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REVIEW

Kerfah R, Plevin MJ, Sounier R, Gans P, Boisbouvier J. Methyl-specific isotopic labeling: a molecular tool box for solution NMR studies of large proteins. Curr Opin Struct Biol.Jun;32:113-22 (2015).

Plevin MJ, Boisbouvier J. Isotope-Labelling of Methyl Groups for NMR Studies of Large Proteins. Book chapter in Recent Developments in Biomolecular NMR, Royal Society of Chemistry, Book serie: Biomolecular Science, Book Editor(s): Clore M and Potts J, DOI:10.1039/9781849735391 (2012).

Tzeng, Shiou-Ru; Pai, Ming-Tao; Kalodimos, Charalampos G. NMR Studies of Large Protein Systems in book Protein NMR techniques (3rd edition), Book Series: Methods in Molecular Biology, Book Editor(s): Shekhtman A and Burz DS, Volume: 831, Pages: 133-140, DOI: 10.1007/978-1-61779-480-3_8 (2012).

Kay L.E.Solution NMR spectroscopy of supra-molecular systems, why bother? A methyl-TROSY view. J. Magn. Res. 210, 159-170 (2011).

Ruschak AM and Kay LE.Methyl groups as probes of supra-molecular strcuture, dynamics and function. J.Biomol NMR. 46(1):75-87 (2010).

Foster MP, McElroy CA, Amero CD.Solution NMR of large molecules and assemblies. Biochemistry. 16;46(2):331-40 (2007).

Sprangers R, Velyvis A, Kay LE. Solution NMR of supramolecular complexes: providing new insights into function. Nat. Methods. (9):697-703 (2007).

Tugarinov V, Kanelis V, Kay LE.Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy. Nat. Protoc. 1(2):749-54 (2006).

LABELLING DEVELOPMENT

Ayala I, Hamelin O, Amero C, Pessey O, Plevin MJ, Gans P, Boisbouvier J. An optimized isotopic labelling strategy of isoleucine-γ2 methyl groups for solution NMR studies of high molecular weight proteins. Chem. Comm. Ed. 48, 1434-1436 (2012).

Religa TL, Ruschak AM, Rosenzweig R, Kay LE. Site-directed methyl group labeling as an NMR probe of structure and dynamics in supramolecular protein systems: applications to the proteasome and to the ClpP protease. J. Am.Chem .Soc. 15;133(23):9063-8 (2011)

Gans P, Hamelin O, Sounier R, Ayala I, Dura MA, Amero C, Noirclerc-Savoye M, Franzetti B, Plevin MJ, Boisbouvier J. Stereospecific Isotopic Labeling of Methyl Groups for NMR Studies of High Molecular Weight Proteins. Angew. Chem. Int. Ed. 49, 1958-1862 (2010).

Godoy-Ruiz R, Guo C, Tugarinov V.Alanine Methyl Groups as NMR Probes of Molecular Structure and Dynamics in High-Molecular-Weight Proteins. J. Am. Soc. 132; 5:18340-18350 (2010)

Ruschak AM, Velyvis A, Kay LE. A simple strategy for 13C, 1H labeling at the Ile γ2 methyl position in highly deuterated proteins. J. Biomol. NMR.48(3):129-35 (2010).

Amero C, Schanda P, Dura A, Ayala I, Marion D, Franzetti B, Brutscher B, Boisbouvier J. Fast Two Dimensional NMR Spectroscopy of High Molecular Weight Protein Assemblies. J. Am. Chem. Soc. 131, 3448-9 (2009).

Ayala I, Sounier R, Use N, Gans P, Boisbouvier J. An efficient protocol for the complete incorporation of methyl specifically protonated alanine in perdeuterated protein. J. Biomol. NMR 43, 111-119 (2009).

Isaacson RL, Simpson PJ, Liu M, Cota E, Zhang X, Freemont P, Matthews S. A new labeling method for methyl transverse relaxation-optimized spectroscopy NMR spectra of alanine residues. J.Am.Chem. Soc.129(50):15428-9 (2007).

Lichtenecker R, Ludwiczek ML, Schmid W, Konrat R. Simplification of protein NOESY spectra using bioorganic precursor synthesis and NMR spectral editing. J. Am. Chem. Soc. 126(17):5348-9 (2004).

Tugarinov V, Kay LE. An isotope labeling strategy for methyl TROSY spectroscopy. J. Biomol. NMR, 28(2):165-72 (2004).

Gross JD, Gelev VM, Wagner G. A sensitive and robust method for obtaining intermolecular NOEs between side chains in large protein complexes. J. Biomol. NMR. 25(3):235-42 (2003).

Tugarinov V, Hwang PM, Ollerenshaw JE, Kay LE. Cross-correlated relaxation enhanced 1H[bond]13C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes. J. Am. Chem. Soc. 125(34):10420-8 (2003).

Gardner KH and Kay LE. Production and incorporation of 15N,13C,2H (1H δ1 methyl) isoleucine into proteins for multidimensional NMR studies. J. Am. Chem. Soc. 119:7599-7600 (1997).

