Published September 8, 2023
| Version v1
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Mechanism-Based Redesign of GAP to Activate Oncogenic Ras
Authors/Creators
- 1. Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
- 2. nstitute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary; Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budafoki út 6-8, Budapest 1111, Hungary
Description
Additional material for Berta et al. J. Am. Chem. Soc. 2023, 145, 37, 20302–20310
- Paths: minimised structures corresponding to the the GTP hydrolysis mechanism.
- MD setup: equilibriated inputs for classical MD simulations for WT and mutant systems in CHARMM/NAMD format, set up for the charmm36m FF.
- NBO: outputs for Natrual Bonding Orbitals analysis carried out for TS and RS structures.
- GAP mutants: optimised TS and RS structures of the most promising designed GAP mutants.
Notes
This project made use of time on ARCHER granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk) and the CAMP HPC cluster of The Francis Crick Institute. The authors acknowledge use of the research computing facility at King's College London, Rosalind (https://rosalind.kcl.ac.uk). Supported by the Ministry for Innovation and Technology and the National Research, Development and Innovation Fund of Hungary (K135231, NKP-2018-1.2.1-NKP-2018-00005, TKP2021-EGA-02, to B.G.V. and K.N.).
Files
GAP_mutants.zip
Additional details
Related works
- Is supplement to
- Journal article: 10.1021/jacs.3c04330 (DOI)