Overview on the Use of NMR to Examine Protein Structure

Vincent Breukels1, Albert Konijnenberg1, Sanne M. Nabuurs1, Jurgen F. Doreleijers1, Nadezda V. Kovalevskaya1, Geerten W. Vuister1

1 Protein Biophysics, Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 17.5
DOI:  10.1002/0471140864.ps1705s64
Online Posting Date:  April, 2011
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Abstract

Any protein structure determination process contains several steps, starting from obtaining a suitable sample, then moving on to acquiring data and spectral assignment, and lastly to the final steps of structure determination and validation. This unit describes all of these steps, starting with the basic physical principles behind NMR and some of the most commonly measured and observed phenomena such as chemical shift, scalar and residual coupling, and the nuclear Overhauser effect. Then, in somewhat more detail, the process of spectral assignment and structure elucidation is explained. Furthermore, the use of NMR to study protein‐ligand interaction, protein dynamics, or protein folding is described. Curr. Protoc. Protein Sci. 64:17.5.1‐17.5.44. © 2011 by John Wiley & Sons, Inc.

Keywords: NMR; protein structure; interactions

     
 
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Table of Contents

  • Introduction
  • Basic Principles
  • Multi‐Dimensional Spectroscopy
  • 15N‐HSQC
  • Instrumentation
  • Sample Preparation
  • Chemical Shift
  • Scalar Coupling, NOE, and Residual Dipolar Coupling
  • Resonance Assignment
  • Fast Methods
  • Structure Determination
  • Relaxation and Dynamic Processes
  • Protein Interactions
  • Protein Folding
  • Conclusions
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Literature Cited

