Ahlawat S, Mote KR, Lakomek N-A, Agarwal V (2022) Solid-State NMR: methods for biological solids. Chem Rev 122:9643–9737. https://doi.org/10.1021/acs.chemrev.1c00852
Alderson TR, Kay LE (2020) Unveiling invisible protein States with NMR spectroscopy. Curr Opin Struct Biol 60:39–49. https://doi.org/10.1016/j.sbi.2019.10.008
Baran MC, Huang YJ, Moseley HNB, Montelione GT (2004) Automated analysis of protein NMR assignments and structures. Chem Rev 104:3541–3556. https://doi.org/10.1021/cr030408p
Barlow DJ, Thornton JM (1988) Helix geometry in proteins. J Mol Biol 201:601–619. https://doi.org/10.1016/0022-2836(88)90641-9
Benjin X, Ling L (2020) Developments, applications, and prospects of cryo-electron microscopy. Protein Sci 29:872–882. https://doi.org/10.1002/pro.3805
Bloembergen N (1948) Nuclear magnetic relaxation. Springer Netherlands, Dordrecht
Castellani F, van Rossum B, Diehl A et al (2002) Structure of a protein determined by solid-state magic-angle-spinning NMR spectroscopy. Nature 420:99–102. https://doi.org/10.1038/nature01070
Article ADS MATH Google Scholar
Choi AR, Kim SY, Yoon SR et al (2007) Substitution of Pro206 and Ser86 residues in the retinal binding pocket of Anabaena sensory rhodopsin is not sufficient for proton pumping function. J Microbiol Biotechnol 17:138–145
Comellas G, Rienstra CM (2013) Protein structure determination by Magic-Angle spinning Solid-State NMR, and insights into the formation, structure, and stability of amyloid fibrils. Annu Rev Biophys 42:515–536. https://doi.org/10.1146/annurev-biophys-083012-130356
Eilers M, Shekar SC, Shieh T et al (2000) Internal packing of helical membrane proteins. Proc Natl Acad Sci 97:5796–5801. https://doi.org/10.1073/pnas.97.11.5796
Article ADS MATH Google Scholar
Furutani Y, Kawanabe A, Jung K-H, Kandori H (2005) FTIR spectroscopy of the All-Trans form of Anabaena sensory rhodopsin at 77 K: hydrogen bond of a water between the schiff base and Asp75. Biochemistry 44:12287–12296. https://doi.org/10.1021/bi050841o
Gaponenko V, Howarth JW, Gasmi-Seabrook G et al (2000) Protein global fold determination using site‐directed spin and isotope labeling. Protein Sci 9:302–309. https://doi.org/10.1110/ps.9.2.302
García-Nafría J, Tate CG (2020) Cryo-Electron microscopy: moving beyond X-Ray crystal structures for drug receptors and drug development. Annu Rev Pharmacol Toxicol 60:51–71. https://doi.org/10.1146/annurev-pharmtox-010919-023545
Gillespie JR, Shortle D (1997) Characterization of long-range structure in the denatured state of Staphylococcal nuclease. I. paramagnetic relaxation enhancement by nitroxide spin labels1. J Mol Biol 268:158–169. https://doi.org/10.1006/jmbi.1997.0954
Good DB, Wang S, Ward ME et al (2014) Conformational dynamics of a seven transmembrane helical protein Anabaena sensory rhodopsin probed by Solid-State NMR. J Am Chem Soc 136:2833–2842. https://doi.org/10.1021/ja411633w
Goodsell DS, Zardecki C, Di Costanzo L et al (2020) RCSB protein data bank: enabling biomedical research and drug discovery. Protein Sci 29:52–65. https://doi.org/10.1002/pro.3730
Güntert P (2009) Automated structure determination from NMR spectra. Eur Biophys J 38:129–143. https://doi.org/10.1007/s00249-008-0367-z
Güntert P, Buchner L (2015) Combined automated NOE assignment and structure calculation with CYANA. J Biomol NMR 62:453–471. https://doi.org/10.1007/s10858-015-9924-9
Güntert P, Braun W, Wüthrich K (1991) Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J Mol Biol 217:517–530. https://doi.org/10.1016/0022-2836(91)90754-T
