Nuclear overhauser spectroscopy of chiral CHD methylene groups

详细信息    查看全文

• 作者：Rafal Augustyniak ; Jan Stanek ; Henri Colaux…
• 关键词：NMR spectroscopy ; Protein structures ; Nuclear Overhauser spectroscopy ; Automatic structure calculation
• 刊名：Journal of Biomolecular NMR
• 出版年：2016
• 出版时间：January 2016
• 年：2016
• 卷：64
• 期：1
• 页码：27-37
• 全文大小：1,624 KB
• 参考文献：Atreya HS, Chary KVR (2001) Selective ‘unlabeling’ of amino acids in fractionally C-13 labeled proteins: an approach for stereospecific NMR assignments of CH3 groups in Val and Leu residues. J Biomol NMR 19:267–272CrossRef
  Bohlen JM, Bodenhausen G (1993) Experimental aspects of chirp NMR-spectroscopy. J Magn Reson A 102:293–301CrossRef ADS
  Cai ML, Liu JH, Gong YX, Krishnamoorthi R (1995) A practical method for stereospecific assignments of gamma-methylene and delta-methylene hydrogens via estimation of vicinal H-1–H-1 coupling-constants. J Magn Reson, Ser B 107:172–178. doi:10.​1006/​jmrb.​1995.​1074 CrossRef
  Carlomagno T, Peti W, Griesinger C (2000) A new method for the simultaneous measurement of magnitude and sign of D-1(CH) and D-1(HH) dipolar couplings in methylene groups. J Biomol NMR 17:99–109. doi:10.​1023/​a:​1008346902500 CrossRef
  Castellani F, van Rossum B, Diehl A, Schubert M, Rehbein K, Oschkinat H (2002) Structure of a protein determined by solid-state magic-angle-spinning NMR spectroscopy. Nature 420:98–102. doi:10.​1038/​nature01070 CrossRef ADS
  Clore GM, Appella E, Yamada M, Matsushima K, Gronenborn AM (1990) 3-dimensional structure of interleukin-8 in solution. Biochemistry 29:1689–1696. doi:10.​1021/​bi00459a004 CrossRef
  Clore GM, Bax A, Gronenborn AM (1991a) Stereospecific assignment of β-methylene protons in larger proteins using 3D 15 N-separated Hartmann–Hahn and 13C-separated rotating frame Overhauser spectroscopy. J Biomol NMR 1:13–22. doi:10.​1007/​bf01874566 CrossRef
  Clore GM, Wingfield PT, Gronenborn AM (1991b) High-resolution 3-dimensional structure of interleukin-1-beta in solution by 3-dimensional and 4-dimensional nuclear-magnetic-resonance spectroscopy. Biochemistry 30:2315–2323. doi:10.​1021/​bi00223a005 CrossRef
  Curley RW, Panigot MJ, Hansen AP, Fesik SW (1994) Stereospecific assignments of glycine in proteins by stereospecific deuteration and N-15 labeling. J Biomol NMR 4:335–340
  Driscoll PC, Gronenborn AM, Clore GM (1989) The influence of stereospecific assignments on the determination of 3-dimensional structures of proteins by nuclear magnetic-resonance spectroscopy—application to the sea-anemone protein BDS-I. FEBS Lett 243:223–233CrossRef
  Emerson SD, Montelione GT (1992) Accurate measurements of proton scalar coupling-constants using C-13 isotropic mixing spectroscopy. J Am Chem Soc 114:354–356. doi:10.​1021/​ja00027a052 CrossRef
  Emsley L, Bodenhausen G (1990a) Gaussian pulse cascades-new analytical functions for rectangular selective inversion and in-phase excitation in NMR. Chem Phys Lett 165:469–476CrossRef ADS
  Emsley L, Bodenhausen G (1990b) Phase-shifts induced by transient Bloch–Siegert effects in NMR. Chem Phys Lett 168:297–303CrossRef ADS
  Folmer RHA, Hilbers CW, Konings RNH, Nilges M (1997) Floating stereospecific assignment revisited: application to an 18 kDa protein and comparison with J-coupling data. J Biomol NMR 9:245–258. doi:10.​1023/​a:​1018670623695 CrossRef
  Gardner KH, Kay LE (1998) The use of H-2, C-13, N-15 multidimensional NMR to study the structure and dynamics of proteins. Annu Rev Biopys Biomol Struct 27:357–406CrossRef
  Geen H, Freeman R (1991) Band-selective radiofrequency pulses. J Magn Reson 93:93–141ADS
  Grzesiek S, Ikura M, Clore GM, Gronenborn AM, Bax A (1992) A 3D triple-resonance NMR technique for qualitative measurement of carbonyl-H-beta J couplings in isotopically enriched proteins. J Magn Reson 96:215–221ADS
  Grzesiek S, Anglister J, Ren H, Bax A (1993) C-13 line narrowing by H-2 decoupling in H-2/C-13/N-15-enriched proteins—application to triple-resonance 4D J-connectivity of sequential amides. J Am Chem Soc 115:4369–4370. doi:10.​1021/​ja00063a068 CrossRef
  Guntert P, Braun W, Billeter M, Wuthrich K (1989) Automated stereospecific H-1-NMR assignments and their impact on the precision of protein-structure determinations in solution. J Am Chem Soc 111:3997–4004CrossRef
