Site-selective 13C labeling of histidine and tryptophan using ribose
Tóm tắt
Experimental studies on protein dynamics at atomic resolution by NMR-spectroscopy in solution require isolated 1H-X spin pairs. This is the default scenario in standard 1H-15N backbone experiments. Side chain dynamic experiments, which allow to study specific local processes like proton-transfer, or tautomerization, require isolated 1H-13C sites which must be produced by site-selective 13C labeling. In the most general way this is achieved by using site-selectively 13C-enriched glucose as the carbon source in bacterial expression systems. Here we systematically investigate the use of site-selectively 13C-enriched ribose as a suitable precursor for 13C labeled histidines and tryptophans. The 13C incorporation in nearly all sites of all 20 amino acids was quantified and compared to glucose based labeling. In general the ribose approach results in more selective labeling. 1-13C ribose exclusively labels His δ2 and Trp δ1 in aromatic side chains and helps to resolve possible overlap problems. The incorporation yield is however only 37% in total and 72% compared to yields of 2-13C glucose. A combined approach of 1-13C ribose and 2-13C glucose maximizes 13C incorporation to 75% in total and 150% compared to 2-13C glucose only. Further histidine positions β, α and CO become significantly labeled at around 50% in total by 3-, 4- or 5-13C ribose. Interestingly backbone CO of Gly, Ala, Cys, Ser, Val, Phe and Tyr are labeled at 40–50% in total with 3-13C ribose, compared to 5% and below for 1-13C and 2-13C glucose. Using ribose instead of glucose as a source for site-selective 13C labeling enables a very selective labeling of certain positions and thereby expanding the toolbox for customized isotope labeling of amino-acids.
Tài liệu tham khảo
Ahlner A, Andresen C, Khan SN, Kay LE, Lundstrom P (2015) Fractional enrichment of proteins using [2-C-13]-glycerol as the carbon source facilitates measurement of excited state C-13 alpha chemical shifts with improved sensitivity. J Biomol NMR 62:341–351
Akke M, Palmer AG (1996) Monitoring macromolecular motions on microsecond–millisecond time scales by R1r–R1 constant-relaxation-time NMR spectroscopy. J Am Chem Soc 118:911–912
Bartlett GJ, Porter CT, Borkakoti N, Thornton JM (2002) Analysis of catalytic residues in enzyme active sites. J Mol Biol 324:105–121
Bogan AA, Thorn KS (1998) Anatomy of hot spots in protein interfaces. J Mol Biol 280:1–9
Boyer JA, Lee AL (2008) Monitoring aromatic picosecond to nanosecond dynamics in proteins via C-13 relaxation: expanding perturbation mapping of the rigidifying core mutation, V54A, in eglin C. Biochemistry 47:4876–4886
Burley SK, Petsko GA (1985) Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science 229:23–28
Burley SK, Petsko GA (1989) Electrostatic interactions in aromatic oligopeptides contribute to protein. Stability Trends Biotech 7:354–359
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) Nmrpipe—a multidimensional spectral processing system based on unix pipes. J Biomol NMR 6:277–293
Eddy MT, Belenky M, Sivertsen AC, Griffin RG, Herzfeld J (2013) Selectively dispersed isotope labeling for protein structure determination by magic angle spinning NMR. J Biomol NMR 57:129–139. doi:10.1007/s10858-013-9773-3
Ferrage F, Piserchio A, Cowburn D, Ghose R (2008) On the measurement of 15N-{1H} nuclear Overhauser effects. J Magn Reson 192:302–313
Fersht A (1977) Enzyme structure and mechanism. W. H. Freeman, New York
Hansen AL, Kay LE (2011) Quantifying millisecond time-scale exchange in proteins by CPMG relaxation dispersion NMR spectroscopy of side-chain carbonyl groups. J Biomol NMR 50:347–355
Hansen AL, Kay LE (2014) Measurement of histidine pK(a) values and tautomer populations in invisible protein states. Proc Natl Acad Sci USA 111:E1705-E1712
Hansen AL, Lundstrom P, Velyvis A, Kay LE (2012) Quantifying millisecond exchange dynamics in proteins by CPMG relaxation dispersion NMR using side-chain H-1 probes. J Am Chem Soc 134:3178–3189
Ishima R, Torchia DA (2003) Extending the range of amide proton relaxation dispersion experiments in proteins using a constant-time relaxation-compensated CPMG approach. J Biomol NMR 25:243–248
Jarymowycz VA, Stone MJ (2006) Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences. Chem Rev 106:1624–1671
Johnson BA (2004) Using NMRView to visualize and analyze the NMR spectra of macromolecules. Meth Mol Biol 278:313–352
