Abayev-Avraham M, Salzberg Y, Gliksberg D, Oren-Suissa M, Rosenzweig R (2023) DNAJB6 mutants display toxic gain of function through unregulated interaction with Hsp70 chaperones. Nat Commun 14:7066
Abramov G, Velyvis A, Rennella E, Wong LE, Kay LE (2020) A methyl-TROSY approach for NMR studies of high-molecular-weight DNA with application to the nucleosome core particle. Proceedings of the National Academy of Sciences 117:12836–12846
Amero C, Asunción Durá M, Noirclerc-Savoye M, Perollier A, Gallet B, Plevin MJ, Vernet T, Franzetti B, Boisbouvier J (2011) A systematic mutagenesis-driven strategy for site-resolved NMR studies of supramolecular assemblies. J Biomol NMR 50:229–236
Aoto PC, Martin BT, Wright PE (2016) NMR characterization of information flow and allosteric communities in the MAP kinase p38γ. Sci Rep 6:28655
Aoto PC, Stanfield RL, Wilson IA, Dyson HJ, Wright PE (2019) A dynamic switch in inactive p38γ leads to an excited state on the pathway to an active kinase. Biochemistry 58:5160–5172
Ayala I, Chiari L, Kerfah R, Boisbouvier J, Gans P, Hamelin O (2020) Asymmetric synthesis of Methyl specifically labelled L -Threonine and application to the NMR studies of high molecular weight proteins. ChemistrySelect 5:5092–5098
Cai M, Huang Y, Yang R, Craigie R, Clore GM (2016) A simple and robust protocol for high-yield expression of perdeuterated proteins in Escherichia coli grown in shaker flasks. J Biomol NMR 66:85–91
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
Dudley JA, Park S, MacDonald ME, Fetene E, Smith CA (2020) Resolving overlapped signals with automated FitNMR analytical peak modeling. J Magn Reson 318:106773
Ernst RR, Anderson WA (1966) Application of fourier transform spectroscopy to magnetic resonance. Rev Sci Instrum 37:93–102
Article ADS MATH Google Scholar
Fischer M, Kloiber K, Häusler J, Ledolter K, Konrat R, Schmid W (2007) Synthesis of a13 C-Methyl‐Group‐Labeled methionine precursor as a useful tool for simplifying protein structural analysis by NMR spectroscopy. ChemBioChem 8:610–612
Geen H, Freeman R (1991) Band-selective radiofrequency pulses. Journal of Magnetic Resonance (1969) 93:93–141
Hansen DF, Kay LE (2011) Determining valine side-chain rotamer conformations in proteins from Methyl 13 C chemical shifts: application to the 360 kda half-proteasome. J Am Chem Soc 133:8272–8281
Hansen DF, Vallurupalli P, Kay LE (2009) Measurement of Methyl group motional parameters of invisible, excited protein States by NMR spectroscopy. J Am Chem Soc 131:12745–12754
Helmus JJ, Jaroniec CP (2013) Nmrglue: an open source Python package for the analysis of multidimensional NMR data. J Biomol NMR 55:355–367
Kerfah R, Hamelin O, Boisbouvier J, Marion D (2015a) CH3-specific NMR assignment of Alanine, isoleucine, leucine and valine Methyl groups in high molecular weight proteins using a single sample. J Biomol NMR 63:389–402
Kerfah R, Plevin MJ, Pessey O, Hamelin O, Gans P, Boisbouvier J (2015b) Scrambling free combinatorial labeling of alanine-β, isoleucine-δ1, leucine-proS and valine-proS Methyl groups for the detection of long range NOEs. J Biomol NMR 61:73–82
Kupce E, Freeman R (1993) Polychromatic selective pulses. J Magn Reson Ser A 102:122–126
Lee W, Rahimi M, Lee Y, Chiu A (2021) POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules. Bioinformatics 37:3041–3042
Lescop E, Schanda P, Brutscher B (2007) A set of BEST triple-resonance experiments for time-optimized protein resonance assignment. J Magn Reson 187:163–169
Article ADS MATH Google Scholar
Maisonneuve P, Caillet-Saguy C, Raynal B, Gilquin B, Chaffotte A, Pérez J, Zinn‐Justin S, Delepierre M, Buc H, Cordier F, Wolff N (2014) Regulation of the catalytic activity of the human phosphatase PTPN 4 by its PDZ domain. FEBS J 281:4852–4865
