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SedNMR: a web tool for optimizing sedimentation of macromolecular solutes for SSNMR

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Abstract

We have proposed solid state NMR (SSNMR) of sedimented solutes as a novel approach to sample preparation for biomolecular SSNMR without crystallization or other sample manipulations. The biomolecules are confined by high gravity—obtained by centrifugal forces either directly in a SSNMR rotor or in a ultracentrifugal device—into a hydrated non-crystalline solid suitable for SSNMR investigations. When gravity is removed, the sample reverts to solution and can be treated as any solution NMR sample. We here describe a simple web tool to calculate the relevant parameters for the success of the experiment.

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References

  • Ader C, Schneider R, Seider K, Etzkorn M, Becker S, Baldus M (2009) Structural rearrangements of membrane proteins probed by water-edited solid-state NMR spectroscopy. J Am Chem Soc 131:170–176

    Google Scholar 

  • Akbey Ü, van Rossum B-J, Oschkinat H (2012) Practical aspects of high-sensitivity multidimensional 13C MAS NMR spectroscopy of perdeuterated proteins. J Magn Reson 217:77–85

    ADS  Google Scholar 

  • Andersson KM, Hovmoller S (2000) The protein content in crystals and packing coefficients in different space groups. Acta Crystallogr D Biol Crystallogr 56:789–790

    Google Scholar 

  • Asami S, Szekely K, Schanda P, Meier BH, Reif B (2012) Optimal degree of protonation for (1)H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency. J Biomol NMR 54:155–168

    Google Scholar 

  • Balbo J, Mereghetti P, Herten D-P, Wade RC (2013) The shape of protein crowders is a major determinant of protein diffusion. Biophys J 104:1576–1584

    Google Scholar 

  • Baldwin AJ, Walsh P, Hansen DF, Hilton GR, Benesch JLP, Sharpe S, Kay LE (2012) Probing dynamic conformations of the high-molecular-weight αB-crystallin heat shock protein ensemble by NMR spectroscopy. J Am Chem Soc 134:15343–15350

    Google Scholar 

  • Barbato G, Ikura M, Kay LE, Pastor RW, Bax A (1992) Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy; the central helix is flexible. Biochemistry 31:5269–5278

    Google Scholar 

  • Bayro MJ, Debelouchina GT, Eddy MT, Birkett NR, MacPhee CE, Rosay MM, Maas W, Dobson CM, Griffin RG (2011) Intermolecular structure determination of amyloid fibrils with magic-angle spinning and dynamic nuclear polarization NMR. J Am Chem Soc 133:13967–13974

    Google Scholar 

  • Bermel W, Bertini I, Felli IC, Matzapetakis M, Pierattelli R, Theil EC, Turano P (2007) A method for Cα direct-detection in protonless NMR. J Magn Reson 188:301–310

    ADS  Google Scholar 

  • Bermel W, Felli IC, Kümmerle R, Pierattelli R (2008) 13C direct-detection biomolecular NMR. Concepts Magn Reson 32A:183–200

    Google Scholar 

  • Bermel W, Bertini I, Felli IC, Peruzzini R, Pierattelli R (2010) Exclusively heteronuclear NMR experiments to obtain structural and dynamic information on proteins. ChemPhysChem 11:689–695

    Google Scholar 

  • Bertini I, Calderone V, Fragai M, Jaiswal R, Luchinat C, Melikian M, Mylonas E, Svergun D (2008) Evidence of reciprocal reorientation of the catalytic and hemopexin-like domains of full-length MMP-12. J Am Chem Soc 130:7011–7021

    Google Scholar 

  • Bertini I, Kursula P, Luchinat C, Parigi G, Vahokoski J, Willmans M, Yuan J (2009) Accurate solution structures of proteins from X-ray data and minimal set of NMR data: calmodulin peptide complexes as examples. J Am Chem Soc 131:5134–5144

    Google Scholar 

  • Bertini I, Bhaumik A, De Paepe G, Griffin RG, Lelli M, Lewandowski JR, Luchinat C (2010a) High-resolution solid-state NMR structure of a 17.6 kDa protein. J Am Chem Soc 132:1032–1040

