Date of Award
Master of Science in Chemistry
Selective nitrosylation of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) at Cys-247 affects gene regulation through the interferon-gamma (IFN- γ) activated inhibitor of translation (GAIT) complex. Oxidized low-density lipoprotein (LDLox) and INF-γ induce assembly of the nitrosylase complex composed of inducible nitric oxide synthase (iNOS), S100A8, and S100A9 proteins. Crystal structure of the complex of GAPDH and S100A8A9 is not known, structural prediction method were employed by protein-protein docking and binding energy calculation with PatchDock and FIREDock respectively. Candidate models were selected, based on a weight factor calculated, from the computational method developed from the "artificial protease" cleavage mapping Fe(III) (s)-1-(p- bromoacetamidobenzyl) EDTA to identify helical domains of GAPDH that may interact with S100A8. Models were also selected based on the Boltzmann distribution according to their binding energy. Interface residue analysis suggest that from the models that matched with experimental data, DCE-9 has highest weight factor of 1.68. Docking complexes without experimental bias has the highest binding energy of -76.04 kcal/mol when compared to other candidate models. Our analysis also suggests that complex that matched with experimental data are less likely to form as their binding energies were much lower when compared to the models that were not selected based on experimental data. It can be inferred from our analysis that artificial cleavage mapping may lead to artefacts and the CHARMM19 force field used in FIREDock may not accurately represent the true binding energy of these complexes.
Turzo, SM Bargeen Alam, "Computational Investigation of Protein Assemblies" (2018). ETD Archive. 1090.