  Güntert P, Billeter M, Ohlenschläger O, Brown L, Wüthrich K (1998) Conformational analysis of protein and nucleic acid fragments with the new grid search algorithm FOUND. J Biomol NMR 12:543–548. doi:10.​1023/​a:​1008391403193 CrossRef
  Hahnke MJ, Richter C, Heinicke F, Schwalbe H (2010) The HN(COCA)HAHB NMR experiment for the stereospecific assignment of H(beta)-protons in non-native states of proteins. J Am Chem Soc 132:918–919. doi:10.​1021/​ja909239w CrossRef
  Herrmann T, Guntert P, Wuthrich K (2002a) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209–227. doi:10.​1016/​s0022-2836(02)00241-3 CrossRef
  Herrmann T, Guntert P, Wuthrich K (2002b) Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J Biomol NMR 24:171–189. doi:10.​1023/​a:​1021614115432 CrossRef
  Kainosho M, Torizawa T, Iwashita Y, Terauchi T, Ono AM, Guntert P (2006) Optimal isotope labelling for NMR protein structure determinations. Nature 440:52–57. doi:10.​1038/​nature04525 CrossRef ADS
  Kazimierczuk K, Zawadzka A, Koźmiński W, Zhukov I (2008) Determination of spin–spin couplings from ultrahigh resolution 3D NMR spectra obtained by optimized random sampling and multidimensional Fourier transformation. J Am Chem Soc 130:5404–5405. doi:10.​1021/​ja800622p CrossRef
  Kazimierczuk K, Stanek J, Zawadzka-Kazimierczuk A, Kozminski W (2010) Random sampling in multidimensional NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 57:420–434. doi:10.​1016/​j.​pnmrs.​2010.​07.​002 CrossRef
  Kordel J, Skelton NJ, Akke M, Chazin WJ (1993) High-resolution solution structure of calcium-loaded calbindin-D(9 k). J Mol Biol 231:711–734CrossRef
  Kordel J, Pearlman DA, Chazin WJ (1997) Protein solution structure calculations in solution: solvated molecular dynamics refinement of calbindin D-9k. J Biomol NMR 10:231–243CrossRef
  Kumar A, Ernst RR, Wüthrich K (1980) A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton–proton cross-relaxation networks in biological macromolecules. Biochem Biophys Res Commun 95:1–6CrossRef
  Kumar A, Grace RCR, Madhu PK (2000) Cross-correlations in NMR. Prog NMR Spectrosc 37:191–319CrossRef
  Kupce E, Freeman R (1995) Adiabatic pulses for wideband inversion and broadband decoupling. J Magn Reson Ser A 115:273–276CrossRef ADS
  Kushlan DM, Lemaster DM (1993) Resolution and sensitivity enhancement of heteronuclear correlation for methylene resonances via H-2-enrichment and decoupling. J Biomol NMR 3:701–708
  Leiting B, Marsilio F, O’Connell JF (1998) Predictable deuteration of recombinant proteins expressed in Escherichia coli. Anal Biochem 265:351–355. doi:10.​1006/​abio.​1998.​2904 CrossRef
  Lemaster DM (1987) Chiral-beta and random fractional deuteration for the determination of protein side-chain conformation by NMR. FEBS Lett 223:191–196. doi:10.​1016/​0014-5793(87)80534-3 CrossRef
  Lemaster DM (1990) Deuterium labeling in NMR structural-analysis of larger proteins. Q Rev Biophys 23:133–174CrossRef
  Lohr F, Schmidt JM, Ruterjans H (1999) Simultaneous measurement of (3)J(HN, H alpha) and (3)J(H alpha, H beta) coupling constants in C-13, N-15-labeled proteins. J Am Chem Soc 121:11821–11826. doi:10.​1021/​ja991356h CrossRef
  Luthy J, Retey J, Arigoni D (1969) Preparation and detection of chiral methyl groups. Nature 221:1213. doi:10.​1038/​2211213a0 CrossRef ADS
  Marino JP, Diener JL, Moore PB, Griesinger C (1997) Multiple-quantum coherence dramatically enhances the sensitivity of CH and CH2 correlations in uniformly C-13-labeled RNA. J Am Chem Soc 119:7361–7366. doi:10.​1021/​ja964379u CrossRef
  Miclet E, Williams DC, Clore GM, Bryce DL, Boisbouvier J, Bax A (2004) Relaxation-optimized NMR spectroscopy of methylene groups in proteins and nucleic acids. J Am Chem Soc 126:10560–10570. doi:10.​1021/​ja047904v CrossRef
  Mueller L (1987) PE-COSY, a simple alternative to E-COSY. J Magn Reson 72:191–196. doi:10.​1016/​0022-2364(87)90188-0 ADS
  Muhandiram DR, Yamazaki T, Sykes BD, Kay LE (1995) Measurement of 2H T1rho relaxation times in uniformly 13C-labeled and fractionally 2H-labeled proteins in solution. J Am Chem Soc 117:11536–11544CrossRef
  Muller L (1979) Sensitivity enhanced detection of weak nuclei using heteronuclear multiple quantum coherence. J Am Chem Soc 101:4481–4484CrossRef
  Neri D, Szyperski T, Otting G, Senn H, Wuthrich K (1989) Stereospecific nuclear magnetic-resonance assignments of the methyl-groups of valine and leucine in the DNA-binding domain of the 434-repressor by biosynthetically directed fractional C-13 labeling. Biochemistry 28:7510–7516CrossRef