Literature Cited
   Almond, A. and Axelsen, J. 2002. Physical interpretation of residual dipolar couplings in neutral aligned media. J. Am. Chem. Soc. 124:9986‐9987.
   Altieri, A. and Byrd, R. 2004. Automation of NMR structure determination of proteins. Curr. Opin. Struct. Biol. 14:547‐553.
   Andrec, M., Du, P., and Levy, R. 2001a. Protein structural motif recognition via NMR residual dipolar couplings. J. Am. Chem. Soc. 123:1222‐1229.
   Andrec, M., Du, P., and Levy, R. 2001b. Protein backbone structure determination using only residual dipolar couplings from one ordering medium. J. Biomol. NMR 21:335‐347.
   Andronesi, O.C., Becker, S., Seidel, K., Heise, H., Young, H.S., and Baldus, M. 2005. Determination of membrane protein structure and dynamics by magic‐angle‐spinning solid‐state NMR spectroscopy. J. Am. Chem. Soc. 127:12965‐12974.
   Atkinson, R. and Kieffer, B. 2004. The role of protein motions in molecular recognition: Insights from heteronuclear NMR relaxation measurements. Prog. Nucl. Mag. Res. Sp. 44:141‐187.
   Ayala, I., Sounier, R., Usé, N., Gans, P., and Boisbouvier, J. 2009. An efficient protocol for the complete incorporation of methyl‐protonated alanine in perdeuterated protein. J. Biomol. NMR 43:111‐119.
   Bagby, S., Tong, K.I., Liu, D., Alattia, J.R., and Ikura, M. 1997. The button test: A small scale method using microdialysis cells for assessing protein solubility at concentrations suitable for NMR. J. Biomol. NMR 10:279‐282.
   Bai, Y., Sosnick, T.R., Mayne, L., and Englander, S.W. 1995. Protein folding intermediates: Native‐state hydrogen exchange. Science 269:192‐197.
   Balambika, R., Inui, T., Sargsyan, H., Arshava, B., Cohen, L.S., Ding, F.X., Becker, J.M., and Naider, F. 2007. Synthesis of a double transmembrane domain fragment of Ste2p by native chemical ligation. Int. J. Pept. Res. Ther. 13:251‐263.
   Bartels, C., Billeter, M., Güntert, P., and Wüthrich, K. 1996. Automated sequence‐specific NMR assignment of homologous proteins using the program GARANT. J. Biomol. NMR 7:207‐213.
   Bartels, C., Güntert, P., Billeter, M., and Wüthrich, K. 1997. GARANT: A general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. J. Comput. Chem. 18:139‐149.
   Baum, J., Dobson, C.M., Evans, P.A., and Hanley, C. 1989. Characterization of a partly folded protein by NMR methods: Studies on the molten globule state of guinea pig alpha‐lactalbumin. Biochemistry 28:7‐13.
   Bax, A., Clore, G., and Gronenborn, A. 1990. 1H‐1H correlation via isotropic mixing of 13C magnetization, a new 3‐dimensional approach for assigning 1H and 13C spectra of 13C ‐enriched proteins. J. Magn. Reson. 88:425‐431.
   Bax, A., Ikura, M., Kay, L.E., and Zhu, G. 1991. Removal of f1‐base‐line distortion and optimization of folding in multidimensional nmr‐spectra. J. Magn. Reson. 91:174‐178.
   Berlin, K., O'Leary, D.P., and Fushman, D. 2009. Improvement and analysis of computational methods for prediction of residual dipolar couplings. J. Magn. Reson. 201:25‐33.
   Bhattacharya, A., Tejero, R., and Montelione, G.T. 2007. Evaluating protein structures determined by structural genomics consortia. Proteins 66:778‐795.
   Billeter, M., Wagner, G., and Wuethrich, K. 2008. Solution NMR structure determination of proteins revisited.J. Biomol. NMR 42:155‐158.
   Bondos, S. and Bicknell, A. 2003. Detection and prevention of protein aggregation before, during, and after purification. Anal. Biochem. 316:223‐231.
   Bouchner, W. 1993. Azara. http://www.ccpn.ac.uk/azara/.
   Breukels, V. and Vuister, G. W. 2010. Binding of calcium is sensed structurally and dynamically throughout the second calcium‐binding domain of the sodium/calcium exchanger. Proteins 78:1813‐1824.
   Brünger, A.T. 2007. Version 1.2 of the Crystallography and NMR system. Nat. Protoc. 2:2728‐2733.
   Brünger, A., Marius Clore, G.M., Gronenborn, A.M., and Saffrich, R. 1993. Assessing the quality of solution nuclear magnetic resonance structures by complete cross‐validation. Science 261:328‐331.
   Bryson, M., Tian, F., Prestegard, J.H., and Valafar, H. 2008. REDCRAFT: A tool for simultaneous characterization of protein backbone structure and motion from RDC data. J. Magn. Reson. 191:322‐334.
   Buchler, N., Zuiderweg, E., Wang, H., and Goldstein, R. 1997. Protein heteronuclear NMR assignments using mean‐field simulated annealing. J. Magn. Reson. 125:34‐42.