SIDE CHAINS DYNAMICS

Kleckner, Ian R.; Gollnick, Paul; Foster, Mark P. Mechanisms of allosteric gene regulation by NMR quantification of microsecond-millisecond protein dynamics. J. Mol. Bio. 415(2):372-381(2011).

Baldwin AJ, Religa TL, Hansen DF, Bouvignies G, Kay LE. 13CHD2 methyl group probes of millisecond time scale exchange in proteins by 1H relaxation dispersion: an application to proteasome gating residue dynamics. J. Am. Chem. Soc. 32(32):10992-5 (2010).

Religa TL, Sprangers R, Kay LE. Dynamic regulation of archaeal proteasome gate opening as studied by TROSY NMR. Science. 328(5974):98-102 (2010).

Sprangers R, Kay LE. Quantitative dynamics and binding studies of the 20S proteasome by NMR. Nature.445(7128):618-22 (2007).

Sprangers R, Gribun A, Hwang PM, Houry WA, Kay LE. Quantitative NMR spectroscopy of supramolecular complexes: dynamic side pores in ClpP are important for product release. Proc. Natl. Acad. Sci. U S A. 102(46):16678-83 (2005).

Korzhnev DM, Kloiber K, Kanelis V, Tugarinov V, Kay LE. Probing slow dynamics in high molecular weight proteins by methyl-TROSY NMR spectroscopy: application to a 723-residue enzyme. J. Am. Chem. Soc. 126(12):3964-73 (2004).

STRUCTURES DETERMINATION

Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen AC, Schmidt E, Kerfah R, Mas G, Colletier JP, Güntert P, Favier A, Schoehn G, Schanda P, Boisbouvier J. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nat Commun. 19;10(1):2697 (2019)

Jung YS, Cai M, Clore GM. Solution Structure of the IIAChitobiose-HPr Complex of the N,N'-Diacetylchitobiose Branch of the Escherichia coli Phosphotransferase System. J. Biol. Chem. 287(28):23819-29 (2012).

Gautier A, Mott HR, Bostock MJ, Kirkpatrick JP, Nietlispach D.Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy. Nat. Struct. Mol.Biol. 17(6):768-74(2010).

Imai S, Osawa M, Takeuchi K, Shimada I. Structural basis underlying the dual gate properties of KcsA. Proc. Natl. Acad. Sci.U S A. 107(14):6216-21 (2010).

Yoshiura C, Kofuku Y, Ueda T, Mase Y, Yokogawa M, Osawa M, Terashima Y, Matsushima K, Shimada I. NMR Analyses of the Interaction between CCR5 and Its Ligand Using Functional Reconstitution of CCR5 in Lipid Bilayers. J. Am. Chem. Soc. 132(19):6768-77(2010).

Baldwin AJ, Hansen DF, Vallurupalli P, Kay LE. Measurement of Methyl Axis Orientations in Invisible, Excited States of Proteins by Relaxation Dispersion NMR Spectroscopy. J Am Chem Soc. 131(33):11939-48 (2009).

Renault M, Saurel O, Czaplicki J, Demange P, Gervais V, Löhr F, Réat V, Piotto M, Milon A. Solution State NMR Structure and Dynamics of KpOmpA, a 210 Residue Transmembrane Domain Possessing a High Potential for Immunological Applications. J. Mol. Biol. 385(1):117-30. (2009).

Yu L, Edalji R, Harlan JE, Holzman TF et. al. Structural Characterization of a Soluble Amyloid beta-Peptide Oligomer. Biochem. 48(9): 1870-1877 (2009).

Guo C, Tugarinov V. Identification of HN-methyl NOEs in large proteins using simultaneous amide-methyl TROSY-based detection. J. Biomol. NMR. 43(1):21-30 (2008).

Delbecq S, Auguin D, Yang YS, Löhr F, Arold S, Schetters T, Précigout E, Gorenflot A, Roumestand C.The solution structure of the adhesion protein Bd37 from Babesia divergens reveals structural homology with eukaryotic proteins involved in membrane trafficking. J. Mol. Biol. 75(2):409-24 (2008).

Hiller S, Garces RG, Malia TJ, Orekhov VY, Colombini M, Wagner G.Solution structure of the integral human membrane protein VDAC-1 in detergent micelles. Science 321(5893):1206-10 (2008).

Wang X, Weldeghiorghis T, Zhang G, Imperiali B, Prestegard JH.Solution structure of Alg13: The sugar donor subunit of a yeast N-acetylglucosamine transferase. Structure.16(6):965-75 (2008)

Gelis I, Bonvin AM, Keramisanou D, Koukaki M, Gouridis G, Karamanou S, Economou A, Kalodimos CG. Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR. Cell.131(4):756-69 (2007).

Hu J, Hu K, Williams DC Jr, Komlosh ME, Cai M, Clore GM.Solution NMR structures of productive and non-productive complexes between the A and B domains of the cytoplasmic subunit of the mannose transporter of the Escherichia coli phosphotransferase system. J. Biol. Chem. 283(16):11024-37 (2008).

