Use of paramagnetic
Journal
Nature chemical biology
ISSN: 1552-4469
Titre abrégé: Nat Chem Biol
Pays: United States
ID NLM: 101231976
Informations de publication
Date de publication:
09 2020
09 2020
Historique:
received:
02
12
2019
accepted:
07
05
2020
pubmed:
10
6
2020
medline:
18
11
2020
entrez:
10
6
2020
Statut:
ppublish
Résumé
In proteins where conformational changes are functionally important, the number of accessible states and their dynamics are often difficult to establish. Here we describe a novel
Identifiants
pubmed: 32514183
doi: 10.1038/s41589-020-0561-6
pii: 10.1038/s41589-020-0561-6
pmc: PMC7442671
mid: NIHMS1592417
doi:
Substances chimiques
Amino Acid Transport System X-AG
0
Fluorine
284SYP0193
Histidine
4QD397987E
Nickel
7OV03QG267
Cysteine
K848JZ4886
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1006-1012Subventions
Organisme : NINDS NIH HHS
ID : R01 NS064357
Pays : United States
Organisme : NIH HHS
ID : S10 OD018509
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : NIA NIH HHS
ID : R37 AG019391
Pays : United States
Organisme : NINDS NIH HHS
ID : R37 NS085318
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM118302
Pays : United States
Commentaires et corrections
Type : CommentIn
Références
Palmer, A. G. Enzyme dynamics from NMR spectroscopy. Acc. Chem. Res. 48, 457–465 (2015).
pubmed: 25574774
pmcid: 4334254
doi: 10.1021/ar500340a
Pervushin, K., Riek, R., Wider, G. & Wuthrich, K. Attenuated T
pubmed: 9356455
doi: 10.1073/pnas.94.23.12366
pmcid: 24947
Jiang, Y. & Kalodimos, C. G. NMR studies of large proteins. J. Mol. Biol. 429, 2667–2676 (2017).
pubmed: 28728982
doi: 10.1016/j.jmb.2017.07.007
Danielson, M. A. & Falke, J. J. Use of
pubmed: 8800468
pmcid: 2899692
doi: 10.1146/annurev.bb.25.060196.001115
Susac, L., Eddy, M. T., Didenko, T., Stevens, R. C. & Wuthrich, K. A2A adenosine receptor functional states characterized by
pubmed: 30463958
doi: 10.1073/pnas.1813649115
pmcid: 6294957
Manglik, A. et al. Structural insights into the dynamic process of β2-adrenergic receptor signaling. Cell 161, 1101–1111 (2015).
pubmed: 25981665
pmcid: 4441853
doi: 10.1016/j.cell.2015.04.043
Di Pietrantonio, C., Pandey, A., Gould, J., Hasabnis, A. & Prosser, R. S. Understanding protein function through an ensemble description: characterization of functional states by
pubmed: 30638528
doi: 10.1016/bs.mie.2018.09.029
Yernool, D., Boudker, O., Folta-Stogniew, E. & Gouaux, E. Trimeric subunit stoichiometry of the glutamate transporters from Bacillus caldotenax and Bacillus stearothermophilus. Biochemistry 42, 12981–12988 (2003).
pubmed: 14596613
doi: 10.1021/bi030161q
Danbolt, N. C. Glutamate uptake. Prog. Neurobiol. 65, 1–105 (2001).
pubmed: 11369436
doi: 10.1016/S0301-0082(00)00067-8
Zerangue, N. & Kavanaugh, M. P. Flux coupling in a neuronal glutamate transporter. Nature 383, 634–637 (1996).
pubmed: 8857541
doi: 10.1038/383634a0
Levy, L. M., Warr, O. & Attwell, D. Stoichiometry of the glial glutamate transporter GLT-1 expressed inducibly in a Chinese hamster ovary cell line selected for low endogenous Na-dependent glutamate uptake. J. Neurosci. 18, 9620–9628 (1998).
