Sparse pseudocontact shift NMR data obtained from a non-canonical amino acid-linked lanthanide tag improves integral membrane protein structure prediction

Chen JL et al (2016) Analysis of the solution conformations of T4 lysozyme by paramagnetic NMR spectroscopy. Phys Chem Chem Phys 18:5850–5859

Article  Google Scholar 

Chin JW et al (2002) Addition of p-azido-L-phenylalanine to the genetic code of Escherichia coli. J Am Chem Soc 124:9026–9027

Article  Google Scholar 

Crick DJ et al (2015) Integral membrane protein structure determination using pseudocontact shifts. J Biomol NMR 61:197–207

Article  Google Scholar 

de la Cruz L et al (2011) Binding of low molecular weight inhibitors promotes large conformational changes in the dengue virus NS2B-NS3 protease: fold analysis by pseudocontact shifts. J Am Chem Soc 133:19205–19215

Article  Google Scholar 

Fernandez C, Hilty C, Wider G, Guntert P, Wuthrich K (2004) NMR structure of the integral membrane protein OmpX. J Mol Biol 336:1211–1221

Article  Google Scholar 

Gardner KH, Kay LE (1998) The Use of 2H, 13C, 15N multidimensional NMR to study the structure and dynamics of proteins. Ann Rev of Biophys Biomol Struct 27:357–406

Article  Google Scholar 

Gautier A, Mott HR, Bostock MJ, Kirkpatrick JP, Nietlispach D (2010) Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy. Nat Struct Mol Biol 17:768–774

Article  Google Scholar 

Goto NK, Kay LE (2000) New developments in isotope labeling strategies for protein solution NMR spectroscopy. Curr Opin Struct Biol 10:585–592

Article  Google Scholar 

Graham B et al (2011) DOTA-amide lanthanide tag for reliable generation of pseudocontact shifts in protein NMR spectra. Bioconjug Chem 22:2118–2125

Article  Google Scholar 

Gront D, Kulp DW, Vernon RM, Strauss CE, Baker D (2011) Generalized fragment picking in Rosetta: design, protocols and applications. PLoS ONE 6:e23294

Article  ADS  Google Scholar 

Hagn F, Nasr ML, Wagner G (2018) Assembly of phospholipid nanodiscs of controlled size for structural studies of membrane proteins by NMR. Nat Protoc 13:79–98

Article  Google Scholar 

Hiller S et al (2008) Solution structure of the integral human membrane protein VDAC-1 in detergent micelles. Science 321:1206–1210

Article  ADS  Google Scholar 

Hyberts SG, Arthanari H, Robson SA, Wagner G (2014) Perspectives in magnetic resonance: NMR in the post-FFT era. J Magn Reson 241:60–73

Article  ADS  Google Scholar 

Jaremko M et al (2016) High-resolution NMR determination of the dynamic structure of membrane proteins. Angew Chem Int Ed Engl 55:10518–10521

Article  Google Scholar 

Jiang WX, Gu XH, Dong X, Tang C (2017) Lanthanoid tagging via an unnatural amino acid for protein structure characterization. J Biomol NMR 67:273–282

Article  Google Scholar 

Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195–202

Article  Google Scholar 

Koehler J, Meiler J (2011) Expanding the utility of NMR restraints with paramagnetic compounds: background and practical aspects. Prog Nucl Magn Reson Spectrosc 59:360–389

Article  Google Scholar 

Kuenze G, Bonneau R, Leman JK, Meiler J (2019) Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints. Structure 27:1721–1734e5

Lange OF et al (2012) Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples. Proc Natl Acad Sci 109:10873–10878

Article  ADS  Google Scholar 

Leman JK, Mueller R, Karakas M, Woetzel N, Meiler J (2013) Simultaneous prediction of protein secondary structure and transmembrane spans. Proteins 81:1127–1140

Article  Google Scholar 

Lin EC, Opella SJ (2014) Covariance spectroscopy in high-resolution multi-dimensional solid-state NMR. J Magn Reson 239:57–60

Article  ADS  Google Scholar 

Loh CT et al (2013) Lanthanide tags for site-specific ligation to an unnatural amino acid and generation of pseudocontact shifts in proteins. Bioconjug Chem 24:260–268

Article  Google Scholar 

MacKenzie KR, Prestegard JH, Engelman DM (1997) A transmembrane helix dimer: structure and implications. Science 276:131–133

Article  Google Scholar 

Miclet E et al (2004) Relaxation-optimized NMR spectroscopy of methylene groups in proteins and nucleic acids. J Am Chem Soc 126:10560–10570

Article  Google Scholar 

Milles S et al (2012) Click strategies for single-molecule protein fluorescence. J Am Chem Soc 134:5187–5195

Article  Google Scholar 

Muntener T, Joss D, Haussinger D, Hiller S (2022) Pseudocontact shifts in biomolecular NMR spectroscopy. Chem Rev 122:9422–9467

Article  Google Scholar 

Nasr ML et al (2017) Covalently circularized nanodiscs for studying membrane proteins and viral entry. Nat Methods 14:49–52

Article  Google Scholar 

Nietlispach D (2005) Suppression of anti-TROSY lines in a sensitivity enhanced gradient selection TROSY scheme. J Biomol NMR 31:161–166

Article  Google Scholar 

Okwei ENN et al (2022) First crystal structure of a non-canonical amino acid linked to a paramagnetic lanthanide tag facilitates protein structure determination using NMR-derived restraints. bioRxiv (2022).