    Google Scholar 

  • Bertini I, Emsley L, Lelli M, Luchinat C, Mao J, Pintacuda G (2010b) Ultra-fast MAS solid-state NMR permits extensive 13C and 1H detection in paramagnetic metalloproteins. J Am Chem Soc 132:5558–5559

    Google Scholar 

  • Bertini I, Case DA, Ferella L, Giachetti A, Rosato A (2011a) A grid-enable web portal for NMR structure refinement with AMBER. Bioinformatics 27:2384–2390

    Google Scholar 

  • Bertini I, Emsley L, Felli IC, Laage S, Lesage A, Lewandoski DA, Marchetti A, Pierattelli R, Pintacuda G (2011b) High-resolution and sensitivity through-bond correlations in ultra-fast MAS solid-state NMR. Chem Sci 2:345–348

    Google Scholar 

  • Bertini I, Gonnelli L, Luchinat C, Mao J, Nesi A (2011c) A new structural model Aß40 fibrils. J Am Chem Soc 133:16013–16022

    Google Scholar 

  • Bertini I, Luchinat C, Parigi G, Ravera E, Reif B, Turano P (2011d) Solid-state NMR of proteins sedimented by ultracentrifugation. Proc Natl Acad Sci USA 108:10396–10399

    ADS  Google Scholar 

  • Bertini I, Engelke F, Gonnelli L, Knott B, Luchinat C, Osen D, Ravera E (2012a) On the use of ultracentrifugal devices for sedimented solute NMR. J Biomol NMR 54:123–127

    Google Scholar 

  • Bertini I, Engelke F, Luchinat C, Parigi G, Ravera E, Rosa C, Turano P (2012b) NMR properties of sedimented solutes. Phys Chem Chem Phys 14:439–447

    Google Scholar 

  • Bertini I, Luchinat C, Parigi G, Ravera E (2013) SedNMR: on the edge between solution and solid state NMR. Acc Chem Res 46:2059–2069

    Google Scholar 

  • Bhaumik A, Luchinat C, Parigi G, Ravera E, Rinaldelli M (2013) NMR crystallography on paramagnetic systems: solved and open issues. Cryst Eng Comm 15:8639–8656

    Google Scholar 

  • Bjerring M, Paaske B, Oschkinat H, Akbey Ü, Nielsen NC (2012) Rapid solid-state NMR of deuterated proteins by interleaved cross-polarization from 1H and 2H nuclei. J Magn Reson 214:324–328

    ADS  Google Scholar 

  • Böckmann A, Gardiennet C, Verel R, Hunkeler A, Loquet A, Pintacuda G, Emsley L, Meier BH, Lesage A (2009) Characterization of different water pools in solid-state NMR protein samples. J Biomol NMR 45:319–327

    Google Scholar 

  • Byeon I-JL, Hou G, Han Y, Suiter CL, Ahn J, Jung J, Byeon C-H, Gronenborn AM, Polenova T (2012) Motions on the millisecond time scale and multiple conformations of HIV-1 capsid protein: implications for structural polymorphism of CA assemblies. JACS 134:6455–6466

    Google Scholar 

  • Cady SD, Schmidt-Rohr K, Wang J, Soto CS, DeGrado WF, Hong M (2010) Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers. Nature 463:689–692

    ADS  Google Scholar 

  • Chou JJ, Li S, Klee CB, Bax A (2001) Solution structure of Ca2 + calmodulin reveals flexible hand-like properties of its domains. Nat Struct Biol 8:990–997

    Google Scholar 

  • Debelouchina GT, Platt GW, Bayro MJ, Radford SE, Griffin RG (2010) Magic angle spinning NMR analysis of beta(2)-microglobulin amyloid fibrils in two distinct morphologies. J Am Chem Soc 132:10414–10423

    Google Scholar 

  • Ding Y, Yao Y, Marassi FM (2013) Membrane protein structure determination in membrana. Acc Chem Res 46:2182–2190

    Google Scholar 

  • Fernández C, Wider G (2003) TROSY in NMR studies of the structure and function of large biological macromolecules. Curr Opin Struct Biol 13:570–580

