Saturation transfer difference NMR on the integral trimeric membrane transport protein GltPh determines cooperative substrate binding.
Amino Acid Transport Systems
/ metabolism
Animals
Aspartic Acid
/ metabolism
Biological Transport
/ physiology
Glutamic Acid
/ metabolism
Hydrogen-Ion Concentration
Kinetics
Magnetic Resonance Spectroscopy
/ methods
Mammals
/ metabolism
Membrane Proteins
/ metabolism
Membrane Transport Proteins
/ metabolism
Proteolipids
/ metabolism
Pyrococcus horikoshii
/ metabolism
Substrate Specificity
/ physiology
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
05 10 2020
05 10 2020
Historique:
received:
06
07
2020
accepted:
04
09
2020
entrez:
6
10
2020
pubmed:
7
10
2020
medline:
5
1
2021
Statut:
epublish
Résumé
Saturation-transfer difference (STD) NMR spectroscopy is a fast and versatile method which can be applied for drug-screening purposes, allowing the determination of essential ligand binding affinities (K
Identifiants
pubmed: 33020522
doi: 10.1038/s41598-020-73443-z
pii: 10.1038/s41598-020-73443-z
pmc: PMC7536232
doi:
Substances chimiques
Amino Acid Transport Systems
0
Membrane Proteins
0
Membrane Transport Proteins
0
Proteolipids
0
proteoliposomes
0
Aspartic Acid
30KYC7MIAI
Glutamic Acid
3KX376GY7L
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
16483Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/M011216/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/P010660/1
Pays : United Kingdom
Organisme : Austrian Science Fund FWF
ID : F3524
Pays : Austria
Organisme : Austrian Science Fund FWF
ID : F3506
Pays : Austria
Références
Danbolt, N. C. Glutamate uptake. Prog. Neurobiol. 65, 1–105 (2001).
pubmed: 11369436
doi: 10.1016/S0301-0082(00)00067-8
pmcid: 11369436
Owe, S. G., Marcaggi, P. & Attwell, D. The ionic stoichiometry of the GLAST glutamate transporter in salamander retinal glia. J. Physiol. 577, 591–599 (2006).
pubmed: 17008380
pmcid: 1890427
doi: 10.1113/jphysiol.2006.116830
Zerangue, N. & Kavanaugh, M. P. Flux coupling in a neuronal glutamate transporter. Nature 383, 634–637 (1996).
pubmed: 8857541
doi: 10.1038/383634a0
pmcid: 8857541
Fairman, W. A., Vandenberg, R. J., Arriza, J. L., Kavanaught, M. P. & Amara, S. G. An excitatory amino-acid transporter with properties of a ligand-gated chloride channel. Nature 375, 599–603 (1995).
pubmed: 7791878
doi: 10.1038/375599a0
pmcid: 7791878
Canul-Tec, J. C. et al. Structure and allosteric inhibition of excitatory amino acid transporter 1. Nature 544, 446–451 (2017).
pubmed: 28424515
pmcid: 5410168
doi: 10.1038/nature22064
Yernool, D., Boudker, O., Jin, Y. & Gouaux, E. Structure of a glutamate transporter homologue from Pyrococcus horikoshii. Nature 431, 811–818 (2004).
pubmed: 15483603
doi: 10.1038/nature03018
pmcid: 15483603
Jensen, S., Guskov, A., Rempel, S., Hänelt, I. & Slotboom, D. J. Crystal structure of a substrate-free aspartate transporter. Nat. Struct. Mol. Biol. 20, 1224–1227 (2013).
pubmed: 24013209
doi: 10.1038/nsmb.2663
pmcid: 24013209
Garaeva, A. A. et al. Cryo-EM structure of the human neutral amino acid transporter ASCT2. Nat. Struct. Mol. Biol. 25, 515–521 (2018).
pubmed: 29872227
doi: 10.1038/s41594-018-0076-y
pmcid: 29872227
Ji, Y., Postis, V. L. G., Wang, Y., Bartlam, M. & Goldman, A. Transport mechanism of a glutamate transporter homologue GltPh. Biochem. Soc. Trans. 44, 898–904 (2016).
pubmed: 27284058
pmcid: 4900748
doi: 10.1042/BST20160055
Boudker, O., Ryan, R. M., Yernool, D., Shimamoto, K. & Gouaux, E. Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter. Nature 445, 387–393 (2007).
pubmed: 17230192
doi: 10.1038/nature05455
pmcid: 17230192
Reyes, N., Ginter, C. & Boudker, O. Transport mechanism of a bacterial homologue of glutamate transporters. Nature 462, 880–885 (2009).
