Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis

• Published in: Angewandte Chemie International Edition Vol. 55; no. 45; pp. 13990 - 13994
• Main Authors: Feng, Yitao, Zhang, Lu, Wu, Shaowen, Liu, Zhijun, Gao, Xin, Zhang, Xu, Liu, Maili, Liu, Jianwei, Huang, Xuhui, Wang, Wenning
• Format: Journal Article
• Language: English
• Published: Germany Blackwell Publishing Ltd 02-11-2016; Wiley Subscription Services, Inc
• Edition: International ed. in English
• Subjects: Carrier Proteins - chemistry; conformational dynamics; Crystal structure; Fluorescence Resonance Energy Transfer; FRET; Glutamine - chemistry; molecular dynamics; Molecular Dynamics Simulation; NMR spectroscopy; Nuclear Magnetic Resonance, Biomolecular; Protein Conformation; protein folding; FRET; protein folding; NMR spectroscopy; molecular dynamics; conformational dynamics
• ISSN: 1433-7851; 1521-3773
• DOI: 10.1002/anie.201606613

The glutamine binding protein (GlnBP) binds l‐glutamine and cooperates with its cognate transporters during glutamine uptake. Crystal structure analysis has revealed an open and a closed conformation for apo‐ and holo‐GlnBP, respectively. However, the detailed conformational dynamics have remained unclear. Herein, we combined NMR spectroscopy, MD simulations, and single‐molecule FRET techniques to decipher the conformational dynamics of apo‐GlnBP. The NMR residual dipolar couplings of apo‐GlnBP were in good agreement with a MD‐derived structure ensemble consisting of four metastable states. The open and closed conformations are the two major states. This four‐state model was further validated by smFRET experiments and suggests the conformational selection mechanism in ligand recognition of GlnBP.
Beyond the two‐state model: By combining NMR residual dipolar coupling studies, MD simulations, Markov state model analysis, and single‐molecule FRET, four conformational states were identified that underlie the conformational dynamics of apo‐GlnBP. An MD‐derived conformational ensemble consisting of four metastable states was in good agreement with the experimental data.