    Google Scholar 

  • Fiaux J, Bertelsen EB, Horwich AL, Wüthrich K (2002) NMR analysis of a 900 KDa GroEL GROES complex. Nature 418:207–211

    ADS  Google Scholar 

  • Fischer MW, Losonczi JA, Weaver JL, Prestegard JH (1999) Domain orientation and dynamics in multidomain proteins from residual dipolar couplings. Biochemistry 38:9013–9022

    Google Scholar 

  • Fragai M, Luchinat C, Martelli T, Ravera E, Sagi I, Solomonov I, Udi Y (2013a) SSNMR of biosilica-entrapped enzymes. Chem Commun. doi:10.1039/c3cc46896h

  • Fragai M, Luchinat C, Parigi G, Ravera E (2013b) Practical considerations over spectral quality in solid state NMR spectroscopy of soluble proteins. J Biomol NMR 57:155–166

    Google Scholar 

  • Gardiennet C, Schütz AK, Hunkeler A, Kunert B, Terradot L, Böckmann A, Meier BH (2012) A sedimented sample of a 59 kDa dodecameric helicase yields high-resolution solid-state NMR spectra. Angew Chem Int Edition 51:7855–7858

    Google Scholar 

  • Garrett RH, Grisham CM (2012) Biochemistry, 5th edn. Brooks/Cole, Belmont

    Google Scholar 

  • Gelis I, Vitzthum V, Dhimole N, Caporini MA, Schedlbauer A, Carnevale D, Connell SR, Fucini P, Bodenhausen G (2013) Solid-state NMR enhanced by dynamic nuclear polarization as a novel tool for ribosome structural biology. J Biomol NMR 56:85–93

    Google Scholar 

  • Giffard M, Hediger S, Lewandowski JR, Bardet M, Simorre JP, Griffin RG, De Paëpe G (2012) Compensated second-order recoupling: application to third spin assisted recoupling. Phys Chem Chem Phys 14:7246–7255

    Google Scholar 

  • Goobes G, Goobes R, Schueler-Furman O, Baker D, Stayton PS, Drobny GP (2006) Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals. Proc Natl Acad Sci USA 103:16083–16088

    ADS  Google Scholar 

  • Goobes G, Goobes R, Shaw WJ, Gibson JM, Long JR, Raghunathan V, Schueler-Furman O, Popham JM, Baker D, Campbell CT, Stayton PS, Drobny GP (2007a) The structure, dynamics, and energetics of protein adsorption: lessons learned from adsorption of statherin to hydroxyapatite. Magn Reson Chem 45:S32–S47

    Google Scholar 

  • Goobes G, Stayton PS, Drobny GP (2007b) Solid-state NMR studies of molecular recognition at protein-mineral interfaces. Progr NMR Spectrosc 50:71–85

    Google Scholar 

  • Guo C, Zhang D, Tugarinov V (2008) An NMR experiment for simultaneous TROSY-based detection of amide and methyl groups in large proteins. J Am Chem Soc 130:10872–10873

    Google Scholar 

  • Habenstein B, Wasmer C, Bousset L, Sourigues Y, Schutz A, Loquet A, Meier BH, Melki R, Bockmann A (2011) Extensive de novo solid-state NMR assignments of the 33 kDa C-terminal domain of the Ure2 prion. J Biomol NMR 51:235–243

    Google Scholar 

  • Habenstein B, Bousset L, Sourigues Y, Kabani M, Loquet A, Meier BH, Melki R, Böckmann A (2012) A native-like conformation for the C-terminal domain of the prion Ure2p within its fibrillar form. Angew Chem Int Ed Engl 51:7963–7966

    Google Scholar 

  • Haeberlen U, Waugh JS (1969) Spin-lattice relaxation in periodically perturbed systems. Phys Rev 185:420–429

    ADS  Google Scholar 

  • Haller JD, Schanda P (2013) Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. J Biomol NMR. doi:10.1007/s10858-013-9787-x

