Evaluation of TOCSY mixing for sensitivity-enhancement in solid-state NMR and application of 4D experiments for side-chain assignments of the full-length 30 kDa membrane protein GlpG

Bak M, Rasmussen JT, Nielsen NC (2000) SIMPSON: a General Simulation Program for solid-state NMR spectroscopy. J Magn Reson 147:296–330

Article  ADS  MATH  Google Scholar 

Baldus M, Meier BH (1996) Total correlation spectroscopy in the Solid State. The Use of Scalar couplings to Determine the through-bond connectivity. J Magn Reson Ser A 121:65–69

Article  ADS  MATH  Google Scholar 

Baldus M, Iuliucci RJ, Meier BH (1997) Probing through-bond connectivities and through-space distances in solids by Magic-Angle-Spinning Nuclear magnetic resonance. J Am Chem Soc 119:1121–1124

Article  Google Scholar 

Blahut J, Brandl MJ, Pradhan T, Reif B, Tošner Z (2022) Sensitivity-enhanced Multidimensional solid-state NMR spectroscopy by optimal-control-based transverse mixing sequences. J Am Chem Soc 144:17336–17340

Article  Google Scholar 

Blahut J, Brandl MJ, Sarkar R, Reif B, Tošner Z (2023) Optimal control derived sensitivity-enhanced CA-CO mixing sequences for MAS solid-state NMR– applications in sequential protein backbone assignments. J Magn Reson Open 16–17:100122

Article  Google Scholar 

Bohg C, Öster C, Utesch T, Bischoff S, Lange S, Shi C, Sun H, Lange A (2021) A combination of solid-state NMR and MD simulations reveals the binding mode of a rhomboid protease inhibitor. Chem Sci 12:12754–12762

Article  Google Scholar 

Bohg C, Öster C, Türkaydin B, Lisurek M, Sanchez-Carranza P, Lange S, Utesch T, Sun H, Lange A (2023) The opening dynamics of the lateral gate regulates the activity of rhomboid proteases. Sci Adv 9:1–11

Article  Google Scholar 

Callon M, Luder D, Malär AA, Wiegand T, Římal V, Lecoq L, Böckmann A, Samoson A, Meier BH (2023) High and fast: NMR protein–proton side-chain assignments at 160 kHz and 1.2 GHz. Chem Sci 14:10824–10834

Article  Google Scholar 

Cavanagh J, Rance M (1990) Sensitivity improvement in isotropic mixing (TOCSY) experiments. J Magn Reson 88:72–85

ADS  MATH  Google Scholar 

Chevelkov V, Lange S, Sawczyc H, Lange A (2023) Accurate determination of Motional amplitudes in Biomolecules by solid-state NMR. ACS Phys Chem Au 3:199–206

Article  MATH  Google Scholar 

Delaglio F, Grzesiek S, Vuister G, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6

Fraga H, Arnaud C, Gauto DF, Audin M, Kurauskas V, Macek P, Krichel C, Guan J, Boisbouvier J, Sprangers R, Breyton C, Schanda P, Solid-State (2017) NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for Resonance assignment of large proteins. ChemPhysChem 18:2697–2703

Article  Google Scholar 

Ghasriani H, Kwok JKC, Sherratt AR, Foo ACY, Qureshi T, Goto NK (2014) Micelle-Catalyzed Domain Swapping in the GlpG rhomboid protease cytoplasmic domain. Biochemistry 53:5907–5915

Article  Google Scholar 

Hyberts SG, Takeuchi K, Wagner G (2010) Poisson-Gap Sampling and Forward Maximum Entropy Reconstruction for enhancing the resolution and sensitivity of protein NMR data. J Am Chem Soc 132:2145–2147

Article  MATH  Google Scholar 

Hyberts SG, Milbradt AG, Wagner AB, Arthanari H, Wagner G (2012) Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling. J Biomol NMR 52:315–327

Article  MATH  Google Scholar 

Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A, Potapenko A, Bridgland A, Meyer C, Kohl SAA, Ballard AJ, Cowie A, Romera-Paredes B, Nikolov S, Jain R, Adler J, Back T, Petersen S, Reiman D, Clancy E, Zielinski M, Steinegger M, Pacholska M, Berghammer T, Bodenstein S, Silver D, Vinyals O, Senior AW, Kavukcuoglu K, Kohli P (2021) Hassabis, D. highly accurate protein structure prediction with AlphaFold. Nature 596:583–589

Article  ADS  Google Scholar 

Klein A, Vasa SK, Söldner B, Grohe K, Linser R (2022) Unambiguous side-chain assignments for solid-state NMR structure elucidation of Nondeuterated Proteins via a combined 5D/4D side-chain-to-backbone experiment. J Phys Chem Lett 13:1644–1651

Article  Google Scholar 

Marchanka A, Stanek J, Pintacuda G, Carlomagno T (2018) Rapid access to RNA resonances by proton-detected solid-state NMR at > 100 kHz MAS. Chem Commun 54:8972–8975

Article  Google Scholar 

Marion D, Ikura M, Tschudin R, Bax A (1989) Rapid recording of 2D NMR spectra without phase cycling. Application to the study of hydrogen exchange in proteins. J Magn Reson 85:393–399

ADS  Google Scholar 

Nimerovsky E, Varkey AC, Kim M, Becker S, Andreas LB (2023) Simplified preservation of Equivalent pathways Spectroscopy. JACS Au 3:2763–2771

Article  Google Scholar 

Nimerovsky E, Kosteletos S, Lange S, Becker S, Lange A, Andreas LB (2024) Homonuclear Simplified Preservation of Equivalent pathways Spectroscopy. J Phys Chem Lett 15:6272–6278