Kasinath V, Valentine KG, Wand AJ (2013) A C-13 Labeling strategy reveals a range of aromatic side chain motion in calmodulin. J Am Chem Soc 135:9560–9563
Kasinath V, Fu YN, Sharp KA, Wand AJ (2015) A sharp thermal transition of fast aromatic-ring dynamics in ubiquitin. Angew Chem Int Edit 54:102-+
Korzhnev DM, Religa TL, Banachewicz W, Fersht AR, Kay LE (2010) A transient and low-populated protein-folding intermediate at atomic resolution. Science 329:1312–1316
Krishna Deepak RN, Sankararamakrishnan R (2016) N-H...N hydrogen bonds involving histidine imidazole nitrogen atoms: a new structural role for histidine residues in proteins. Biochemistry 55:3774–3783. doi:10.1021/acs.biochem.6b00253
Levitt M, Perutz MF (1988) Aromatic rings act as hydrogen-bond acceptors. J Mol Biol 201:751–754
Lichtenecker RJ, Weinhaupl K, Schmid W, Konrat R (2013) Alpha-Ketoacids as precursors for phenylalanine and tyrosine labelling in cell-based protein overexpression. J Biomol NMR 57:327–331
Lindskog S (1997) Structure and mechanism of carbonic anhydrase. Pharmacol Ther 74:1–20
Lo Conte L, Chothia C, Janin J (1999) The atomic structure of protein-protein recognition sites. J Mol Biol 285:2177–2198
Loria JP, Rance M, Palmer AG (1999) A relaxation-compensated Carr-Purcell-Meiboom-Gill sequence for characterizing chemical exchange by NMR spectroscopy. J Am Chem Soc 121:2331–2332
Lundstrom P et al (2007) Fractional C-13 enrichment of isolated carbons using [1-C-13]- or [2-C-13]-glucose facilitates the accurate measurement of dynamics at backbone C-alpha and side-chain methyl positions in proteins. J Biomol NMR 38:199–212
Lundstrom P, Hansen DF, Vallurupalli P, Kay LE (2009a) Accurate measurement of alpha proton chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy. J Am Chem Soc 131:1915–1926
Lundstrom P, Lin H, Kay LE (2009b) Measuring (13)C(beta) chemical shifts of invisible excited states in proteins by relaxation dispersion NMR spectroscopy. J Biomol NMR 44:139–155
Lundstrom P, Ahlner A, Blissing AT (2012a) Isotope labeling methods for large systems isotope labeling. Biomol Nmr 992:3–15
Lundstrom P, Ahlner A, Blissing AT (2012b) Isotope labeling methods for relaxation measurements isotope. Labeling Biomol Nmr 992:63–82
Mahadevi AS, Sastry GN (2013) Cation-pi interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 113:2100–2138
Milbradt AG, Arthanari H, Takeuchi K, Boeszoermenyi A, Hagn F, Wagner G (2015) Increased resolution of aromatic cross peaks using alternate C-13 labeling and TROSY. J Biomol NMR 62:291–301
Millet O, Muhandiram DR, Skrynnikov NR, Kay LE (2002) Deuterium spin probes of side-chain dynamics in proteins. 1. Measurement of five relaxation rates per deuteron in C-13-labeled and fractionally H-2-enriched proteins in solution. J Am Chem Soc 124:6439–6448
Mittermaier A, Kay LE (2006) Review - New tools provide new insights in NMR studies of protein dynamics. Science 312:224–228
Miyanoiri Y, Takeda M, Jee J, Ono AM, Okuma K, Terauchi T, Kainosho M (2011) Alternative SAIL-Trp for robust aromatic signal assignment and determination of the chi(2) conformation by intra-residue NOEs. J Biomol NMR 51:425–435
Muhandiram DR, Yamazaki T, Sykes BD, Kay LE (1995) Measurement of H-2 T-1 and T-1P relaxation-times in uniformly C-13-labeled and fractionally H-2-labeled proteins in solution. J Am Chem Soc 117:11536–11544
Mulder FAA, Hon B, Mittermaier A, Dahlquist FW, Kay LE (2002) Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme. J Am Chem Soc 124:1443–1451
Neudecker P et al (2012) Structure of an intermediate state in protein folding and aggregation. Science 336:362–366
Palmer AG (2004) NMR characterization of the dynamics of biomacromolecules. Chem Rev 104:3623–3640
Paquin R, Ferrage F, Mulder FAA, Akke M, Bodenhausen G (2008) Multiple-timescale dynamics of side-chain carboxyl and carbonyl groups in proteins by C-13 nuclear spin relaxation. J Am Chem Soc 130:15805-+
Pelton JG, Torchia DA, Meadow ND, Roseman S (1993) Tautomeric states of the active-site histidines of phosphorylated and unphosphorylated Iii(Glc), a signal-transducing protein from Escherichia-coli, using 2-dimensional heteronuclear nmr. Techniq Prot Sci 2:543–558
Preimesberger MR, Majumdar A, Rice SL, Que L, Lecomte JT (2015) Helix-capping histidines: diversity of N-H...N hydrogen bond strength revealed by (2 h)JNN scalar couplings. Biochemistry 54:6896–6908. doi:10.1021/acs.biochem.5b01002
