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Can we use molecular dynamics to simulate biomolecular recognition?

dataset
posted on 2023-04-11, 06:41 authored by Malin LükingMalin Lüking, David van der Spoel, Johan Elf, Gareth A. Tribello

This Dataset contains starting structures, inout files and scripts to prepare and run normal and biased simulations on the LacI Transcriptionfactor and DNA (with different sequences). The starting structures (based on the crystal structure with PDB ID 1EFA), input files for GROMACS and PLUMED and scripts for prepartion and analysis are also available on GitHub. In this dataset, one can additionally find the trajetories of the simulations that were run to produce the linked publication.

The trajectories include the follwing sets:


Unbiased simulations 

5 replica of 50 ns each


NMR restraint simulations 

2 DNA sequences: specific, OSymL and non-specific NOD

3 replica of 250 ns each


Metadynamics simulations

OSymL (specific DNA sequence)

bias on selected contacts between the protein and the DNA

bias on selected contacts between the protein and the DNA and between the two hinge helices

bias on selected contacts between the protein and the DNA and between the two hinge helices and the hinge helixity


NOD (non-specific DNA sequence)

bias on selected contacts between the protein and the DNA and between the two hinge helices and the hinge helixity


Code contains the scripts used for preparing, running and analysing the simulations. It is also available on GitHub (https://github.com/mallu2/Transcriptionfactor_unbinding).  

Funding

Knut and Alice Wallenberg Foundation 2016.0077

SNIC 2021/3-8

The physics of genetic information processing

Swedish Research Council

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History

Publisher

Uppsala University