A homogeneous dataset of polyglutamine and glutamine rich aggregating peptides simulations

Published: 10 March 2021| Version 1 | DOI: 10.17632/2tmsbchh42.1
Contributors:
Exequiel Barrera, Francesco Zonta, Sergio Pantano

Description

This dataset contains a collection of molecular dynamics (MD) simulations of polyglutamine (polyQ) and glutamine-rich (Q-rich) peptides in the multi microsecond timescale. Primary data from coarse-grained simulations performed using the SIRAH force field has been processed to provide fully atomistic coordinates. The dataset encloses MD trajectories of polyQs of 4 (Q4), 11 (Q11), and 36 (Q36) amino acids long. In the case of Q11, simulations in presence of Q5 and QEQQQ peptides, which modulate aggregation, are also included. The dataset also comprises MD trajectories of the gliadin related p31-43 peptide, and Insulin’s C-peptide at pH=7 and pH=3.2, which constitute examples of Q-rich and Q-poor aggregating peptides. The dataset grants molecular insights on the role of glutamines in the spontaneous and unbiased ab-initio aggregation of a series of peptides using a homogeneous set of simulations. The dataset is provided in Protein Data Bank (pdb) format. Further analyses of the trajectories can be performed directly using any molecular visualization/analysis software suites.

Files

Steps to reproduce

The dataset is provided in Protein Data Bank (pdb) format. Further analyses of the trajectories can be performed directly using any molecular visualization/analysis software suites.

Institutions

  • Institut Pasteur Montevideo
  • ShanghaiTech University
  • Consejo Nacional de Investigaciones Cientificas y Tecnicas

Categories

Protein Aggregation, Coarse Grained Model, Molecular Dynamics

Licence