Molecular operating environment 2010

Monomeric DJ1/PGK1 complex structure was derived by overlaying the CRT0063465-PGK1 costructure with the C106-sulfinic acid-bound DJ1 structure, and with PDB DJ1 structure (1P5F.PDB), aligning protein units through overlay of bound CRT0063465 (CRT0063465 fragment in the case of the DJ1 structure). The resulting complex, containing only bound CRT0063465 from the PGK1 crystal structure, showed protein–protein steric clashes, so the DJ1 structure was subjected to local energy minimization in loop regions contacting PGK1. The full complex underwent constrained energy minimization, keeping the ligand structure rigid. To construct the DJ1 dimeric complex, two units of the minimized monomeric complex were overlain with the dimer DJ1 crystal structure 1SOA.PDB, using DJ1 sequence. Structural alignment guided positioning of protein units. Constrained minimization was conducted on the final dimeric complex, again keeping both ligand structures fixed. Calculations were performed using Molecular Operating Environment (MOE) 2010.10 from Chemical Computing Group Inc., using the Amber99 forcefield.