Structural Analysis of UCH37 and its Complexes

Molecular models were generated using Modeller[59 (link)] and MacroModel (Schrodinger, New York, NY). PfUCH37 was modelled using an ensemble of available UCH37 X-ray crystal structures (PDB IDs: 3A7S and 3IHR, 44% and 36% sequence identity respectively), including the complex of TsUCH37 with ubiquitin (37% sequence identity; PDB ID: 4IG7). The structures of PfUCH37 and TsUCH37 (PDB ID: 4IG7) were minimized using the MMF94s forcefield in Sybyl-X 2.1.1 (Certara L.P., St Louis, MO), with the final structure having more than 95% of residues in the allowed region of a Ramachandran plot. Ubiquitin and Nedd8 were docked into the structures of UCH37 using Piper (Schrodinger, New York, NY), with the available X-ray crystal structure of TsUCH37 in complex with ubiquitin (PDB ID: 4IG7) used to guide protein docking. The models of the complexes were minimised using the MMF94s forcefield in Sybyl-X 2.1.1 as described above. The quality of all the models were confirmed with Verify3D[60 (link)]. The structural consequences of the differences in interfacial residues were analysed to assess the structural importance of the residues[41 (link),61 (link)–63 (link)]. Interactions were calculated using Arpeggio[64 (link)] and model structures were examined using Pymol.