pubmed: 9822723
pmcid: 6793325
doi: 10.1523/JNEUROSCI.18-23-09620.1998
Akyuz, N., Altman, R. B., Blanchard, S. C. & Boudker, O. Transport dynamics in a glutamate transporter homologue. Nature 502, 114–118 (2013).
pubmed: 23792560
pmcid: 3829612
doi: 10.1038/nature12265
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
Liu, J. J., Horst, R., Katritch, V., Stevens, R. C. & Wuthrich, K. Biased signaling pathways in β2-adrenergic receptor characterized by
pubmed: 22267580
pmcid: 3292700
doi: 10.1126/science.1215802
Clore, G. M. & Iwahara, J. Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. Chem. Rev. 109, 4108–4139 (2009).
pubmed: 19522502
pmcid: 2825090
doi: 10.1021/cr900033p
Bondarenko, V. et al.
pubmed: 31525026
pmcid: 7092367
Solomon, I. Relaxation processes in a system of two spins. Phys. Rev. 99, 559–565 (1955).
doi: 10.1103/PhysRev.99.559
Bloembergen, N. Proton relaxation times in paramagnetic solutions. J. Chem. Phys. 27, 572–573 (1957).
doi: 10.1063/1.1743771
Matei, E. & Gronenborn, A. M.
doi: 10.1002/anie.201508464
Hull, W. E. & Sykes, B. D. Fluorotyrosine alkaline phosphatase: internal mobility of individual tyrosines and the role of chemical shift anisotropy as a
pubmed: 1195374
doi: 10.1016/S0022-2836(75)80105-7
Hull, W. E. & Sykes, B. D. Dipolar nuclear spin relaxation of
doi: 10.1063/1.431367
Gerig, J. T. Fluorine-proton Overhauser effects in fluorine-labeled macromolecular systems. J. Am. Chem. Soc. 99, 1721–1725 (1977).
doi: 10.1021/ja00448a006
Todd, R. J., Van Dam, M. E., Casimiro, D., Haymore, B. L. & Arnold, F. H. Cu(II)-binding properties of a cytochrome c with a synthetic metal-binding site: His-X3-His in an α-helix. Proteins 10, 156–161 (1991).
pubmed: 1654548
doi: 10.1002/prot.340100209
Didenko, T., Liu, J. J., Horst, R., Stevens, R. C. & Wuthrich, K. Fluorine-19 NMR of integral membrane proteins illustrated with studies of GPCRs. Curr. Opin. Struct. Biol. 23, 740–747 (2013).
pubmed: 23932201
pmcid: 3805696
doi: 10.1016/j.sbi.2013.07.011
McIlwain, B. C., Vandenberg, R. J. & Ryan, R. M. Characterization of the inward- and outward-facing substrate binding sites of the prokaryotic aspartate transporter, GltPh. Biochemistry 55, 6801–6810 (2016).
pubmed: 27951659
doi: 10.1021/acs.biochem.6b00795
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
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: 5320997
Georgieva, E. R., Borbat, P. P., Ginter, C., Freed, J. H. & Boudker, O. Conformational ensemble of the sodium-coupled aspartate transporter. Nat. Struct. Mol. Biol. 20, 215–221 (2013).
pubmed: 23334289
pmcid: 3565060
doi: 10.1038/nsmb.2494
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
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
Suh, S.-S., Haymore, B. L. & Arnold, F. H. Characterization of His-X3-His sites in α-helices of synthetic metal-binding bovine somatotropin. Protein Eng. Des. Sel. 4, 301–305 (1991).
doi: 10.1093/protein/4.3.301
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
Machtens, J. P. et al. Mechanisms of anion conduction by coupled glutamate transporters. Cell 160, 542–553 (2015).
pubmed: 25635461
doi: 10.1016/j.cell.2014.12.035
Cavanagh, J., Fairbrother, W. J., Palmer, A. G., Rance, M. & Skelton, N. J. in Protein NMR Spectroscopy 2nd edn 333–404 (Academic Press, 2007).
