Glutamine-binding protein (GlnBp) is one of the ligand-specific periplasmic binding proteins in the Escherichia coli permease systems, predicted to play an important role in transferring Gln from the pe-riplasmic space to the cytoplasmic space. In this paper, the interaction of the key residues in GlnBp with the ligand Gln and the functional difference between the two hinges in GlnBp were evaluated through molecular dynamics simulation sampling, and the binding free energy of GlnBp with Gln was calculated by the MM-PBSA method. The results show that the main impetus to bind Gln lies in the van der Waals’(VDW) interactions between Gln and Phe13, Phe50, Thr118, Ile69, as well as the electrostatic interactions between Arg75, Thr70, Asp157, Gly68, Lys115, Ala67, His156 and ligand Gln. The hinge region 85～89 whose fluctuation is larger than the hinge region 181～185 has a more flexibility which can provide a structural ba-sis to bind ligand Gln, while the main function of the hinge region 181～185 was proposed to restrict ligand Gln in the pocket of GlnBp. It is found that the result predicted with the MM-PBSA method agrees well with experimental data. The relationship between the structure and function of GlnBp is well illustrated, which provides us with some important structural information on the open-close mechanism of GlnBp and the transportation of Gln.

Key words: GlnBp, open-close motion, molecular dynamics simulation, MM-PBSA, binding free energy