Orton HW, Huber T, Otting G (2020) Paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra. Magnetic Resonance 1:1–12

Article  Google Scholar 

Otomo T, Ito N, Kyogoku Y, Yamazaki T (1999) NMR observation of selected segments in a larger protein: central-segment isotope labeling through intein-mediated ligation. Biochemistry 38:16040–16044

Article  Google Scholar 

Oxenoid K, Chou JJ (2005) The structure of phospholamban pentamer reveals a channel-like architecture in membranes. Proc Natl Acad Sci USA 102:10870–10875

Article  ADS  Google Scholar 

Oxenoid K, Kim HJ, Jacob J, Sonnichsen FD, Sanders CR (2004) NMR assignments for a helical 40 kDa membrane protein. J Am Chem Soc 126:5048–5049

Article  Google Scholar 

Palmer MR et al (2015) Sensitivity of nonuniform sampling NMR. J Phys Chem B 119:6502–6515

Article  Google Scholar 

Park SH et al (2015) Paramagnetic relaxation enhancement of membrane proteins by incorporation of the metal-chelating unnatural amino acid 2-amino-3- (8-hydroxyquinolin-3-yl)propanoic acid (HQA). J Biomol NMR 61:185–196

Article  Google Scholar 

Pervushin K, Riek R, Wider G, Wuethrich K (1997) Attenuated T2 relaxation by mutual cancellation of dipole–dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc Natl Acad Sci USA 94:12366–12371

Article  ADS  Google Scholar 

Romanelli A, Shekhtman A, Cowburn D, Muir TW (2004) Semisynthesis of a segmental isotopically labeled protein splicing precursor: NMR evidence for an unusual peptide bond at the N-extein-intein junction. Proc Natl Acad Sci USA 101:6397–6402

Article  ADS  Google Scholar 

Schmitz C, Vernon R, Otting G, Baker D, Huber T (2012) Protein structure determination from pseudocontact shifts using ROSETTA. J Mol Biol 416:668–677

Article  Google Scholar 

Seigneuret M, Kainosho M (1993) Localisation of methionine residues in bacteriorhodopsin by carbonyl 13C-NMR with sequence-specific assignments. FEBS Lett 327:7–12

Article  Google Scholar 

Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213–223

Article  Google Scholar 

Simons KT, Kooperberg C, Huang E, Baker D (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268:209–225

Article  Google Scholar 

Sprangers R, Gribun A, Hwang PM, Houry WA, Kay LE (2005) Quantitative NMR spectroscopy of supramolecular complexes: dynamic side pores in ClpP are important for product release. Proc Natl Acad Sci USA 102:16678–16683

Article  ADS  Google Scholar 

Stanton-Cook M, Su X, Otting G, Huber T (2018) PyParaTools—software for working with paramagnetic NMR data

Suiter CL et al (2014) Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range. J Biomol NMR 59:57–73

Article  Google Scholar 

Susac L, Horst R, Wuthrich K (2014) Solution-NMR characterization of outer-membrane protein A from E. coli in lipid bilayer nanodiscs and detergent micelles. Chembiochem 15:995–1000 (2014).

Tian C et al (2005) Membrane protein preparation for TROSY NMR screening. Methods Enzymol 394:321–334

Article  Google Scholar 

Trbovic N et al (2005) Efficient strategy for the rapid backbone assignment of membrane proteins. J Am Chem Soc 127:13504–13505

Article  Google Scholar 

Tugarinov V, Kay LE (2005) Methyl groups as probes of structure and dynamics in NMR studies of high-molecular-weight proteins. ChemBioChem 6:1567–1577

Article  Google Scholar 

Tugarinov V, Hwang PM, Kay LE (2004a) Nuclear magnetic resonance spectroscopy of high-molecular-weight proteins. Annu Rev Biochem 73:107–146

Article  Google Scholar 

Tugarinov V, Sprangers R, Kay LE (2004b) Line narrowing in methyl-TROSY using zero-quantum 1H–13C NMR spectroscopy. J Am Chem Soc 126:4921–4925

Article  Google Scholar 

Weigelt J, Miles CS, Dixon NE, Otting G (1998) Backbone NMR assignments and secondary structure of the N-terminal domain of DnaB helicase from E. coli. J Biomol NMR 11:233–234 (1998).

Williams CJ et al (2018) MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci 27:293–315

Article  Google Scholar 

Yagi H, Tsujimoto T, Yamazaki T, Yoshida M, Akutsu H (2004) Conformational change of H+-ATPase beta monomer revealed on segmental isotope labeling NMR spectroscopy. J Am Chem Soc 126:16632–16638

Article  Google Scholar 

Young TS, Ahmad I, Yin JA, Schultz PG An enhanced system for unnatural amino acid mutagenesis in E. coli. J Mol Biol 395:361–74 (2010).

Zhao B, Baisden JT, Zhang Q (2020) Probing excited conformational states of nucleic acids by nitrogen CEST NMR spectroscopy. J Magn Reson 310:106642

Article  Google Scholar 

Zhou Y et al (2008) NMR solution structure of the integral membrane enzyme DsbB: functional insights into DsbB-catalyzed disulfide bond formation. Mol Cell 31:896–908

Article  Google Scholar 

Zuger S, Iwai H (2005) Intein-based biosynthetic incorporation of unlabeled protein tags into isotopically labeled proteins for NMR studies. Nat Biotechnol 23:736–740

留言 (0)

沒有登入
gif