Article  MATH  Google Scholar 

Öster C, Walkowiak GP, Hughes DE, Spoering AL, Peoples AJ, Catherwood AC, Tod JA, Lloyd AJ, Herrmann T, Lewis K, Dowson CG, Lewandowski JR (2018) Structural studies suggest aggregation as one of the modes of action for teixobactin. Chem Sci 9:8850–8859

Article  Google Scholar 

Öster C, Lange S, Hendriks K, Lange A (2024) Detecting Bound Ions in Ion Channels by Solid-State NMR Experiments on 15 N-Labelled Ammonium Ions. in Methods in Molecular Biology vol. 2796 23–34

Paluch P, Augustyniak R, Org M-L, Vanatalu K, Kaldma A, Samoson A, Stanek J (2022) NMR assignment of Methyl Groups in immobilized proteins using multiple-bond 13 C homonuclear transfers, Proton Detection, and very fast MAS. Front Mol Biosci 9:1–18

Article  Google Scholar 

Rienstra CM, Zhou DH, Rienstra CM (2008) High-performance solvent suppression for Proton detected solid-state NMR. J Magn Reson 192:167–172

Article  ADS  MATH  Google Scholar 

Sawczyc H, Tatsuta T, Öster C, Kosteletos S, Lange S, Bohg C, Langer T, Lange A (2024) Lipid-polymer nanoparticles to probe the native-like environment of intramembrane rhomboid protease GlpG and its activity. Nat Commun 15:7533

Article  Google Scholar 

Schleucher J, Sattler M, Griesinger C (1993) Coherence selection by gradients without Signal Attenuation: application to the three-dimensional HNCO experiment. Angew Chemie Int Ed Engl 32:1489–1491

Article  MATH  Google Scholar 

Shaka A, Keeler J, Freeman R (1983) Evaluation of a new broadband decoupling sequence: WALTZ-16. J Magn Reson 53:313–340

ADS  MATH  Google Scholar 

Shaka A, Lee C, Pines A (1988) Iterative schemes for bilinear operators; application to spin decoupling. J Magn Reson 77:274–293

ADS  MATH  Google Scholar 

Sherratt AR, Blais DR, Ghasriani H, Pezacki JP, Goto NK (2012) Activity-based protein profiling of the escherichia coli GlpG rhomboid protein delineates the catalytic core. Biochemistry 51:7794–7803

Article  Google Scholar 

Shi C, Öster C, Bohg C, Li L, Lange S, Chevelkov V, Lange A (2019) Structure and Dynamics of the rhomboid protease GlpG in Liposomes studied by solid-state NMR. J Am Chem Soc 141:17314–17321

Article  MATH  Google Scholar 

Skinner SP, Fogh RH, Boucher W, Ragan TJ, Mureddu LG, Vuister GW (2016) CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis. J Biomol NMR 66:111–124

Article  Google Scholar 

Stanek J, Andreas LB, Jaudzems K, Cala D, Lalli D, Bertarello A, Schubeis T, Akopjana I, Kotelovica S, Tars K, Pica A, Leone S, Picone D, Xu Z, Dixon NE, Martinez D, Berbon M, El Mammeri N, Noubhani A, Saupe S, Habenstein B, Loquet A, Pintacuda G (2016) NMR spectroscopic assignment of backbone and side-chain protons in fully protonated proteins: Microcrystals, Sedimented assemblies, and amyloid fibrils. Angew Chemie Int Ed 55:15504–15509

Article  Google Scholar 

Tan KO, Agarwal V, Lakomek N-A, Penzel S, Meier BH, Ernst M (2018) Efficient low-power TOBSY sequences for fast MAS. Solid State Nucl Magn Reson 89:27–34

Article  ADS  Google Scholar 

Varadi M, Bertoni D, Magana P, Paramval U, Pidruchna I, Radhakrishnan M, Tsenkov M, Nair S, Mirdita M, Yeo J, Kovalevskiy O, Tunyasuvunakool K, Laydon A, Žídek A, Tomlinson H, Hariharan D, Abrahamson J, Green T, Jumper J, Birney E, Steinegger M, Hassabis D, Velankar S (2024) AlphaFold protein structure database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Res 52:D368–D375

Article  Google Scholar 

Verel R, Ernst M, Meier BH (2001) Adiabatic Dipolar recoupling in solid-state NMR: the DREAM Scheme. J Magn Reson 150:81–99

Article  ADS  MATH  Google Scholar 

Wang Y, Zhang Y, Ha Y (2006) Crystal structure of a rhomboid family intramembrane protease. Nature 444:179–180

Article  ADS  MATH  Google Scholar 

Wu Z, Yan N, Feng L, Oberstein A, Yan H, Baker RP, Gu L, Jeffrey PD, Urban S, Shi Y (2006) Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry. Nat Struct Mol Biol 13:1084–1091

Article  Google Scholar 

Xiang S, Chevelkov V, Becker S, Lange A (2014) Towards automatic protein backbone assignment using proton-detected 4D solid-state NMR data. J Biomol NMR 60:85–90

Article  Google Scholar 

Xiang S, Biernat J, Mandelkow E, Becker S, Linser R (2016) Backbone assignment for minimal protein amounts of low structural homogeneity in the absence of deuteration. Chem Commun 52:4002–4005

Article  Google Scholar 

Zhou Z, Kümmerle R, Qiu X, Redwine D, Cong R, Taha A, Baugh D, Winniford B (2007) A new decoupling method for accurate quantification of polyethylene copolymer composition and triad sequence distribut

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