  Neuhaus D, Williamson MP (2000) The nuclear Overhauser effect in structural and conformational analysis, 2nd edn. Wiley, New York
  Nietlispach D et al (1996) An approach to the structure determination of larger proteins using triple resonance NMR experiments in conjunction with random fractional deuteration. J Am Chem Soc 118:407–415. doi:10.​1021/​ja952207b CrossRef
  Oktaviani NA, Otten R, Dijkstra K, Scheek RM, Thulin E, Akke M, Mulder FAA (2011) 100% complete assignment of non-labile (1)H, (13)C, and (15)N signals for calcium-loaded calbindin D(9 k) P43G. Biomol NMR Assign 5:79–84. doi:10.​1007/​s12104-010-9272-3 CrossRef
  Orts J, Vögeli B, Riek R, Güntert P (2013) Stereospecific assignments in proteins using exact NOEs. J Biomol NMR 57:211–218. doi:10.​1007/​s10858-013-9780-4 CrossRef
  Ostler G et al (1993) Stereospecific assignments of the leucine methyl resonances in the H-1-NMR spectrum of lactobacillus-casei dihydrofolate-reductase. FEBS Lett 318:177–180CrossRef
  Palmer AG, Cavanagh J, Wright PE, Rance M (1991) Sensitivity improvement in proton-detected 2-dimensional heteronuclear correlation NMR-spectroscopy. J Magn Reson 93:151–170. doi:10.​1016/​0022-2364(91)90036-s ADS
  Paquin R, Ferrage F, Mulder FAA, Akke M, Bodenhausen G (2008) Multiple-timescale dynamics of side-chain carboxyl and carbonyl groups in proteins by 13C nuclear spin relaxation. J Am Chem Soc 130:15805CrossRef
  Piotto M, Saudek V, Sklenar V (1992) Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J Biomol NMR 2:661–665. doi:10.​1007/​BF02192855 CrossRef
  Plevin MJ, Hamelin O, Boisbouvier J, Gans P (2011) A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins. J Biomol NMR 49:61–67. doi:10.​1007/​s10858-010-9463-3 CrossRef
  Pristovsek P, Franzoni L (2006) Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data. J Comput Chem 27:791–797. doi:10.​1002/​jcc.​20389 CrossRef
  Shaka AJ, Keeler J, Frenkiel T, Freeman R (1983) An improved sequence for broad-band decoupling—WALTZ-16. J Magn Reson 52:335–338ADS
  Shaka AJ, Barker PB, Freeman R (1985) Computer-optimized decoupling scheme for wideband applications and low-level operation. J Magn Reson 64:547–552ADS
  Shaka AJ, Lee CJ, Pines A (1988) Iterative schemes for bilinear operators—application to spin decoupling. J Magn Reson 77:274–293ADS
  Stanek J, Augustyniak R, Kozminski W (2012) Suppression of sampling artefacts in high-resolution four-dimensional NMR spectra using signal separation algorithm. J Magn Reson 214:91–102. doi:10.​1016/​j.​jmr.​2011.​10.​009 CrossRef ADS
  States DJ, Haberkorn RA, Ruben DJ (1982) A two-dimensional nuclear Overhauser experiment with pure absorption phase in 4 quadrants. J Magn Reson 48:286–292ADS
  Svensson LA, Thulin E, Forsén S (1992) Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography. J Mol Biol 223:601–606CrossRef
  Takeda M, Terauchi T, Kainosho M (2012) Conformational analysis by quantitative NOE measurements of the beta-proton pairs across individual disulfide bonds in proteins. J Biomol NMR 52:127–139. doi:10.​1007/​s10858-011-9587-0 CrossRef
  Vallurupalli P, Hansen DF, Lundstrom P, Kay LE (2009) CPMG relaxation dispersion NMR experiments measuring glycine H-1(alpha) and C-13(alpha) chemical shifts in the ‘invisible’ excited states of proteins. J Biomol NMR 45:45–55. doi:10.​1007/​s10858-009-9310-6 CrossRef
  Vögeli B, Segawa TF, Leitz D, Sobol A, Choutko A, Trzesniak D, van Gunsteren W, Riek R (2009) Exact distances and internal dynamics of perdeuterated ubiquitin from NOE buildups. J Am Chem Soc 131:17215–17225. doi:10.​1021/​ja905366h
  Vuister GW, Bax A (1992) Resolution enhancement and spectral editing of uniformly C-13-enriched proteins by homonuclear broad-band C-13 decoupling. J Magn Reson 98:428–435. doi:10.​1016/​0022-2364(92)90144-v ADS
  Wagner G, Braun W, Havel TF, Schaumann T, Go N, Wuthrich K (1987) Protein structures in solution by nuclear-magnetic-resonance and distance geometry—the polypeptide fold of the basic pancreatic trypsin-inhibitor determined using 2 different algorithms, DISGEO and DISMAN. J Mol Biol 196:611–639. doi:10.​1016/​0022-2836(87)90037-4 CrossRef
  Yamazaki T, Yoshida M, Nagayama K (1993) Complete assignments of magnetic resonances of ribonuclease-H from Escherichia-coli by double-resonance and triple-resonance 2D and 3D NMR spectroscopies. Biochemistry 32:5656–5669. doi:10.​1021/​bi00072a023 CrossRef
  