  • Harbison GS, Smith SO, Pardoen JA, Courtin JML, Lugtenburg J, Herzfeld J, Mathies RA, Griffin RG (1985) Solid-state carbon-13 NMR detection of a perturbed 6-s-trans chromophore in bacteriorhodopsin. Biochemistry 24:6955–6962

    Google Scholar 

  • Hefke F, Bagaria A, Reckel S, Ullrich SJ, Dötsch V, Glaubitz C, Güntert P (2011) Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm. J Biomol NMR 49:75–84

    Google Scholar 

  • Hong M (2006) Solid-state NMR studies of the structure, dynamics, and assembly of β-sheet membrane peptides and α-helical membrane proteins with antibiotic activities. Acc Chem Res 39:176–183

    Google Scholar 

  • Hong M, Schmidt-Rohr K (2013) Magic-angle-spinning NMR techniques for measuring long-range distances in biological macromolecules. Acc Chem Res 46:2154–2163

    Google Scholar 

  • Hong M, Zhang Y, Hu F (2011) Membrane protein structure and dynamics from NMR spectroscopy. Annu Rev Phys Chem 63:1–24

    Google Scholar 

  • Hu B, Lafon OTJ, Chen Q, Amoureux J-P (2011) Broad-band homo-nuclear correlations assisted by 1H irradiation for biomolecules in very high magnetic field at fast and ultra-fast MAS frequencies. J Magn Reson 212:320–329

    ADS  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

    Google Scholar 

  • Kennedy SD, Bryant RG (1990) Structural effects of hydration: studies of Lysozyme by 13C solids NMR. Biopolymers 29:1801–1806

    Google Scholar 

  • Kervern G, Steuernagel S, Engelke F, Pintacuda G, Emsley L (2007) Absence of Curie relaxation in paramagnetic solids yields long 1H coherence lifetimes. J Am Chem Soc 129:14118–14119

    Google Scholar 

  • Ketchem RR, Hu W, Cross TA (1993) High-resolution conformation of gramicidin-A in a lipid bilayer by solid-state NMR. Science 261:1457–1460

    ADS  Google Scholar 

  • Knight MJ, Webber AL, Pell AJ, Guerry P, Barbet-Massin E, Bertini I, Felli IC, Gonnelli L, Pierattelli R, Emsley L, Lesage A, Hermann T, Pintacuda G (2011) Fast resonance assignment and fold determination of human superoxide dismutase by high-resolution proton-detected solid state MAS NMR spectroscopy. Angew Chem Int Edition 50:11697–11701

    Google Scholar 

  • Knight MJ, Pell AJ, Bertini I, Felli IC, Gonnelli L, Pierattelli R, Hermann T, Emsley L, Pintacuda G (2012) Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR. Proc Natl Acad Sci USA 109:11095–11100

    ADS  Google Scholar 

  • Knight MJ, Felli IC, Pierattelli R, Emsley L, Pintacuda G (2013) Magic angle spinning NMR of paramagnetic proteins. Acc Chem Res 46:2108–2116

    Google Scholar 

  • Koenig SH, Brown RD III (1990) Field-cycling relaxometry of protein solutions and tissue: implications for MRI. Progr NMR Spectrosc 22:487–567

    Google Scholar 

  • Laage S, Marchetti A, Sein J, Pierattelli R, Sass HJ, Grzesiek S, Lesage A, Pintacuda G, Emsley L (2008) Band-selective 1H–13C cross-polarization in fast MAS solid-state NMR spectroscopy. J Am Chem Soc 130:17216–17217

    Google Scholar 

  • Lamley JM, Lewandowski JR (2012) Simultaneous acquisition of homonuclear and heteronuclear long-distance contacts with time-shared third spin assisted recoupling. J Magn Reson 218:30–34

    ADS  Google Scholar 

  • Lange V, Becker-Baldus J, Kunert B, van Rossum BJ, Casagrande F, Engel A, Roske Y, Scheffel FM, Schneider E, Oschkinat H (2010) A MAS NMR study of the bacterial ABC transporter ArtMP. ChemBioChem 11:547–555

    Google Scholar 

  • Lewandowski JR (2013) Advances in solid-state relaxation methodology for probing site-specific protein dynamics. Acc Chem Res 46:2018–2027