pubmed: 19924125
pmcid: 2934767
doi: 10.1038/nature08616
Akyuz, N. et al. Transport domain unlocking sets the uptake rate of an aspartate transporter. Nature 518, 68–73 (2015).
pubmed: 25652997
pmcid: 4351760
doi: 10.1038/nature14158
Verdon, G. & Boudker, O. Crystal structure of an asymmetric trimer of a bacterial glutamate transporter homolog. Nat. Struct. Mol. Biol. 19, 355–357 (2012).
pubmed: 22343718
pmcid: 3633560
doi: 10.1038/nsmb.2233
Psakis, G. et al. Expression screening of integral membrane proteins from Helicobacter pylori 26695. Protein Sci. 16, 2667–2676 (2007).
pubmed: 17965189
pmcid: 2222815
doi: 10.1110/ps.073104707
Hänelt, I., Jensen, S., Wunnicke, D. & Slotboom, D. J. Low affinity and slow Na+ binding precedes high affinity aspartate binding in the secondary-active transporter GltPh. J. Biol. Chem. 290, 15962–15972 (2015).
pubmed: 25922069
pmcid: 4481202
doi: 10.1074/jbc.M115.656876
Silverstein, N., Ewers, D., Forrest, L. R., Fahlke, C. & Kanner, B. I. Molecular determinants of substrate specificity in sodium-coupled glutamate transporters. J. Biol. Chem. 290, 28988–28996 (2015).
pubmed: 26475859
pmcid: 4661411
doi: 10.1074/jbc.M115.682666
Reyes, N., Oh, S. & Boudker, O. Binding thermodynamics of a glutamate transporter homolog. Nat. Struct. Mol. Biol. 20, 634–640 (2013).
pubmed: 23563139
pmcid: 3711778
doi: 10.1038/nsmb.2548
Venkatesan, S. K. et al. Refinement of the central steps of substrate transport by the aspartate transporter GltPh: Elucidating the role of the Na2 sodium binding site. PLoS Comput. Biol. 11, 2 (2015).
doi: 10.1371/journal.pcbi.1004551
Mayer, M. & Meyer, B. Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew. Chemie - Int. Ed. 38, 1784–1788 (1999).
doi: 10.1002/(SICI)1521-3773(19990614)38:12<1784::AID-ANIE1784>3.0.CO;2-Q
Mayer, M. & Meyer, B. Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. J. Am. Chem. Soc. 123, 6108–6117 (2001).
pubmed: 11414845
doi: 10.1021/ja0100120
pmcid: 11414845
Viegas, A., Manso, J., Nobrega, F. L. & Cabrita, E. J. Saturation-transfer difference (STD) NMR: A simple and fast method for ligand screening and characterization of protein binding. J. Chem. Educ. 88, 990–994 (2011).
doi: 10.1021/ed101169t
Mari, S., Serrano-Gómez, D., Cañada, F. J., Corbí, A. L. & Jiménez-Barbero, J. 1D saturation transfer difference NMR experiments on living cells: The DC-SIGN/oligomannose interaction. Angew. Chemie Int. Ed. 44, 296–298 (2004).
doi: 10.1002/anie.200461574
Claasen, B., Axmann, M., Meinecke, R. & Meyer, B. Direct observation of ligand binding to membrane proteins in living cells by a saturation transfer double difference (STDD) NMR spectroscopy method shows a significantly higher affinity of integrin αIIbβ 3 in native platelets than in liposomes. J. Am. Chem. Soc. 127, 916–919 (2005).
pubmed: 15656629
doi: 10.1021/ja044434w
pmcid: 15656629
Airoldi, C., Giovannardi, S., Laferla, B., Jiménez-Barbero, J. & Nicotra, F. Saturation transfer difference NMR experiments of membrane proteins in living cells under HR-MAS conditions: The interaction of the SGLT1 co-transporter with its ligands. Chem. A Eur. J. 17, 13395–13399 (2011).
doi: 10.1002/chem.201102181
Cox, B. D. et al. Structural analysis of CXCR4—Antagonist interactions using saturation-transfer double-difference NMR. Biochem. Biophys. Res. Commun. 466, 28–32 (2015).
pubmed: 26301631
doi: 10.1016/j.bbrc.2015.08.084
pmcid: 26301631
Venkitakrishnan, R. P., Benard, O., Max, M., Markley, J. L. & Assadi-Porter, F. M. Use of NMR Saturation Transfer Difference Spectroscopy to Study Ligand Binding to Membrane Proteins. In Membrane Protein Structure and Dynamics 47–63 (Humana Press, Totowa, 2012).
