An efficient perturbation method to predict the functionally key sites of glutamine binding protein |
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| Affiliation: | 1. Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, SK-812 37 Bratislava, Slovak Republic;2. Department of Chemistry, Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Trieda A. Hlinku 1, SK-949 74 Nitra, Slovak Republic;3. LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal;4. Institute of Organic Chemistry, Catalysis and Petrochemistry, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, SK-812 37 Bratislava, Slovak Republic;1. Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK;1. Japan Fine Ceramics Center, 2-4-1 Mutsuno, Atsuta-ku, Nagoya, Aichi 456-8587, Japan;2. Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan;3. Japan Atomic Energy Agency, 4002 Narita-cho, Oarai-machi, Ibaraki 311-1393, Japan;1. Mechanical Engineering Department, American University of Beirut, Beirut, Lebanon;2. Department of Civil Engineering, The University of Jordan, Queen Rania Street, Amman, Jordan;1. Department of Emergency, Xiamen Hospital of Traditional Chinese Medicine, Xiamen 361009, Fujian, PR China;2. Department of Medicine, Shandong Medical College, Jinan, 250002, Shandong, PR China;3. Department of Spine (Second), Traditional Chinese Medical Hospital of Xinjiang Uygur Autonomous Region, Urumqi, 830000, Xinjiang, PR China;4. Nuclear Medicine Department, Qilu Hospital of Shandong University, NO. 107 Wenhua West Road, Jinan, 250012, Shandong PR China;1. Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland;2. Department of Medical Chemistry, Medical University of Gdańsk, Dębinki 1, 80-211, Gdańsk, Poland |
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| Abstract: | Glutamine-Binding Protein (GlnBP) of Escherichia coli, an important member of the periplasmic binding protein family, is responsible for the first step in the active transport of glutamine across the cytoplasmic membrane. In this work, the functionally key regulation sites of GlnBP were identified by utilizing a perturbation method proposed by our group, in which the residues whose perturbations markedly change the binding free energy between GlnBP and glutamine are considered to be functionally key residues. The results show that besides the substrate binding sites, some other residues distant from the binding pocket, including the ones in the hinge regions between the two domains, the front- and back- door channels and the exposed region, are important for the function of glutamine binding and transport. The predicted results are well consistent with the theoretical and experimental data, which indicates that our method is an effective approach to identify the key residues important for both ligand binding and long-range allosteric signal transmission. This work can provide some insights into the function performance of GlnBP and the physical mechanism of its allosteric regulation. |
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| Keywords: | Glutamine binding protein Gaussian network model Thermodynamic cycle Key residues Conformational transition |
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