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Published September 12, 2022 | Version v1
Journal article Open

Research data on "Reconstitution of microtubule into GTP-responsive nanocapsules"

  • 1. RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
  • 2. Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
  • 3. Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China; State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
  • 4. Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
  • 5. PolitoBIOMedLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
  • 6. Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland.
  • 7. Department of Physical Sciences, Aoyama Gakuin University, Kanagawa 252-5258, Japan.
  • 8. RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679–5198 Japan.
  • 9. RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.

Description

This repository contains the set of data shown in the paper "Reconstitution of microtubule into GTP-responsive nanocapsules", published on Nature Communications (DOI: 10.1038/s41467-022-33156-5).

All the input data needed to run the simulations and get the results are organized in 3 different folders:

 * `00-MDPFiles/`

  in this folder there are the mdp files for each step for Gromacs-MD simulations: energy minimization, nvt, npt, production with restraints and production without restraints.

 * `01-TubulinSystems/`

  the folder contains all the necessary files for the tubulin assembly MD simulations with and without glue (`SystemA_Glue/`, `SystemA_noGlue/`, `SystemB_Glue/`, `SystemB_noGlue/`).

 * `02-OnlyGlue/` 

  the folder contains all the files needed for the the atomistic MD simulations of the glue in water.
 

Files

TubulinNCs.zip

Files (224.6 MB)

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md5:80b021a30dcf90c03e5d2bbb422b0425
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Additional details

Related works

Cites
Journal article: 10.1038/s41467-022-33156-5 (DOI)

Funding

DYNAPOL – Modeling approaches toward bioinspired dynamic materials 818776
European Commission