DOI: 10.5281/zenodo.16610780
title: Modelling Data related to the article "Phosphorylation of SNAP-25 at Ser187 is Enhanced Following its Cleavage by Botulinum Neurotoxin Serotype A, Promoting the Dominant-Negative Effect of the Resulting Fragment."

description: This dataset accompanies the molecular dynamics (MD) study of the SNARE complex in its wild-type and modified forms, as well as umbrella sampling simulations of a model peptide designed to explore the impact of serine phosphorylation on helical stability. The data have been generated using the Amber20 package with CUDA-accelerated pmemd, and system preparation and analysis were performed using AmberTools21.

SNARE Complex MD Simulations

Four different SNARE complexes were simulated:





SNAP-25 (wild-type)




pSNAP-25_Ser187 (phosphorylated at Ser187)




SNAP_1-197 (cleaved at the C-terminal helix of SNAP-25, residues 198–204 removed)




pSNAP_1-197_Ser187 (cleaved and phosphorylated at Ser187)



Included Files (per complex)





Topology file (geom.prmtop) with TIP4Pew water and neutralizing ions




Initial coordinates (geom.inpcrd) of the fully solvated system




Post-heatup coordinates (heatup_1.rst, heatup_2.rst) representing the solvated and heated up system before production




Two production trajectories and their topology file  (stripped_1500_1.nc, stripped_1500_2.nc, stripped_1500.prmtop) per system (750 ns each), recorded every 40 ps→ Trajectories are provided in a stripped format: ions removed, and only the 1500 closest water molecules retained per frame to reduce file size.



Each simulation was conducted in the NPT ensemble (Anderson thermostat and Berendsen barostat), using a 2 fs timestep and periodic boundary conditions. The SHAKE algorithm was applied to constrain hydrogen-involving bonds. Analyses focus on the last 300 ns of each replicate to ensure equilibrium sampling.

Umbrella Sampling Simulations

Two 10-residue model peptides were simulated to probe the impact of phosphorylation on α-helical stability:





Model peptide : (peptide) ACE-LYS-ALA-ASP-SER-ASN-LYS-THR-ARG-NME




Phosphorylated model peptide: (pho_peptide) same sequence with Ser → phosphoserine (SEP)



Umbrella sampling was used to stretch the peptide by biasing the distance between the α-carbons of the N-terminal lysine and the C-terminal arginine across 17 windows (10.0 to 18.0 Å, spaced by 0.5 Å), using a harmonic force constant of 8.0 kcal/mol/Å² (Amber input). Each peptide system was independently simulated 50 times.

Included Files (per peptide type)





Topology and initial coordinate files




50 replicate umbrella sampling sets, each containing:





potential of mean force (PMF) output




WHAM metadata file




For each window of each replicate:





reaction coordinate trajectory




final restart file of the equilibrated window







These umbrella sampling simulations were performed with the same solvent model, force fields, and equilibration protocol as the SNARE systems.

Force Field Parameters





Protein: ff14SB




Phosphorylated serine: adapted from Homeyer et al.




Solvent: TIP4Pew water model




Electrostatics: Particle Mesh Ewald (PME), 12.0 Å real-space cutoff