Journal of Data Mining in Genomics & Proteomics

Abstract

Structural Characterization of FAD-binding Domain of CglE, a Putative Dehydrolipoamide Dehydrogenase in Meningitic E. coli K1

Yi-Ming Wang and Hong Cao

To characterize the structural features of FAD-binding domain of E. coli K1 CglE, a dehydrolipoamide dehydrogenase (DLDH) by homology modeling. Sequence similarity of N-terminal residues 1-70 with the a-subunit of FAD-binding domain from CglE of E. coli K1 and other DLDHs provided a basis for the design of the FAD-binding domain of CglE. As a result of finding no single satisfied template for the homology modeling for CglE, two templates (PDB code 2q7vA and 1jehA) were obtained by an online homology modeling procedure for multi-templates modeling. To obtain a high quality target protein, a computational bioinformatic software Accelrys Discovery Studio client 2.5 and several automated online servers were utilized. Due to the relatively low identity of the alignments, two templates were taken into consideration attempting to improve the homology model. The quality of the refined model was assessed on the basis of both geometric and energetic aspects including MD simulations, energy minimizations, Ramachandran Plot and other measurements.