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

<p>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 &alpha;-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&nbsp;<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to&nbsp;<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado &amp; Pantano JCTC 2020</a>. Briefly, simulations were performed in triplicate for 5 &mu;s 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 &alpha;-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.&nbsp;</p> <p>The information is divided into five tar files containing each system&#39;s data (only protein coordinates are reported). Additionally, the Sirah Tools&#39; &nbsp;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.&nbsp;</p> <p>To take a quick look at the trajectories:</p> <p>1- Untar the tar file of interest&nbsp;</p> <p>2- Open the trajectory on VMD using the command line:</p> <p>vmd &quot;your_protein&quot;.psf &nbsp;&quot;your_protein&quot;.xtc -e sirah_vmdtk.tcl</p> <p><br> Note that using the tcl script you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.</p> <p>This dataset contains simulations associated to a manuscript with the same title and by the same authors.</p> <p>For questions, kindly contact Florencia Klein (fklein@pasteur.edu.uy), Exequiel Barrera (ebarrera@pasteur.edu.uy), or&nbsp;Sergio Pantano (spantano@pasteur.edu.uy).</p>