain all parameter, input, and metadata files for performing the respective molecular dynamics simulations. For definitions and details about these files see NAMD (https://www.ks.uiuc.edu/Research/namd/) and the user guide (https://www.ks.uiuc.edu/Research/namd/2.14/ug/). The 2_relax/ subdirectories contain the inputs and results of the initial relaxation stage. For definitions and details about these files see NAMD (https://www.ks.uiuc.edu/Research/namd/) and the user guide (https://www.ks.uiuc.edu/Research/namd/2.14/ug/). The 3_heat1/ subdirectories contain the inputs and results of the first heating stage. For definitions and details about these files see NAMD (https://www.ks.uiuc.edu/Research/namd/) and the user guide (https://www.ks.uiuc.edu/Research/namd/2.14/ug/). The 4_heat2/ subdirectories contain the inputs and results of the second heating stage. For definitions and details about these files see NAMD (https://www.ks.uiuc.edu/Research/namd/) and the user guide (https://www.ks.uiuc.edu/Research/namd/2.14/ug/). The 5_prun/ subdirectories contain subdirectories with the results of 1 nanosecond chunks (prun000001/, prun000002/), the last chunk (prun_last), and fitted coordinates at every 1 nanosecond of the simulation without water molecules and ions (pdbs/). For definitions and details about these files see NAMD (https://www.ks.uiuc.edu/Research/namd/) and the user guide (https://www.ks.uiuc.edu/Research/namd/2.14/ug/). The coordinate (pdb) files in the pdbs/ directory can be visualized with PyMol (https://www.schrodinger.com/products/pymol), ChimeraX (https://www.rbvi.ucsf.edu/chimerax/), or any other program that reads pdb files. 2. Relationship between files, if important: None 3. Additional related data collected that was not included in the current data package: None 4. Are there multiple versions of the dataset (molecular dynamics simulations)? No METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: The starting point for all molecular dynamics simulations of the tripartite complex was the crystal structure of the Syt1?SNARE?complexin-1 complex at 1.85 ? resolution (PDB ID 5W5C (https://www.rcsb.org/structure/5w5c)). Prior to the simulations, the Syt1_C2A domain, the crystallographic water molecules, Mg2+, and glycerol molecules were deleted from the crystal structure. Specifically, the following residues were included in the simulations of the tripartite interface: Syt1_C2B[270-419], synaptobrevin-2[29-66], Stx1A[191-244], SNAP-25A[10-74 & 141-194], complexin-1 [51-75]. For all simulations the NAMD (https://www.ks.uiuc.edu/Research/namd/) program was used. See also the user guide for NAMD (https://www.ks.uiuc.edu/Research/namd/2.14/ug/) The starting model was placed in a 111 ? 111 ? 111 ? periodic boundary condition box. The empty space in the box was filled with 41204 water molecules using the VMD solvate plugin. The system has a total of 130,133 atoms. The system was charge-neutralized and ionized by addition of 129 potassium and 112 chloride ions, corresponding to a salt concentration of ~ 145 mM. Identical to the primary interface simulations, the CHARMM36 all-hydrogen force fields and parameters were used with a non-bonded cutoff of 11 ?. Five independent 1-?sec simulations were performed using different initial random number seeds. The CHARMM36 all-hydrogen force fields and parameters?were used (https://www.charmm-gui.org) with a non-bonded cutoff of 11 ?. A constant pressure method was used by adjusting the size of the box. The Particle Mesh Ewald method was used to accelerate the calculation of long-range electrostatic nonbonded energy terms. Langevin dynamics (with a friction term and a random force term) was used to maintain the temperature of the simulation. All hydrogen-heavy-atom bonds were kept rigid using the Rattle method as implemented in NAMD. The system was equilibrated by the following procedure: (1) relaxation step, ramping up the temperature from 0 to 50 K for 50 picoseconds with a 1 femtosecond time step; (2) first heating step, ramping up the temperature from 50 to 100 K for 50 picoseconds with a 1 femtosecond time step; (3) second heating step, ramping up the temperature from 100 to 250 K for 150 picoseconds with a 1 femtosecond time step. For all simulations, 1-nanosecond chunks were run at a temperature of 300 K with a time step of 1 femtosecond. Five independent 1-?sec simulations were performed by using different initial random number seeds. Note that two simulations of resulted in a dissociation event. All simulations were performed on the Stanford Sherlock Cluster using 4 nodes, each node consisting of dual 10-core CPU 2.4 Ghz Intel processors, i.e. a total of 80 CPUs were used for each simulation. The MPI-parallel NAMD2 2.14b1 executable was used. To visualize the results, only protein components are shown, and all structures were fitted to each other, and displayed with PyMOL 2.5.1. The molecular dynamics simulations were performed with the following Unix shell commands: cd cd 2_relax relax.inp >& relax.log cd ../3_heat heat1.inp >& heat1.log cd ../4_heat heat2.inp >& heat2.log cd ../5_prun/prun000001 prun.inp1 >& prun.log cd ../5_prun/prun000002 prun.inp1 >& prun.log ? 2. Methods for processing the data: n/a 3. Instrument- or software-specific information needed to interpret the data: VMD 1.9.4 (http://www.ks.uiuc.edu/Research/vmd/) NAMD 2.14b (https://www.ks.uiuc.edu/Research/namd/) PyMol 2.5.1 (https://www.schrodinger.com/products/pymol) ChimeraX (https://www.rbvi.ucsf.edu/chimerax/) 4. Standards and calibration information, if appropriate: n/a 5. Environmental/experimental conditions: n/a 6. Describe any quality-assurance procedures performed on the data: n/a 7. People involved with sample collection, processing, analysis and/or submission: Axel T. Brunger.