Robust AMBER Force Field Parameters for Glutathionylated Cysteines.
Zineb ElftmaouiEmmanuelle BignonPublished in: International journal of molecular sciences (2023)
S-glutathionylation is an oxidative post-translational modification, which is involved in the regulation of many cell signaling pathways. Increasing amounts of studies show that it is crucial in cell homeostasis and deregulated in several pathologies. However, the effect of S-glutathionylation on proteins' structure and activity is poorly understood, and a drastic lack of structural information at the atomic scale remains. Studies based on the use of molecular dynamics simulations, which can provide important information about modification-induced modulation of proteins' structure and function, are also sparse, and there is no benchmarked force field parameters for this modified cysteine. In this contribution, we provide robust AMBER parameters for S-glutathionylation, which we tested extensively against experimental data through a total of 33 μs molecular dynamics simulations. We show that our parameter set efficiently describes the global and local structural properties of S-glutathionylated proteins. These data provide the community with an important tool to foster new investigations into the effect of S-glutathionylation on protein dynamics and function, in a common effort to unravel the structural mechanisms underlying its critical role in cellular processes.
Keyphrases
- molecular dynamics simulations
- molecular docking
- single cell
- cell therapy
- healthcare
- electronic health record
- single molecule
- signaling pathway
- big data
- mental health
- multidrug resistant
- high glucose
- drug induced
- machine learning
- cell proliferation
- bone marrow
- oxidative stress
- social media
- endothelial cells
- mesenchymal stem cells
- binding protein
- fluorescent probe
- deep learning
- endoplasmic reticulum stress
- neural network