    Google Scholar 

  • Lewandowski JR, Sein J, Sass HJ, Grzesiek S, Blackledge M, Emsley L (2010) Measurement of site-specific 13C spin-lattice relaxation in a crystalline protein. J Am Chem Soc 132:8252–8254

    Google Scholar 

  • Lewandowski JR, Dumez JN, Akbey Ü, Franks WT, Emsley L, Oschkinat H (2011a) 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

    Google Scholar 

  • Lewandowski JR, Sass HJ, Grzesiek S, Blackledge M, Emsley L (2011b) Site-specific measurement of slow motions in proteins. J Am Chem Soc 133:16762–16765

    Google Scholar 

  • Linden AH, Franks WT, Akbey Ü, Lange S, van Rossum B-J, Oschkinat H (2011) Cryogenic temperature effects and resolution upon slow cooling of protein preparations in solid state NMR. J Biomol NMR 51:283–292

    Google Scholar 

  • Loening NM, Bjerring M, Nielsen NC, Oschkinat H (2012) A comparison of NCO and NCA transfer methods for biological solid-state NMR spectroscopy. J Magn Reson 214:81–90

    ADS  Google Scholar 

  • Long JR, Shaw WJ, Stayton PS, Drobny GP (2001) Structure and dynamics of hydrated statherin on hydroxyapatite as determined by solid-state NMR. Biochemistry 40:15451–15455

    Google Scholar 

  • Lopez del Amo JM, Schmidt M, Fink U, Dasari M, Fändrich M, Reif B (2012) An asymmetric dimer as the basic subunit in Alzheimer’s disease amyloid β fibrils. Angew Chem Int Edition Engl 51:6136–6139

    Google Scholar 

  • Loquet A, Giller K, Becker S, Lange A (2010) Supramolecular interactions probed by (13)C-(13)C solid-state NMR spectroscopy. J Am Chem Soc 132:15164–15166

    Google Scholar 

  • Loquet A, Sgourakis NG, Gupta R, Giller K, Riedel D, Goosmann C, Griesinger C, Kolbe M, Baker D, Becker S, Lange A (2012) Atomic model of the type III secretion system needle. Nature 486:276–279

    ADS  Google Scholar 

  • Loquet A, Habenstein B, Lange A (2013) Structural investigations of molecular machines by solid-state NMR. Acc Chem Res 46:2070–2079

    Google Scholar 

  • Luchinat C, Parigi G, Ravera E, Rinaldelli M (2012) Solid state NMR crystallography through paramagnetic restraints. J Am Chem Soc 134:5006–5009

    Google Scholar 

  • Luchinat C, Parigi G, Ravera E (2013) Water and protein dynamics in sedimented systems: a relaxometric investigation. Chem Phys Chem 14:3156–3161

    Google Scholar 

  • Lundh S (1980) Concentrated protein solutions in the analytical ultracentrifuge. J Polym Sci Polym Phys Edition 18:1963–1978

    ADS  Google Scholar 

  • Lundh S (1985) Ultacentrifugation of concentrated biopolymer solutions and effect of ascorbate. Arch Biochem Biophys 241:265–274

    Google Scholar 

  • Lv G, Kumar A, Giller K, Orcellet ML, Riedel D, Fernandez CO, Becker S, Lange A (2012) Structural comparison of mouse and human α-synuclein amyloid fibrils by solid-state NMR. J Mol Biol 420:99–111

    Google Scholar 

  • Mainz A, Jehle S, van Rossum BJ, Oschkinat H, Reif B (2009) Large protein complexes with extreme rotational correlation times investigated in solution by magic-angle-spinning NMR spectroscopy. J Am Chem Soc 131:15968–15969

    Google Scholar 

  • Mainz A, Bardiaux B, Kuppler F, Multhaup G, Felli IC, Pierattelli R, Reif B (2012) Structural and mechanistic implications of metal-binding in the small heat-shock protein αB-crystallin. J Biol Chem 287:1128–1138