Hass MA, Ubbink M (2014) Structure determination of protein–protein complexes with long-range anisotropic paramagnetic NMR restraints. Curr Opin Struct Biol 24:45–53. https://doi.org/10.1016/j.sbi.2013.11.010
Hu Y, Cheng K, He L et al (2021) NMR-Based methods for protein analysis. Anal Chem 93:1866–1879. https://doi.org/10.1021/acs.analchem.0c03830
Iwahara J, Schwieters CD, Clore GM (2004) Ensemble approach for NMR structure refinement against 1H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule. J Am Chem Soc 126:5879–5896. https://doi.org/10.1021/ja031580d
Janik R, Peng X, Ladizhansky V (2007) 13 C–13 C distance measurements in U–13 C, 15 N-labeled peptides using rotational resonance width experiment with a homogeneously broadened matching condition. J Magn Reson 188:129–140. https://doi.org/10.1016/j.jmr.2007.06.005
Kermani AA (2021) A guide to membrane protein X-ray crystallography. FEBS J 288:5788–5804. https://doi.org/10.1111/febs.15676
Klukowski P, Riek R, Güntert P (2022) Rapid protein assignments and structures from Raw NMR spectra with the deep learning technique ARTINA. Nat Commun 13:6151. https://doi.org/10.1038/s41467-022-33879-5
Article ADS MATH Google Scholar
Kuszewski J, Schwieters CD, Garrett DS et al (2004) Completely automated, highly Error-Tolerant macromolecular structure determination from multidimensional nuclear overhauser enhancement spectra and chemical shift assignments. J Am Chem Soc 126:6258–6273. https://doi.org/10.1021/ja049786h
Lacabanne D, Orelle C, Lecoq L et al (2019) Flexible-to-rigid transition is central for substrate transport in the ABC transporter BmrA from Bacillus subtilis. Commun Biol 2:1–9. https://doi.org/10.1038/s42003-019-0390-x
Ladizhansky V (2017) Applications of solid-state NMR to membrane proteins. Biochim Biophys Acta BBA - Proteins Proteom 1865:1577–1586. https://doi.org/10.1016/j.bbapap.2017.07.004
Ladizhansky V, Palani RS, Mardini M, Griffin RG (2024) Dipolar recoupling in rotating solids. Chem Rev 124:12844–12917. https://doi.org/10.1021/acs.chemrev.4c00373
Laurents DV (2022) AlphaFold 2 and NMR spectroscopy: partners to understand protein structure, dynamics and function. Front Mol Biosci 9. https://doi.org/10.3389/fmolb.2022.906437
Lee S, Chirikjian GS (2004) Interhelical angle and distance preferences in globular proteins. Biophys J 86:1105. https://doi.org/10.1016/S0006-3495(04)74185-5
Liang B, Bushweller JH, Tamm LK (2006) Site-Directed parallel Spin-Labeling and paramagnetic relaxation enhancement in structure determination of membrane proteins by solution NMR spectroscopy. J Am Chem Soc 128:4389–4397. https://doi.org/10.1021/ja0574825
Maciejewski MW, Schuyler AD, Gryk MR et al (2017) NMRbox: A resource for biomolecular NMR computation. Biophys J 112:1529–1534. https://doi.org/10.1016/j.bpj.2017.03.011
Mandala VS, Williams JK, Hong M (2018) Structure and dynamics of membrane proteins from Solid-State NMR. Annu Rev Biophys 47:201–222. https://doi.org/10.1146/annurev-biophys-070816-033712
Manolikas T, Herrmann T, Meier BH (2008) Protein structure determination from 13 C Spin-Diffusion Solid-State NMR spectroscopy. J Am Chem Soc 130:3959–3966. https://doi.org/10.1021/ja078039s
Maveyraud L, Mourey L (2020) Protein X-ray crystallography and drug discovery. Molecules 25:1030. https://doi.org/10.3390/molecules25051030
Milikisiyants S, Wang S, Munro RA et al (2017) Oligomeric structure of Anabaena sensory rhodopsin in a lipid bilayer environment by combining Solid-State NMR and Long-range DEER constraints. J Mol Biol 429:1903–1920. https://doi.org/10.1016/j.jmb.2017.05.005
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