June 24, Mon 2013
1:00 pm, MRB 200 Conference Room
Dr. Jooyoung Lee
Center for In Silico Protein Science, Korea Institute for Advanced Study
High-accuracy protein structure modeling and its application to molecular replacement of crystal phasing
We have solved the crystal structures of predicted fructose-specific enzyme IIBfruc fromEscherichia coli (EcEIIBfruc) and d-glycero-d-manno-heptose-1,7-bisphosphate phosphatase from Burkholderia thailandensis (BtGmhB) of which the X-ray data contain various crystallographic problems. The bottleneck of the structural determination by X-ray crystallography was the phasing of the diffraction data. The obstacles were overcome by molecular replacement (MR) using the GOT (Global-Optimization-based Template-based modeling of proteins) models combined with the exhaustive search by brute-force automation of phasing trials. The determined crystal structure of EcEIIBfruc reveals that the core structure of the protein resembles that of enzyme IIBcellobiose from E. coli(EcIIBcel). The spatially aligned conserved residues of Cys10 and Thr17 of EcEIIBfruc with those of EcIIBcel suggest that the catalytic mechanism of EcEIIBfruc is similar to that ofEcIIBcel. The crystal structure of metal-free BtGmhB shows the importance of zinc and magnesium ions for both structural and functional reasons. This study suggests that the current computational approach can be applied to many unsolved MR problems where better 3D protein models are required or/and the MR solution is limited by the ambiguity in the crystallographic data.