    Google Scholar 

  • Mainz A, Religa TL, Sprangers R, Linser R, Kay LE, Reif B (2013) NMR spectroscopy of soluble protein complexes at one mega-dalton and beyond. Angew Chem Int Edition 52:8746–8751

    Google Scholar 

  • Marassi FM, Opella SJ (2000) A solid-state NMR index of helical membrane protein structure and topology. J Magn Reson 144:150–155

    ADS  Google Scholar 

  • Marassi FM, Ramamoorthy A, Opella SJ (1997) Complete resolution of the solid-state NMR spectrum of a uniformly 15 N-labeled membrane protein in phospholipid bilayers. Proc Natl Acad Sci USA 94:8551–8556

    ADS  Google Scholar 

  • Marassi FM, Das BB, Lu GJ, Nothnagel HJ, Park SH, Son WS, Tian Y, Opella SJ (2011) Structure determination of membrane proteins in five easy pieces. Methods 55:363–369

    Google Scholar 

  • Martin RW, Zilm KW (2003) Preparation of protein nanocrystals and their characterization by solid state NMR. J Magn Reson 165:162–174

    ADS  Google Scholar 

  • Matti Mariq M, Waugh JS (1979) NMR in rotating solids. J Chem Phys 70:3300–3316

    ADS  Google Scholar 

  • Matzapetakis M, Turano P, Theil EC, Bertini I (2007) 13C-13C NOESY spectra of a 480 kDa protein: solution NMR of ferritin. J Biomol NMR 38:237–242

    Google Scholar 

  • Murray DT, Das N, Cross TA (2013) Solid state NMR strategy for characterizing native membrane protein structures. Acc Chem Res 46:2172–2181

    Google Scholar 

  • Nielsen AB, Székely K, Gath J, Ernst M, Nielsen NC, Meier BH (2012) Simultaneous acquisition of PAR and PAIN spectra. J Biomol NMR 52:283–288

    Google Scholar 

  • Oliphant TE (2007) Python for scientific computing. Comput Sci Eng 9:10–20

    Google Scholar 

  • Opella SJ (2013) Structure determination of membrane proteins in their native phospholipid bilayer environment by rotationally aligned solid-state NMR spectroscopy. Acc Chem Res 46:2145–2153

    Google Scholar 

  • Opella SJ, Marassi FM (2004) Structure determination of membrane proteins by NMR spectroscopy. NMR Spectrosc Chem Rev 104:3587–3606

    Google Scholar 

  • Parthasarathy S, Long F, Miller Y, Xiao Y, McElheny D, Thurber K, Ma B, Nussinov R, Ishii Y (2011) Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer’s ß by solid-state NMR spectroscopy. J Am Chem Soc 133:3390–3400

    Google Scholar 

  • Pauli J, van Rossum B, Forster H, de Groot HJ, Oschkinat H (2000) Sample optimization and identification of signal patterns of amino acid side chains in 2D RFDR spectra of the alpha-spectrin SH3 domain. J Magn Reson 143:411–416

    ADS  Google Scholar 

  • Petkova AT, Ishii Y, Balbach JJ, Antzutkin ON, Leapman RD, Delaglio F, Tycko R (2002) A structural model for Alzheimer’s beta-amyloid fibrils based on experimental constraints from solid state NMR. Proc Natl Acad Sci USA 99:16742–16747

    ADS  Google Scholar 

  • Petkova AT, Baldus M, Belenky M, Hong M, Griffin RG, Herzfeld J (2003) Backbone and side chain assignment strategies for multiply labeled membrane peptides and proteins in the solid state. J Magn Reson 160:1–12

    ADS  Google Scholar 

  • Polenova T (2011) Protein NMR spectroscopy: spinning into focus. Nat Chem 3:759–760

    Google Scholar 

  • Poon DKY, Withers SG, McIntosh LP (2007) Direct demonstration of the flexibility of the glycosylated proline-threonine linker in the Cellulomonas fimi xylanase Cex through NMR spectroscopic analysis. J Biol Chem 282:2091–2100