doi: 10.1007/978-1-62703-023-6_4
Meinecke, R. & Meyer, B. Determination of the binding specificity of an integral membrane protein by saturation transfer difference NMR: RGD peptide ligands binding to integrin αIIbβ3. J. Med. Chem. 44, 3059–3065 (2001).
pubmed: 11543674
doi: 10.1021/jm0109154
pmcid: 11543674
Fredriksson, K. et al. Nanodiscs for INPHARMA NMR characterization of GPCRs: Ligand binding to the Human A2A Adenosine Receptor. Angew. Chemie Int. Ed. 56, 5750–5754 (2017).
doi: 10.1002/anie.201612547
Igonet, S. et al. Enabling STD-NMR fragment screening using stabilized native GPCR: A case study of adenosine receptor. Sci. Rep. 8, 1–14 (2018).
doi: 10.1038/s41598-018-26113-0
Yong, K. J. et al. Determinants of ligand subtype-selectivity at α 1A-Adrenoceptor revealed using saturation transfer difference (STD) NMR. ACS Chem. Biol. 13, 1090–1102 (2018).
pubmed: 29537256
doi: 10.1021/acschembio.8b00191
pmcid: 29537256
Vaid, T. M., Chalmers, D. K., Scott, D. J. & Gooley, P. INPHARMA based determination of ligand binding modes at α1-adrenergic receptors explains the molecular basis of subtype selectivity. Chem. A Eur. J. https://doi.org/10.1002/chem.202000642 (2020).
doi: 10.1002/chem.202000642
Bumbak, F. et al. Conformational changes in tyrosine 11 of neurotensin are required to activate the neurotensin receptor 1. ACS Pharmacol. Transl. Sci. https://doi.org/10.1021/acsptsci.0c00026 (2020).
doi: 10.1021/acsptsci.0c00026
pubmed: 32832871
pmcid: 32832871
Koch, H. P. & Larsson, H. P. Small-scale molecular motions accomplish glutamate uptake in human glutamate transporters. J. Neurosci. 25, 1730–1736 (2005).
pubmed: 15716409
pmcid: 6725926
doi: 10.1523/JNEUROSCI.4138-04.2005
Grewer, C. et al. The individual subunits of the glutamate transporter EAAC1 homotrimer function independently of each other. Biochemistry 44, 11913–11923 (2005).
pubmed: 16128593
pmcid: 2459315
doi: 10.1021/bi050987n
Erkens, G. B., Hänelt, I., Goudsmits, J. M. H., Slotboom, D. J. & Van Oijen, A. M. Unsynchronised subunit motion in single trimeric sodium-coupled aspartate transporters. Nature 502, 119–123 (2013).
pubmed: 24091978
doi: 10.1038/nature12538
pmcid: 24091978
Ruan, Y. et al. Direct visualization of glutamate transporter elevator mechanism by high-speed AFM. Proc. Natl. Acad. Sci. USA. 114, 1584–1588 (2017).
pubmed: 28137870
doi: 10.1073/pnas.1616413114
pmcid: 28137870
Claridge, T. D. W. High-Resolution NMR Techniques in Organic Chemistry. In Protein-Ligand Screening by NMR 421–455 (Elsevier Inc., Amsterdam, 2016).
Angulo, J., Enríquez-Navas, P. M. & Nieto, P. M. Ligand-receptor binding affinities from saturation transfer difference (STD) NMR. Chem. A Eur. J. 16, 7803–7812 (2010).
doi: 10.1002/chem.200903528
Wang, Y., Sen Liu, D. & Wyss, D. F. Competition STD NMR for the detection of high-affinity ligands and NMR-based screening. Magn. Reson. Chem. 42, 485–489 (2004).
pubmed: 15137040
doi: 10.1002/mrc.1381
pmcid: 15137040
Cantor, C. R. & Schimmel, P. R. Biophysical Chemistry: Part III. In Ligand interactions at equilibrium 849–1371 (WH Freeman and Co., Oxford, 1980).
Cheng, Y. & Prusoff, W. H. Relationship between the inhibition constant (KI) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction. Biochem. Pharmacol. 22, 3099–3108 (1973).
pubmed: 4202581
doi: 10.1016/0006-2952(73)90196-2
pmcid: 4202581
Postis, V. et al. The use of SMALPs as a novel membrane protein scaffold for structure study by negative stain electron microscopy. Biochim. Biophys. Acta Biomembr. 1848, 496–501 (2015).
doi: 10.1016/j.bbamem.2014.10.018
Vold, R. L., Waugh, J. S., Klein, M. P. & Phelps, D. E. Measurement of spin relaxation in complex systems. J. Chem. Phys. 48, 3831–3832 (1968).
doi: 10.1063/1.1669699