May 11, Wed 2011
11:00 am, MRB 200 Conference Room
Dr. Ling Wu
University of Minnesota
Structural studies of Metalloproteinase and Protien-Ligand Binding systems
Acutolysin A is a snake venom zinc metalloproteinase possessing only one catalytic domain. The catalytic zinc ion, in the active site, is coordinated in a tetrahedral manner with three imidazole nitrogen atoms of histidine and one oxygen atom. It is uncertain whether this oxygen atom is a water molecule or a hydroxide ion just from the three-dimensional X-ray crystal structure. The identity of the fourth ligand of zinc is theoretically determined for the first time by performing both combined quantum mechanical and molecular mechanical (QM/MM) simulation and high-level quantum mechanical calculations. All of the results obtained indicate that the fourth ligand in the active site of the reported X-ray crystal structure is a water molecule rather than a hydroxide anion. (Postdoc work) The complement system is a key part of the innate and adaptive immune system. Activation of C3 by the C3 convertases is a central amplification step in complement activation. Experiments have shown that C3 is unable to progress through the C3 pathway when M351T mutation is present. Since the mutation site is 15 angstroms away from the binding site so we would not expect to see an effect from the mutation on binding. However, we do see that the mutation causes a significant increase in binding affinity between C3 and Compstatin. In order to explore the differences of the structural and energetic contributions in the binding process between the compstatin and wild type complement C3c and mutated one, molecular dynamics simulations and free energy calculations were performed. Base on the analysis in our work, we believe that the stronger binding of mutated complement C3c tocompstatin than the wild type C3c is the outcome of the additional hydrogen bonds formed by Gly345 and Ser388 and hydrophobic interaction with more residues involved (His10 of compstatin and Met346, Pro347 and Gln490 of mutated C3c), which is caused by the significant secondary structure changes in the binding site of the M351T mutation structure.