Mayer, M. & Meyer, B. Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew. Chem. Int. Ed. 38, 1784–1788 (1999).
doi: 10.1002/(SICI)1521-3773(19990614)38:12<1784::AID-ANIE1784>3.0.CO;2-Q
Spoerner, M. et al. Conformational states of human rat sarcoma (Ras) protein complexed with its natural ligand GTP and their role for effector interaction and GTP hydrolysis. J. Biol. Chem. 285, 39768–39778 (2010).
pubmed: 20937837
pmcid: 3000958
doi: 10.1074/jbc.M110.145235
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
Ye, L., Van Eps, N., Zimmer, M., Ernst, O. P. & Prosser, R. S. Activation of the A2A adenosine G-protein-coupled receptor by conformational selection. Nature 533, 265–268 (2016).
pubmed: 27144352
doi: 10.1038/nature17668
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
Sali, A. & Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779–815 (1993).
pubmed: 8254673
doi: 10.1006/jmbi.1993.1626
Jo, S., Lim, J. B., Klauda, J. B. & Im, W. CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys. J. 97, 50–58 (2009).
pubmed: 19580743
pmcid: 2711372
doi: 10.1016/j.bpj.2009.04.013
Klauda, J. B. et al. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J. Phys. Chem. B 114, 7830–7843 (2010).
pubmed: 20496934
pmcid: 2922408
doi: 10.1021/jp101759q
Shi, L., Quick, M., Zhao, Y., Weinstein, H. & Javitch, J. A. The mechanism of a neurotransmitter:sodium symporter—inward release of Na
pubmed: 18570870
pmcid: 2826427
doi: 10.1016/j.molcel.2008.05.008
Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781–1802 (2005).
pubmed: 16222654
pmcid: 2486339
doi: 10.1002/jcc.20289
Essmann, U. et al. A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577–8593 (1995).
doi: 10.1063/1.470117
Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).
pubmed: 8744570
doi: 10.1016/0263-7855(96)00018-5
McGibbon, RobertT. et al. MDTraj: a modern open library for the analysis of molecular dynamics trajectories. Biophys. J. 109, 1528–1532 (2015).
pubmed: 26488642
pmcid: 4623899
doi: 10.1016/j.bpj.2015.08.015
Ritchie, T. K. et al. Reconstitution of membrane proteins in phospholipid bilayer nanodiscs. Methods Enzymol. 464, 211–231 (2009).
pubmed: 19903557
pmcid: 4196316
doi: 10.1016/S0076-6879(09)64011-8
Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).
pubmed: 16182563
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
pubmed: 28250466
pmcid: 5494038
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
pubmed: 26278980
pmcid: 6760662
doi: 10.1016/j.jsb.2015.08.008
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife 7, 42166 (2018).
doi: 10.7554/eLife.42166
Voss, N. R., Yoshioka, C. K., Radermacher, M., Potter, C. S. & Carragher, B. DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy. J. Struct. Biol. 166, 205–213 (2009).
pubmed: 19374019
pmcid: 2768396
doi: 10.1016/j.jsb.2009.01.004
Lander, G. C. et al. Appion: an integrated, database-driven pipeline to facilitate EM image processing. J. Struct. Biol. 166, 95–102 (2009).
pubmed: 19263523
pmcid: 2775544
doi: 10.1016/j.jsb.2009.01.002
Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EM density maps. Nat. Methods 11, 63–65 (2014).
pubmed: 24213166
doi: 10.1038/nmeth.2727
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
doi: 10.1002/jcc.20084
pubmed: 15264254
Afonine, P. V. et al. phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J. Appl. Crystallogr. 43, 669–676 (2010).
pubmed: 20648263
pmcid: 2906258
doi: 10.1107/S0021889810015608
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
pubmed: 20383002
pmcid: 2852313
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).
pubmed: 20057044