Abstract

Article info 2015 3 (3)    003  (03)   pp.  123 ~ 130
Title High-accuracy protein structure modeling and its application to molecular replacement of crystallographic phasing
Authors Keehyung Joo1,+, Mi-Sun Kim2,+, Jimin Park2,+, Jooyoung Lee1,* and Dong Hae Shin2,*
Institutions 1Center for in silico Protein Science and School of Computational Sciences, Korea Institute for Advanced Study, Seoul 130-722, Korea, 2Collegy of Pharmacy and Graduate School of Pharmaceutical Sciences, Global Top5 Research Program, Ewha Womans University, Seoul 120-750, Korea. *Correspondence: dhshin55@ewha.ac.kr, jlee@kias.re.kr +These authors contributed equally to this work.
Abstract We have solved the crystal structures of predicted fructose-specific enzyme IIBfruc from Escherichia 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 bruteforce automation of phasing trials. 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.