Abstract
Sulfur-containing sites in proteins are of great importance for both protein structure and function, including enzymatic catalysis, signaling pathways, and recognition of ligands and protein partners. Selenium-77 is an NMR active spin-1/2 nucleus that shares many physiochemical properties with sulfur and can be readily introduced into proteins at sulfur sites without significant perturbations to the protein structure. The sulfur-containing amino acid methionine is commonly found at protein–protein or protein–ligand binding sites. Its selenium-containing counterpart, selenomethionine, has a broad chemical shift dispersion useful for NMR-based studies of complex systems. Methods such as (1H)-77Se-13C double cross polarization or {77Se}-13C REDOR could be valuable to map the local environment around selenium sites in proteins but have not been demonstrated to date. In this work, we explore these dipolar transfer mechanisms for structural characterization of the GB1 V39SeM variant of the model protein GB1 and demonstrate that 77Se-13C based correlations can be used to map the local environment around selenium sites in proteins. We have found that the general detection limit is ~ 5 Å, but longer range distances up to ~ 7 Å can be observed as well. This study establishes a framework for the future characterization of selenium sites at protein–protein or protein–ligand binding interfaces.
Data availability
All data generated or analyzed during this study are included in this published article (and its supplementary information files). Original data is available upon request from the corresponding author.
References
Andreas LB et al (2016) Structure of fully protonated proteins by proton-detected magic-angle spinning NMR. Proc Natl Acad Sci 113:9187
Bak M, Rasmussen JT, Nielsen NC (2000) SIMPSON: a general simulation program for solid-state NMR spectroscopy. J Magn Reson 147:296–330
Baldus M, Petkova AT, Herzfeld J, Griffin RG (1998) Cross polarization in the tilted frame: assignment and spectral simplification in heteronuclear spin systems. Mol Phys 95:1197–1207
Beno BR, Yeung K-S, Bartberger MD, Pennington LD, Meanwell NA (2015) A survey of the role of noncovalent sulfur interactions in drug design. J Med Chem 58:4383–4438
Bertani P, Raya J, Bechinger B (2014) 15N chemical shift referencing in solid state NMR. Solid State Nucl Magn Reson 61–62:15–18
Boles JO, Tolleson WH, Schmidt JC, Dunlap RB, Odom JD (1992) Selenomethionyl dihydrofolate-reductase from Escherichia coli—comparative biochemistry and se-77 nuclear-magnetic-resonance spectroscopy. J Biol Chem 267:22217–22223
Chen H, Viel S, Ziarelli F, Peng L (2013) 19F NMR: a valuable tool for studying biological events. Chem Soc Rev 42:7971–7982
Chen Q et al (2020) 77Se NMR probes the protein environment of selenomethionine. J Phys Chem B 124:601–616
Duddeck H (1995) Selenium-77 nuclear magnetic resonance spectroscopy. Prog Nucl Magn Reson Spectrosc 27:1–323
Etzkorn M, Böckmann A, Lange A, Baldus M (2004) Probing molecular interfaces using 2D magic-angle-spinning NMR on protein mixtures with different uniform labeling. J Am Chem Soc 126:14746–14751
Gajda J et al (2006) Structure and dynamics of L-selenomethionine in the solid state. J Phys Chem B 110:25692–25701
Gullion T, Schaefer J (1989) Rotational-echo double-resonance NMR. J Magn Reson 1969(81):196–200
Guo C, Hou G, Lu X, Polenova T (2017) Mapping protein–protein interactions by double-REDOR-filtered magic angle spinning NMR spectroscopy. J Biomol NMR 67:95–108
Hatfield DL, Tsuji PA, Carlson BA, Gladyshev VN (2014) Selenium and selenocysteine: roles in cancer, health, and development. Trends Biochem Sci 39:112–120
Hou G, Yan S, Trébosc J, Amoureux J-P, Polenova T (2013) Broadband homonuclear correlation spectroscopy driven by combined R2nv sequences under fast magic angle spinning for NMR structural analysis of organic and biological solids. J Magn Reson 232:18–30
Jedrychowski MP et al (2020) Facultative protein selenation regulates redox sensitivity, adipose tissue thermogenesis, and obesity. Proc Natl Acad Sci 117:10789
Li F et al (2014) Redox active motifs in selenoproteins. Proc Natl Acad Sci 111:6976
Lim JM, Kim G, Levine RL (2019) Methionine in proteins: it’s not just for protein initiation anymore. Neurochem Res 44:247–257
Liu J, Rozovsky S (2016) 77Se NMR spectroscopy of selenoproteins. In: Hatfield DL, Schweizer U, Tsuji PA, Gladyshev VN (eds) Selenium: its molecular biology and role in human health. Springer International Publishing, Cham, pp 187–198
Manta B, Gladyshev VN (2017) Regulated methionine oxidation by monooxygenases. Free Radical Biol Med 109:141–155
Morcombe CR, Zilm KW (2003) Chemical shift referencing in MAS solid state NMR. J Magn Reson 162:479–486
Nasim MJ, Zuraik MM, Abdin AY, Ney Y, Jacob C (2021) Selenomethionine: a pink Trojan redox horse with implications in aging and various age-related diseases. Antioxidants 10:882
Potrzebowski MJ, Katarzyński R, Ciesielski W (1999) Selenium-77 and carbon-13 high-resolution solid-state NMR studies of selenomethionine. Magn Reson Chem 37:173–181
Rozovsky S (2013) 77Se NMR spectroscopy of selenoproteins. Biochalcogen chemistry: the biological chemistry of sulfur, selenium, and tellurium. American Chemical Society, Washington, pp 127–142
Schaefer J, McKay RA, Stejskal EO (1979) Double-cross-polarization NMR of solids. J Magn Reson 1969(34):443–447
Schaefer SA et al (2013) 77Se enrichment of proteins expands the biological nmr toolbox. J Mol Biol 425:222–231
Schaefer-Ramadan S, Thorpe C, Rozovsky S (2014) Site-specific insertion of selenium into the redox-active disulfide of the flavoprotein augmenter of liver regeneration. Arch Biochem Biophys 548:60–65
Strub M-P et al (2003) Selenomethionine and selenocysteine double labeling strategy for crystallographic phasing. Structure 11:1359–1367
Struppe J, Zhang Y, Rozovsky S (2015) 77Se Chemical shift tensor of l-selenocystine: experimental NMR measurements and quantum chemical investigations of structural effects. J Phys Chem B 119:3643–3650
Yang J, Tasayco ML, Polenova T (2008) Magic angle spinning NMR experiments for structural studies of differentially enriched protein interfaces and protein assemblies. J Am Chem Soc 130:5798–5807
Zhang MJ, Vogel HJ (1994a) 2-dimensional NMR-studies of selenomethionyl calmodulin. J Mol Biol 239:545–554
Zhang M, Vogel HJ (1994b) Two-dimensional NMR studies of selenomethionyl calmodulin. J Mol Biol 239:545–554
Acknowledgements
Research reported in this publication was supported by the National Science Foundation under Grant No. MCB-1616178 to Sharon Rozovsky. Dr. Qingqing Chen acknowledges support by chemical biology training grant award T32-GM133395 from the National Institute of General Medical Sciences. Instrumentation was supported by National Institute of General Medical Sciences under awards number P20GM104316 and P30GM110758.
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Quinn, C.M., Xu, S., Hou, G. et al. 77Se-13C based dipolar correlation experiments to map selenium sites in microcrystalline proteins. J Biomol NMR 76, 29–37 (2022). https://doi.org/10.1007/s10858-022-00390-4
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DOI: https://doi.org/10.1007/s10858-022-00390-4