5D solid-state NMR spectroscopy for facilitated resonance assignment

Ahlawat S, Mopidevi SMV, Taware PP, Raran-Kurussi S, Mote KR, Agarwal V (2023) Assignment of aromatic side-chain spins and characterization of their distance restraints at fast MAS. J Struct Biology: X 7:100082

Google Scholar 

Akbey Ü et al (2009) Optimum levels of exchangeable protons in perdeuterated proteins for proton detection in MAS solid-state NMR spectroscopy. J Biomol NMR 46:67–73

Article  Google Scholar 

Andreas LB et al (2015) Protein residue linking in a single spectrum for magic-angle spinning NMR assignment. J Biomol NMR 62:253–261

Article  Google Scholar 

Andreas LB et al (2016) Structure of fully protonated proteins by proton-detected magic-angle spinning NMR. Proc Natl Acad Sci USA 113:9187–9192

Article  ADS  Google Scholar 

Asami S, Reif B (2013) Proton-detected solid-state NMR spectroscopy at aliphatic sites: application to crystalline systems. Acc Chem Res 46:2089–2097

Article  Google Scholar 

Barbet-Massin E et al (2013) Out-and-back 13 C-13 C scalar transfers in protein resonance assignment by proton-detected solid-state NMR under ultra-fast MAS. J Biomol NMR 56:379–386

Article  Google Scholar 

Barbet-Massin E et al (2014) Rapid Proton-Detected NMR assignment for proteins with fast Magic Angle Spinning. J Am Chem Soc 136:11

Article  Google Scholar 

Becker LM et al (2023) The rigid core and flexible surface of ayloid fibrils probed by magic-angel-spinning NMR spectroscopy of aromatic residues. Angew Chem Int Ed e202219314

Bertarello A et al (2020) Picometer resolution structure of the coordination sphere in the metal-binding site in a metalloprotein by NMR. J Am Chem Soc 142:16757–16765

Article  Google Scholar 

Blahut J, Brandl MJ, Pradhan T, Reif B, Tosner 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 

Böckmann A, Ernst M, Meier BH (2015) Spinning proteins, the faster, the better? J Magn Reson 253:71–79

Article  ADS  Google Scholar 

Cala-De Paepe D, Stanek J, Jaudzems K, Tars K, Andreas LB, Pintacuda G (2017) Is protein deuteration beneficial for proton detected solid-state NMR at and above 100 kHz magic-angle spinning? Solid State Nucl Magn Reson 87:126–136

Article  Google Scholar 

Chevelkov V, Rehbein K, Diehl A, Reif B (2006) Ultrahigh Resolution in Proton Solid-State NMR spectroscopy at high levels of Deuteration. Angew Chem Int Ed 45:3878–3881

Article  Google Scholar 

Chevelkov V, Faelber K, Schrey A, Rehbein K, Diehl A, Reif B (2007) Differential line broadening in MAS solid-state NMR due to dynamic interference. J Am Chem Soc 129:10195–10200

Article  Google Scholar 

Chevelkov V, Fink U, Reif B (2009) Accurate determination of Order parameters from 1H,15 N Dipolar Couplings in MAS solid-state NMR experiments. J Am Chem Soc 131:14018–14022

Article  Google Scholar 

Chevelkov V, Giller K, Becker S, Lange A (2013) Efficient CO-CA transfer in highly deuterated proteins by band-selective homonuclear cross-polarization. J Magn Reson 230:205–211

Article  ADS  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. Journal of Biomolecular NMR 6

Fraga H et al (2017) Solid-state 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 

Gallo A, Franks WT, Lewandowski JR (2019) A suite of solid-state NMR experiments to utilize orphaned magnetization for assignment of proteins using parallel high and low gamma detection. J Magn Reson

Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P (2017) Protein conformational dynamics studied by 15 N and 1H R1ρ relaxation dispersion: application to wild-type and G53A ubiquitin crystals. Solid State Nucl Magn Reson 87:86–95

Article  Google Scholar 

Grohe K et al (2019) Exact distance measurements for structure and dynamics in solid proteins by fast-magic-angle-spinning NMR. Chem Commun 55:7899–7902

Article  ADS  Google Scholar 

Grohe K et al (2020) Protein Motional Details revealed by complementary Structural Biology techniques. Structure 28:1–11

Article  Google Scholar 

Helmus JJ, Jaroniec CP (2013) Nmrglue: an open source Python package for the analysis of multidimensional NMR data. J Biomol NMR 55:355–367

Article  Google Scholar 

Huber M, Böckmann A, Hiller S, Meier BH (2012) 4D solid-state NMR for protein structure determination. Phys Chem Chem Phys 14:5239–5246

Article  Google Scholar 

Hyberts SG, Robson SA, Wagner G (2013) Exploring signal-to-noise ratio and sensitivity in non-uniformly sampled multi-dimensional NMR spectra. J Biomol NMR 55:167–178

Article  Google Scholar 

Jain MG et al (2017) Selective 1H-1H Distance Restraints in fully protonated proteins by very fast Magic-Angle spinning solid-state NMR. J Phys Chem Lett 8

Kazimierczuk K, Zawadzka A, Koźmiński W (2009) Narrow peaks and high dimensionalities: exploiting the advantages of random sampling. J Magn Reson 197:219–228

Article  ADS  Google Scholar 

Klein A et al (2022a) Atomic-resolution Chemical Characterization of (2x)72 kDa Tryptophan Synthase via Four- and Five-Dimensional 1H-Detected Solid-State NMR. Proc Natl Acad Sci USA 119:e2114690119

