Jorge Antonio Amador Balderas
jorgeamador.bsky.social
Jorge Antonio Amador Balderas
@jorgeamador.bsky.social
PhD student at the Computer Chemistry Center in FAU
Molecular Dynamics Simulations on DNA Repair Systems
Which leads to some ligands binding differently to the metal, with some of them (like the best inhibitor) binding in a bidentate fashion, which would block the entrance of water to the binding site, leading to inhibition (4/4)
December 23, 2024 at 5:58 PM
Also, Tyr or Phe doesn't make a critical difference in binding, as the enzyme prioritizes "filling" the hydrophobic pocket with the aromatic ring above other interactions. This also applies to ligands where Tyr and Phe had a D-configuration, with the Zn binding mode being the biggest difference(3/4)
December 23, 2024 at 5:56 PM
Interestingly, there are no critical differences that allow us to distinguish between the binding of the inhibitors and the dipeptide, there is no clear trend where the molecules that are the best inhibitors to bind more or less tightly than the rest of the ligands (2/4)
December 23, 2024 at 5:50 PM
Among other things, we analyzed the binding of the slowly hydrolyzed dipeptide Gly-Tyr/Phe; and inhibitors that are similar to the dipeptide (Tyr or Phe at the C-terminus and aminocarbonyl or hydroxyaminocarbonyl at the N-terminus) (1/4)
December 23, 2024 at 5:47 PM