Assessing SIRAH's Capability to Simulate Intrinsically Disordered Proteins and Peptides

This dataset contains the structures, topologies, and trajectory files of coarse-grained molecular dynamics simulations of five Intrinsically Disordered Proteins (IDPs). We explored the dynamics of α-synuclein (randomly generated conformers), p31-43(PDB is: 6QAX), PaaA2 antitoxin (PDB id:3ZBE), Amyloid-beta 1-40 (PDB id: 2FLM), and Insulin C-peptide (PDB id: 1T0C) using the SIRAH force field running with the Gromacs 18.4 under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Briefly, simulations were performed in triplicate for 5 μs at 300 K and 1 atm in the NPT ensemble. We used a time-step of 20 fs, a direct cutoff for non-bonded interactions of 1.2 nm, and Particle Mesh Ewald summation for long-range electrostatics. For α-synuclein and p31-43, initial conformations were obtained from models built on arbitrary conformations and heated up to 340 K. For PaaA2 antitoxin, Amyloid-beta 1-40, and Proinsulin C-peptide, three different NMR conformers were arbitrarily selected. 

The information is divided into five tar files containing each system's data (only protein coordinates are reported). Additionally, the Sirah Tools'  tcl script with macros for selections and analyses is also included. Please visit http://www.sirahff.com for step-by-step tutorials on running and analyzing CG simulations with SIRAH. 

To take a quick look at the trajectories:

1- Untar the tar file of interest 

2- Open the trajectory on VMD using the command line:

vmd "your_protein".psf  "your_protein".xtc -e sirah_vmdtk.tcl

Note that using the tcl script you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

This dataset contains simulations associated to a manuscript with the same title and by the same authors.

For questions, kindly contact Florencia Klein ([e-mail]), Exequiel Barrera ([e-mail]), or Sergio Pantano ([e-mail]).