• 作者单位：Rafal Augustyniak (1) (2) (3)
  Jan Stanek (4)
  Henri Colaux (1) (2) (3)
  Geoffrey Bodenhausen (1) (2) (3) (5)
  Wiktor Koźmiński (4)
  Torsten Herrmann (6)
  Fabien Ferrage (1) (2) (3)
  
  1. Département de chimie, Ecole Normale Supérieure – PSL Research University, 24 rue Lhomond, 75005, Paris, France
  2. Sorbonne Universités, UPMC Université Paris 6, 4 Place Jussieu, 75005, Paris, France
  3. UMR 7203 LBM, CNRS, 75005, Paris, France
  4. Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
  5. Ecole Polytechnique Fédérale de Lausanne, Institut des Sciences et Ingénierie Chimiques, BCH, 1015, Lausanne, Switzerland
  6. Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, Université de Lyon/UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, 5 rue de la Doua, 69100, Villeurbanne, France
  
• 刊物类别：Physics and Astronomy
• 刊物主题：Physics
  Biophysics and Biomedical Physics
  Polymer Sciences
  Biochemistry
  
• 出版者：Springer Netherlands
• ISSN：1573-5001

文摘

Nuclear magnetic resonance spectroscopy (NMR) can provide a great deal of information about structure and dynamics of biomolecules. The quality of an NMR structure strongly depends on the number of experimental observables and on their accurate conversion into geometric restraints. When distance restraints are derived from nuclear Overhauser effect spectroscopy (NOESY), stereo-specific assignments of prochiral atoms can contribute significantly to the accuracy of NMR structures of proteins and nucleic acids. Here we introduce a series of NOESY-based pulse sequences that can assist in the assignment of chiral CHD methylene protons in random fractionally deuterated proteins. Partial deuteration suppresses spin-diffusion between the two protons of CH₂ groups that normally impedes the distinction of cross-relaxation networks for these two protons in NOESY spectra. Three and four-dimensional spectra allow one to distinguish cross-relaxation pathways involving either of the two methylene protons so that one can obtain stereospecific assignments. In addition, the analysis provides a large number of stereospecific distance restraints. Non-uniform sampling was used to ensure optimal signal resolution in 4D spectra and reduce ambiguities of the assignments. Automatic assignment procedures were modified for efficient and accurate stereospecific assignments during automated structure calculations based on 3D spectra. The protocol was applied to calcium-loaded calbindin D_9k. A large number of stereospecific assignments lead to a significant improvement of the accuracy of the structure.