Sprangers R, Kay LE. Probing supramolecular structure from measurement of methyl (1)H-(13)C residual dipolar couplings. J Am Chem Soc.129(42):12668-9 (2007).

Sounier R, Blanchard L, Wu Z, Boisbouvier J. “High-Accuracy Distance Measurement Between Remote Methyls in Specifically Protonated Proteins”. J. Am. Chem. Soc. 129, 472-3 (2007).

Tugarinov V, Choy WY, Orekhov VY, Kay LE. Solution NMR-derived global fold of a monomeric 82-kDa enzyme. Proc. Natl. Acad. Sci. U S A.102(3):622-7 (2005).

Tugarinov V, Kay LE, Ibraghimov I, Orekhov VY. High-resolution four-dimensional 1H-13C NOE spectroscopy using methyl-TROSY, sparse data acquisition, and multidimensional decomposition. J. Am.Chem. Soc. 127(8):2767-75 (2005).

ASSIGNMENTS

Monneau YR, Rossi P, Bhaumik A, Huang C, Jiang Y, Saleh T, Xie T, Xing Q, Kalodimos CG. Automatic methyl assignment in large proteins by the MAGIC algorithm. J. Biomol. NMR, 0(0), 1–13 (2017).


Hu W, Namanja AT, Wong S, Chen Y. Selective editing of Val and Leu methyl groups in high molecular weight protein NMR. J. Biomol. NMR. 3(2):113-24 (2012).


Amero CD, Durá MA, Noirclerc-Savoye M, Perollier A, Gallet B, Plevin MJ, Vernet T, Franzetti B, Boisbouvier J. A Systematic Mutagenesis-driven Strategy for Site-Resolved NMR Studies of Supramolecular Assemblies. J. Biomol NMR. 50, 229-236 (2011).

Plevin MJ, Hamelin O, Boisbouvier J., Gans P. A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins. J. Biomol. NMR 49:61-67 (2011).

Sahakyan AB, Vranken WF, Cavalli A, Vendruscolo M. Structure-based prediction of methyl chemical shifts in proteins. J Biomol NMR. 50(4):331-46 (2011)

Venditti V, Fawzi NL, Clore GM. Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear Overhauser enhancement spectroscopy. J. Biomol. NMR. 51(3):319-28 (2011).

Velyvis A, Schachman HK, Kay LE. Assignment of Ile, Leu, and Val methyl correlations in supra-molecular systems: an application to aspartate transcarbamoylase. J. Am. Chem. Soc.131(45):16534-43 (2009).

Xu Y, Liu M, Simpson PJ, Isaacson R, Cota E, Marchant J, Yang D, Zhang X, Freemont P, Matthews S. Automated Assignment in Selectively Methyl-Labeled Proteins. J. Am. Chem. Soc.131(27):9480-1(2009).

Tugarinov V, Kay LE. Ile, Leu, and Val methyl assignments of the 723-residue malate synthase G using a new labeling strategy and novel NMR methods. J. Am. Chem. Soc. 125(45):13868-78 (2003).

OTHER LIQUID STATE DEVELOPMENTS & APPLICATIONS


Macek P, Kerfah R, Boeri Erba E, Crublet E, Moriscot C, Schoehn G, Amero C, Boisbouvier J. Unraveling self-assembly pathways of the 468-kDa proteolytic machine TET2. Sci Adv. 7;3(4):e1601601 (2017).


Stoffregen MC, Schwer MM, Renschler FA, Wiesner S. Structure. Methionine Scanning as an NMR Tool for Detecting and Analyzing Biomolecular Interaction Surfaces.Structure.20(4):573-81 (2012).

Esposito D, Sankar A, Morgner N, Robinson CV, Rittinger K, Driscoll PC. Solution NMR Investigation of the CD95/FADD Homotypic Death Domain Complex Suggests Lack of Engagement of the CD95 C Terminus.Structure.18(10):1378-90 (2010).


Plevin MJ, Bryce DL, Boisbouvier J. Direct Detection of CH/pi Interactions in Proteins. Nature Chem. 2, 466-471 (2010).

Ruschak AM, Religa TL, Breuer S, Witt S, Kay LE. The proteasome antechamber maintains substrates in an unfolded state.Nature. 467(7317):868-71(2010).

Orts J, Grimm SK, Griesinger C, Wendt KU, Bartoschek S, Carlomagno T. Specific methyl group protonation for the measurement of pharmacophore-specific interligand NOE interactions. Chemistry.14 (25):7517-20 (2008).

SOLID STATE NMR APPLICATIONS

Huber M, Hiller S, Schanda P, Ernst M, Böckmann A, Verel R, Meier BH. A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination.Chem. Phys. Chem. 12, 915-918 (2011).

Schanda P., Huber M., Boisbouvier J., Meier B.H., Ernst M. Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion. Angew. Chem. Int. Ed. 50, 11005-11009 (2011).

Agarwal V, Xue Y, Reif B, Skrynnikov NR. Protein side-chain dynamics as observed by solution- and solid-state NMR spectroscopy: a similarity revealed. J. Am. Chem. Soc. 130(49):16611-21 (2008).