Maisonneuve P, Caillet-Saguy C, Vaney M-C, Bibi-Zainab E, Sawyer K, Raynal B, Haouz A, Delepierre M, Lafon M, Cordier F, Wolff N (2016) Molecular basis of the interaction of the human protein tyrosine phosphatase Non-receptor type 4 (PTPN4) with the Mitogen-activated protein kinase p38γ. J Biol Chem 291:16699–16708
Mishra SH, Frueh DP (2015) Assignment of Methyl NMR resonances of a 52 kda protein with residue-specific 4D correlation maps. J Biomol NMR 62:281–290
Monneau YR, Rossi P, Bhaumik A, Huang C, Jiang Y, Saleh T, Xie T, Xing Q, Kalodimos CG (2017) Automatic Methyl assignment in large proteins by the MAGIC algorithm. J Biomol NMR 69:215–227
Mulder FAA (2009) Leucine side-chain conformation and dynamics in proteins from 13 C NMR chemical shifts. Chembiochem: Eur J Chem Biology 10:1477–1479
Nerli S, De Paula VS, McShan AC, Sgourakis NG (2021) Backbone-independent NMR resonance assignments of Methyl probes in large proteins. Nat Commun 12:691
Pritišanac I, Degiacomi MT, Alderson TR, Carneiro MG, Siegal ABE, Baldwin G AJ (2017) Automatic assignment of Methyl-NMR spectra of supramolecular machines using graph theory. J Am Chem Soc 139:9523–9533
Pritišanac I, Würz JM, Alderson TR, Güntert P (2019) Automatic structure-based NMR Methyl resonance assignment in large proteins. Nat Commun 10:4922
Article ADS MATH Google Scholar
Salzmann M, Pervushin K, Wider G, Senn H, Wüthrich K (2000) NMR assignment and secondary structure determination of an octameric 110 kda protein using TROSY in triple resonance experiments. J Am Chem Soc 122:7543–7548
Schanda P, Kupče Ē, Brutscher B (2005) SOFAST-HMQC experiments for recording Two-dimensional deteronuclear correlation spectra of proteins within a few seconds. J Biomol NMR 33:199–211
Schanda P, Van Melckebeke H, Brutscher B (2006) Speeding up Three-Dimensional protein NMR experiments to a few minutes. J Am Chem Soc 128:9042–9043
Sever AIM, Alderson TR, Rennella E, Aramini JM, Liu ZH, Harkness RW, Kay LE (2023) Activation of caspase-9 on the apoptosome as studied by methyl-TROSY NMR. Proc Natl Acad Sci USA 120:e2310944120
Shaka AJ, Keeler J, Freeman R (1983) Evaluation of a new broadband decoupling sequence: WALTZ-16. Journal of Magnetic Resonance (1969) 53:313–340
Shukla VK, Siemons L, Hansen DF (2023) Intrinsic structural dynamics dictate enzymatic activity and Inhibition. Proc Natl Acad Sci USA 120:e2310910120
Siemons L, Mackenzie HW, Shukla VK, Hansen DF (2019a) Intra-residue methyl–methyl correlations for valine and leucine residues in large proteins from a 3D-HMBC-HMQC experiment. J Biomol NMR 73:749–757
Siemons L, Uluca-Yazgi B, Pritchard RB, McCarthy S, Heise H, Hansen DF (2019b) Determining isoleucine side-chain rotamer-sampling in proteins from 13 C chemical shift. Chem Commun 55:14107–14110
Sprangers R, Kay LE (2007) Quantitative dynamics and binding studies of the 20S proteasome by NMR. Nature 445:618–622
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
Tugarinov V, Kay LE (2003a) 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 125:13868–13878
Tugarinov V, Kay LE (2003b) Side chain assignments of Ile Δ1 Methyl groups in high molecular weight proteins: an application to a 46 Ns tumbling molecule. J Am Chem Soc 125:5701–5706
Tugarinov V, Hwang PM, Ollerenshaw JE, Kay LE (2003) Cross-Correlated relaxation enhanced 1H– 13 C NMR spectroscopy of Methyl groups in very high molecular weight proteins and protein complexes. J Am Chem Soc 125:10420–10428
Tugarinov V, Sprangers R, Kay LE (2007) Probing Side-Chain dynamics in the proteasome by relaxation violated coherence transfer NMR spectroscopy. J Am Chem Soc 129:1743–1750
Tugarinov V, Baber JL, Clore GM (2023) A methyl-TROSY based 13 C relaxation dispersion NMR experiment for studies of chemical exchange in proteins. J Biomol NMR 77:83–91
Comments (0)