Official Project Description
Tumor necrosis factor α (TNFα) is a cytokine that belongs to a superfamily of trimeric proteins.
This protein has been shown to be important in regulating autoimmune diseases such as arthritis and Crohn’s disease through interactions with the TNF receptor.
In regard to cancer, TNF is a double-dealer.
On one hand, TNF could be an endogenous tumor promoter, because TNF stimulates cancer cells’ growth, proliferation, invasion and metastasis, and tumor angiogenesis.
On the other hand, TNF could be a cancer killer.
In it’s apo state TNFα has shown to be symmetrical, but small ligand inhibitors bind the TNFα disrupt this symmetry by forcing one of the monomers to be below the other two, which disrupts the binding interface to form the TNFα-receptor complex.
In this project, we want to determine the stability of the trimer and get a sense of the free energy landscape.
We also want to determine if the asymmetry found in the inhibited conformation requires the presence of an inhibitor or if the apo trimer can visit inhibited states in the absence of the ligand.
In particular we are interested in learning about the effect the volume of the binding pocket has on forming the asymmetrical TNFα complex.
The initial starting structures are 50 diverse seeds from HREMD simulations started from a crystal structure.
This is a project run by Roivant Sciences (formerly Silicon Therapeutics) as was officially announced in this press release: https://foldingathome.org/2021/04/20/maximizing-the-impact-of-foldinghome-by-engaging-industry-collaborators/ All data is being made publicly available as soon as it is received at https://console.cloud.google.com/storage/browser/stxfah-bucket.