Reynolds WF, Peat IR, Freedman MH, Lyerla JR Jr (1973) Determination of the tautomeric form of the imidazole ring of L-histidine in basic solution by carbon-13 magnetic resonance spectroscopy. J Am Chem Soc 95:328–331
Ruschak AM, Kay LE (2010) Methyl groups as probes of supra-molecular structure, dynamics and function. J Biomol NMR 46:75–87. doi:10.1007/s10858-009-9376-1
Sathyamoorthy B, Singarapu KK, Garcia AE, Szyperski T (2013) Protein conformational space populated in solution probed with aromatic residual dipolar C-13-H-1 Couplings. Chembiochem 14:684–688
Schörghuber J, Sara T, Bisaccia M, Schmid W, Konrat R, Lichtenecker RJ (2015) Novel approaches in selective tryptophan isotope labeling by using Escherichia coli overexpression media. Chembiochem 16:746–751
Schörghuber J, Geist L, Platzer G, Konrat R, Lichtenecker RJ (2017) Highly selective stable isotope labeling of histidine residues by using a novel precursor in E. coli-Based overexpression systems. Chembiochem 18:1487–1491. doi:10.1002/cbic.201700192
Schwender J, Ohlrogge JB, Shachar-Hill Y (2003) A flux model of glycolysis and the oxidative pentosephosphate pathway in developing Brassica napus embryos. J Biol Chem 278:29442–29453. doi:10.1074/jbc.M303432200
Takeda M, Ono AM, Terauchi T, Kainosho M (2010) Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination. J Biomol NMR 46:45–49
Teilum K, Brath U, Lundstrom P, Akke M (2006) Biosynthetic C-13 labeling of aromatic side chains in proteins for NMR relaxation measurements. J Am Chem Soc 128:2506–2507
Tugarinov V, Kay LE (2005) Methyl groups as probes of structure and dynamics in NMR studies of high-molecular-weight proteins. Chembiochem 6:1567
Tugarinov V, Kanelis V, Kay LE (2006) Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy. Nat Prot 1:749–754. doi:10.1038/nprot.2006.101
Valley CC, Cembran A, Perlmutter JD, Lewis AK, Labello NP, Gao J, Sachs JN (2012) The methionine-aromatic motif plays a unique role in stabilizing protein structure. J Biol Chem 287:34979–34991
Vila JA, Arnautova YA, Vorobjev Y, Scheraga HA (2011) Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH. Proc Natl Acad Sci USA 108:5602–5607. doi:10.1073/pnas.1102373108
Wallerstein J, Weininger U, Khan MA, Linse S, Akke M (2015) Site-specific protonation kinetics of acidic side chains in proteins determined by pH-dependent carboxyl (13)C NMR relaxation. J Am Chem Soc 137:3093–3101
Weininger U (2017) Site-selective 13C labeling of proteins using erythrose. J Biomol NMR 67:191–200. doi:10.1007/s10858-017-0096-7
Weininger U, Diehl C, Akke M (2012a) C-13 relaxation experiments for aromatic side chains employing longitudinal- and transverse-relaxation optimized NMR spectroscopy. J Biomol NMR 53:181–190
Weininger U, Liu Z, McIntyre DD, Vogel HJ, Akke M (2012b) Specific 12CbD212CgD2S13CeHD2 isotopomer labeling of methionine to characterize protein dynamics by 1H and 13C NMR relaxation dispersion. J Am Chem Soc 134:18562–18565. doi:10.1021/ja309294u
Weininger U, Respondek M, Akke M (2012c) Conformational exchange of aromatic side chains characterized by L-optimized TROSY-selected C-13 CPMG relaxation dispersion. J Biomol NMR 54:9–14
Weininger U, Respondek M, Low C, Akke M (2013) Slow Aromatic ring flips detected despite near-degenerate NMR frequencies of the exchanging nuclei. J Phys Chem B 117:9241–9247
Weininger U, Brath U, Modig K, Teilum K, Akke M (2014a) Off-resonance rotating-frame relaxation dispersion experiment for C-13 in aromatic side chains using L-optimized TROSY-selection. J Biomol NMR 59:23–29
Weininger U, Modig K, Akke M (2014b) Ring flips revisited: C-13 relaxation dispersion measurements of aromatic side chain dynamics and activation barriers in basic pancreatic trypsin inhibitor. Biochemistry 53:4519–4525
Weininger U, Modig K, Geitner AJ, Schmidpeter PAM, Koch JR, Akke M (2017) Dynamics of aromatic side chains in the active site of FKBP12. BioChemistry 56:334–343. doi:10.1021/acs.biochem.6b01157
Wuthrich K (2001) The way to NMR structures of proteins. Nat Struct Biol 8:923–925. doi:10.1038/Nsb1101-923
Yang CJ, Takeda M, Terauchi T, Jee J, Kainosho M (2015) Differential large-amplitude breathing motions in the interface of FKBP12 drug complexes. Biochemistry 54:6983–6995. doi:10.1021/acs.biochem.5b00820
Zuiderweg ERP (2002) Mapping protein-protein interactions in solution by. NMR spectroscopy biochemistry 41:1–7. doi:10.1021/bi011870b