    Google Scholar 

  • Qiang W, Yau W-M, Luo Y, Mattson MP, Tycko R (2012) Antiparallel β-sheet architecture in Iowa-mutant β-amyloid fibrils. Proc Natl Acad Sci USA 109:4443–4448

    ADS  Google Scholar 

  • Quillin ML, Matthews BW (2000) Accurate calculation of the density of proteins. Acta Cryst D 56:791–794

    Google Scholar 

  • Ravera E, Corzilius B, Michaelis VK, Rosa C, Griffin RG, Luchinat C, Bertini I (2013a) Dynamic nuclear polarization of sedimented solutes. J Am Chem Soc 135:1641–1644

    Google Scholar 

  • Ravera E, Parigi G, Mainz A, Religa TL, Reif B, Luchinat C (2013b) Experimental determination of microsecond reorientation correlation times in protein solutions. J Phys Chem B 117:3548–3553

    Google Scholar 

  • Riek R, Wider G, Pervushin K, Wüthrich K (1999) Polarization transfer by cross-correlated relaxation in solution NMR with very large molecules. Proc Natl Acad Sci USA 96:4918–4923

    ADS  Google Scholar 

  • Rivas G, Minton AP (2011) Beyond the second virial coefficient: sedimentation equilibrium in highly non-ideal solutions. Methods 54:167–174

    Google Scholar 

  • Roerich A, Drobny GP (2013) Solid-state NMR studies of biomineralization peptides and proteins. Acc Chem Res 46:2136–2144

    Google Scholar 

  • Rothen A (1944) Ferritin and apoferritin in the ultracentrifuge: studies on the relationship of ferritin and apoferritin; precision measurements of the rates of sedimentation of apoferritin. J Biol Chem 152:679–693

    Google Scholar 

  • Schanda P, Meier BH, Ernst M (2010) Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. J Am Chem Soc 132:15957–15967

    Google Scholar 

  • Sharma M, Yi MG, Dong H, Qin HJ, Peterson E, Busath DD, Zhou HX, Cross TA (2010) Insight into the mechanism of the influenza A proton channel from a structure in a lipid bilayer. Science 330:509–512

    ADS  Google Scholar 

  • Skrynnikov NR, Goto NK, Yang D, Choy W-Y, Tolman JR, Mueller GA, Kay LE (2000) Orienting domains in proteins using dipolar couplings measured by liquid-state NMR: differences in solution and crystal forms of maltodextrin binding protein loaded with β-cyclodextrin. J Mol Biol 295:1265–1273

    Google Scholar 

  • Sun SJ, Siglin A, Williams JC, Polenova T (2009) Solid-state and solution NMR studies of the CAP-Gly domain of mammalian dynactin and its interaction with microtubules. J Am Chem Soc 131:10113–10126

    Google Scholar 

  • Tugarinov V, Choy WY, Orekhov VY, Kay LE (2005a) Solution NMR-derived global fold of a monomeric 82-kDa enzyme. Proc Natl Acad Sci USA 102:622–627

    ADS  Google Scholar 

  • Tugarinov V, Kay LE, Ibraghimov I, Orekhov VY (2005b) High-resolution four-dimensional 1H-13C NOE spectroscopy using methyl-TROSY, sparse data acquisition, and multidimensional decomposition. J Am Chem Soc 127:2767–2775

    Google Scholar 

  • Tugarinov V, Kanelis V, Kay LE (2006) Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy. Nat Protoc 1:749–754

    Google Scholar 

  • Tycko R, Ishii Y (2003) Constraints on supramolecular structure in amyloid fibrils from two-dimensional solid-state NMR spectroscopy with uniform isotopic labeling. J Am Chem Soc 125:6606–6607

    Google Scholar 

  • Ullrich SJ, Glaubitz C (2013) Perspectives in enzymology of membrane proteins by solid-state NMR. Acc Chem Res 46:2164–2171

    Google Scholar 

  • Van Holde KE, Baldwin RL (1958) Rapid attainment of sedimentation equilibrium. J Phys Chem 62:734–743

    Google Scholar 

  • Venturi L, Woodward N, Hibberd D, Marighedo N, Gravelle A, Ferrante G, Hills BP (2008) Multidimensional cross-correlation relaxometry of aqueous protein systems. Appl Magn Reson 33:213–234