Article  Google Scholar 

Klein A, Vasa SK, Söldner B, Grohe K, Linser R (2022b) 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 

Klukowski P, Riek R, Guntert P (2022) Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA. Nat Commun 13:6151

Article  ADS  Google Scholar 

Knight MJ et al (2011) Fast resonance assignment and fold determination of human superoxide dismutase by high-resolution proton-detected solid-state MAS NMR spectroscopy. Angew Chem Int Ed 50:11697–11701

Article  Google Scholar 

Knight MJ et al (2012) Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR. Proc Natl Acad Sci USA 109:11095–11100

Article  ADS  Google Scholar 

Kosiński K, Stanek J, Górka MJ, Żerko S, Koźmiński W (2017) Reconstruction of non-uniformly sampled five-dimensional NMR spectra by signal separation algorithm. J Biomol NMR 68:129–138

Article  Google Scholar 

Kulminskaya N, Vasa SK, Giller K, Becker S, Linser R (2015) Asynchronous through-bond homonuclear isotropic mixing: application to carbon-carbon transfer in perdeuterated proteins under MAS. J Biomol NMR 63:245–253

Article  Google Scholar 

Kulminskaya N, Vasa SK, Giller K, Becker S, Kwan A, Sunde M, Linser R (2016) Access to side-chain Carbon Information in Deuterated solids under fast MAS through Non-Rotor-Synchronized Mixing. Chem Commun 52:268–271

Article  Google Scholar 

Kurauskas V et al (2017) Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. Nat Commun 8:1–11

Article  Google Scholar 

Lalli D et al (2017) Proton-Based structural analysis of a Heptahelical transmembrane protein in lipid bilayers. J Am Chem Soc 139:13006–13012

Article  Google Scholar 

Lee W, Tonelli M, Markley JL (2014) NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31:1325–1327

Article  Google Scholar 

Lee W, Bahrami A, Dashti HT, Eghbalnia HR, Tonelli M, Westler WM, Markley JL (2019) I-PINE web server: an integrative probabilistic NMR assignment system for proteins. J Biomol NMR 73:213–222

Article  Google Scholar 

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

Article  Google Scholar 

Lewandowski JR, Dumez JN, Akbey Ü, Lange S, Emsley L, Oschkinat H (2011) Enhanced resolution and coherence lifetimes in the solid-state NMR spectroscopy of perdeuterated proteins under ultrafast magic-angle spinning. J Phys Chem Lett 2:2205–2211

Article  Google Scholar 

Linser R (2011) Side-chain to backbone correlations from solid-state NMR of Perdeuterated Proteins through combined excitation and long-range magnetization transfers. J Biomol NMR 51:221–226

Article  Google Scholar 

Linser R, Chevelkov V, Diehl A, Reif B (2007) Sensitivity enhancement using paramagnetic relaxation in MAS solid-state NMR of Perdeuterated Proteins. J Magn Reson 189:209–216

Article  ADS  Google Scholar 

Linser R, Fink U, Reif B (2010a) Assignment of dynamic regions in biological solids enabled by spin-state selective NMR experiments. J Am Chem Soc 132:8891–8893

Article  Google Scholar 

Linser R, Fink U, Reif B (2010b) Narrow carbonyl resonances in Proton-Diluted Proteins facilitate NMR assignments in the solid state. J Biomol NMR 47:1–6

Article  Google Scholar 

Linser R, Bardiaux B, Higman V, Fink U, Reif B (2011a) Structure calculation from unambiguous long-range Amide and Methyl 1H – 1H Distance Restraints for a microcrystalline protein with MAS solid-state NMR spectroscopy. J Am Chem Soc 133:5905–5912

Article  Google Scholar 

Linser R et al (2011b) Proton-Detected solid-state NMR spectroscopy of fibrillar and membrane proteins. Angew Chem Int Ed 50:4508–4512

Article  Google Scholar 

Linser R et al (2014) Solid-state NMR structure determination from Diagonal-Compensated, sparsely nonuniform-sampled 4D Proton-Proton Restraints. J Am Chem Soc 136:11002–11010

Article  Google Scholar 

Lu M et al (2020) Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR. Nat Struct Mol Biol 27:863–869

Article  Google Scholar 

Ma P et al (2014) Probing transient Conformational States of Proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angew Chem Int Ed 53:4312–4317

Article  Google Scholar 

Malär AA et al (2019) Quantifying proton NMR coherent linewidth in proteins under fast MAS conditions: a second moment approach. PhysChemChemPhys 21:18850–18865

Google Scholar 

Mandala VS, Williams JK, Hong M (2018) Structure and Dynamics of membrane proteins from solid-state NMR. Annu Rev Biophys 47:201–222

Article  Google Scholar 

Medeiros-Silva J, Mance D, Daniëls M, Jekhmane S, Houben K, Baldus M, Weingarth M (2016) 1H-Detected solid-state NMR studies of Water-Inaccessible Proteins in Vitro and in situ. Angew Chem. Int Ed 55

Nimerovsky E, Najbauer EE, Movellan KT, Xue K, Becker S, Andreas LB (2022) Modest offset difference internuclear selective transfer via Homonuclear Dipolar Coupling. J Phys Chem Lett 13:1540–1546

Article  Google Scholar 

Orton HW et al (2020) Protein NMR resonance assignment without spectral analysis: 5D SOlid-state automated projection SpectroscopY (SO-APSY). Angew Chem Int Ed 59:2380–2384

Article 

留言 (0)

沒有登入
gif