Published November 1, 2023 | Version v3

Dataset for Simulation-guided engineering of split GFPs with efficient β-strand photodissociation

  • 1. Uppsala University
  • 2. Wayne State University
  • 3. Stanford University

Description

Files associated with performed experiments and simulations, including source data from experimental measurements and simulations, starting structures, parameters, simulation input files, and short videos of simulation trajectories. 

Simulation files include:

  • Initial coordinates of the GFP chromophore for geometry optimization and RESP calculations in GAUSSIAN
  • Parameter and starting files for QM/MM calculations around the conical intersection in TeraChem
  • Parameter, coordinate and input files for regular MD and simulated annealing simulations in AMBER
  • Parameter, coordinate and input files for umbrella sampling simulations of isomerization in AMBER
  • Results files from TeraChem

Additionally, short videos are included of simulations of the cis and trans conformations.

Experimental source data include: 

  • UV-vis data from strand-exchange experiments
  • Mass spectrometry data
  • Fluorescence data

Files

ExperimentalMeasurements.zip

Files (5.1 GB)

Name Size
md5:a1ad5d623de86b1c84d802f085571c4b
306.4 MB Preview Download
md5:97f8b3335f7131dcd3d69412524175a3
4.7 GB Preview Download
md5:46d5f68368a19afad5d00b0dd7a673fb
1.9 MB Download
md5:ab24efd1a12ee7f9990f1281ec7456d7
2.3 MB Download
md5:9b85360ce529d89420276ddf5ea00703
2.5 MB Download
md5:a82bcb4686c83bb03646f746c2a895d6
26.8 kB Download