    Google Scholar 

  • Voss NR, Gerstein M (2005) Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly. J Mol Biol 346:477–492

    Google Scholar 

  • Wassenaar TA, van Dijk M, Loureiro-Ferreira N, van der Schot G, de Vries SJ, Schmitz C, van der Zwan J, Boelens R, Giachetti A, Ferella L, Rosato A, Bertini I, Herrmann T, Jonker HRA, Bagaria A, Jaravine V, Guntert P, Schwalbe H, Vranken WF, Doreleijers JF, Vriend G, Vuister GW, Franke D, Kikhney A, Svergun DI, Fogh RH, Ionides J, Laue ED, Spronk C, Jurksa S, Verlato M, Badoer S, Dal Pra S, Mazzucato M, Frizziero E, Bonvin AMJJ (2012) WeNMR: structural biology on the grid. J Grid Comput 10:743–767

    Google Scholar 

  • Webber AL, Pell AJ, Barbet-Massin E, Knight MJ, Bertini I, Felli IC, Pierattelli R, Emsley L, Lesage A, Pintacuda G (2012) Combination of DQ and ZQ coherences for sensitive through-bond NMR correlation experiments in biosolids under ultra-fast MAS. ChemPhysChem 13:2405–2411

    Google Scholar 

  • Weingarth M, Baldus M (2013) Solid-state NMR-based approaches for supramolecular structure elucidation. Acc Chem Res 46:2164–2171

    Google Scholar 

  • Westfeld T, Verel R, Ernst M, Böckmann A, Meier BH (2012) Properties of the DREAM scheme and its optimization for application to proteins. J Biomol NMR 53:103–112

    Google Scholar 

  • Wider G (2005) NMR techniques used with very large biological macromolecules in solution. Methods Enzymol 394:382–398

    Google Scholar 

  • Yan S, Suiter CL, Hou G, Zhang H, Polenova T (2013) Probing structure and dynamics of protein assemblies by magic angle spinning NMR spectroscopy. Acc Chem Res 46:2047–2058

    Google Scholar 

  • Yang J, Aslimovska L, Glaubitz C (2011) Molecular dynamics of proteorhodopsin in lipid bilayers by solid-state NMR. J Am Chem Soc 133:4874–4881

    Google Scholar 

  • Zinkevich T, Chevelkov V, Reif B, Saalwachter K, Krushelnitsky A (2013) Internal protein dynamics on ps to mus timescales as studied by multi-frequency N solid-state NMR relaxation. J Biomol NMR. doi:10.1007/s10858-013-9782-2

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Acknowledgments

This work has been supported by the EC contracts East-NMR No. 228461, WeNMR No. 261572 and Bio-NMR No. 261863, INSTRUCT (European FP7 e-Infrastructure Grant, Contract No. 211252, http://www.instruct-fp7.eu/), the project PRIN (2009FAKHZT_001) “Biologia strutturale meccanicistica: avanzamenti metodologici e biologici” and Ente Cassa Risparmio Firenze. We thank Frank Engelke (Bruker Biospin), Paolo Santino (Agilent Tech.), Yusuke Nishiyama (Jeol) and F. David Doty (Doty Scientific) for providing rotor specifications.

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Authors and Affiliations

  1. Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy

    Lucio Ferella, Claudio Luchinat, Enrico Ravera & Antonio Rosato

  2. Fondazione Farmacogenomica FiorGen Onlus, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy

    Claudio Luchinat

  3. Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy

    Claudio Luchinat, Enrico Ravera & Antonio Rosato

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  1. Lucio Ferella
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  2. Claudio Luchinat
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  3. Enrico Ravera
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Correspondence to Claudio Luchinat.

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Ferella, L., Luchinat, C., Ravera, E. et al. SedNMR: a web tool for optimizing sedimentation of macromolecular solutes for SSNMR. J Biomol NMR 57, 319–326 (2013). https://doi.org/10.1007/s10858-013-9795-x

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  • DOI: https://doi.org/10.1007/s10858-013-9795-x

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