   Cavalli, A., Salvatella, X., Dobson, C.M., and Vendruscolo, M. 2007. Protein structure determination from NMR chemical shifts. Proc. Natl. Acad. Sci. U.S.A. 104:9615‐9620.
   Cavanagh, J., Fairbrother, W.J., Palmer, A.G., Rance, M., and Skelton, N.J. 2007. Protein NMR Spectroscopy: Principles and Practice, 2nd ed. Elsevier Academic Press, Amsterdam.
   Chen, J., Mandelshtam, V., and Shaka, A. 2000. Regularization of the two‐dimensional filter diagonalization method: FDM2K. J. Magn. Reson. 146:363‐368.
   Clark, E. 1998. Refolding of recombinant proteins. Curr. Opin. Biotechnol. 9:157‐163.
   Cornilescu, G., Delaglio, F., and Bax, A. 1999. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13:289‐302.
   de la Torre, J., Huertas, M., and Carrasco, B. 2000. HYDRONMR: Prediction of NMR relaxation of globular proteins from atomic‐level structures and hydrodynamic calculations. J. Magn. Reson. 147:138‐146.
   Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., and Bax, A. 1995. NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6:277‐293.
   Delaglio, F., Kontaxis, G., and Bax, A. 2000. Protein structure determination using molecular fragment replacement and NMR dipolar couplings. J. Am. Chem. Soc. 122:2142‐2143.
   Diercks, T., Daniels, M., and Kaptein, R. 2005. Extended flip‐back schemes for sensitivity enhancement in multidimensional HSQC‐type out‐and‐back experiments. J. Biomol. NMR 33:243‐259.
   diGuan, C., Li, P., Riggs, P.D., and Inouye, H. 1988. Vectors that facilitate the expression and purification of foreign peptides in Escherichia coli by fusion to maltose‐binding protein. Gene 67:21‐30.
   Dominguez, C., Boelens, R., and Bonvin, A. 2003. HADDOCK: A protein‐protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125:1731‐1737.
   Doreleijers, J. F., Raves, M.L., Rullmann, T., and Kaptein, R. 1999. Completeness of NOEs in protein structure: a statistical analysis of NMR. J. Biomol. NMR 14:123‐132.
   Doreleijers, J.F., Vranken, W.F., Schulte, C., Lin, J., Wedell, J.R., Penkett, C.J., Vuister, G.W., Vriend, G., Markley, J.L., and Ulrich, E.L. 2009. The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries. J. Biomol. NMR 45:389‐396.
   Dosset, P., Hus, J.C., Blackledge, M., and Marion, D. 2000. Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J. Biomol. NMR 16:23‐28.
   Dosset, P., Hus, J., Marion, D., and Blackledge, M. 2001. A novel interactive tool for rigid‐body modeling of multi‐domain macromolecules using residual dipolar couplings. J. Biomol. NMR 20:223‐231.
   Durst, F.G., Ou, H.D., Loehr, F., Doetsch, V., and Straub, W.E. 2008. The better tag remains unseen. J. Am. Chem. Soc. 130:14932.
   Engh, R. and Huber, R. 1991. Accurate bond and angle parameters for x‐ray protein‐structure refinement. Acta Crystallogr. A 47:392‐400.
   Ericsson, U.B., Hallberg, B.M., DeTitta, G.T., Dekker, N., and Nordlund, P. 2006. Thermofluor‐based high‐throughput stability optimization of proteins for structural studies. Anal. Biochem. 357:289‐298.
   Fahmy, A. and Wagner, G. 2002. TreeDock: A tool for protein docking based on minimizing van der Waals energies. J. Am. Chem. Soc. 124:1241‐1250.
   Felli, I.C. and Brutscher, B. 2009. Recent advances in solution NMR: Fast methods and heteronuclear direct detection. Chemphyschem 10:1356‐1368.
   Fernandes, M., Bernado, P., Pons, M., and de la Torre, J. 2001. An analytical solution to the problem of the orientation of rigid particles by planar obstacles. Application to membrane systems and to the calculation of dipolar couplings in protein NMR spectroscopy. J. Am. Chem. Soc. 123:12037‐12047.
   Fernandez, C. and Wider, G. 2003. TROSY in NMR studies of the structure and function of large biological macromolecules. Curr. Opin. Struct. Biol. 13:570‐580.
   Flinders, J. and Dieckmann, T. 2006. NMR spectroscopy of ribonucleic acids. Prog. Nucl. Mag. Res. Sp. 48:137‐159.
   Gardner, K.H. and Kay, L.E. 1997. Production and incorporation of N‐15, C‐13, H‐2 (H‐1‐delta 1 methyl) isoleucine into proteins for multidimensional NMR studies. J. Am. Chem. Soc. 119:7599‐7600.
   Gardner, K.H. and Kay, L.E. 1998. The use of 2H, 13C, 15N multidimensional NMR to study the structure and dynamics of proteins. Annu. Rev. Biophys. Biomol. Struct. 27:357‐406.
   Gelis, I., Bonvin, A.M., Keramisanou, D., Koukaki, M., Gouridis, G., Karamanou, S., Economou, A., and Kalodimos, C.G. 2007. Structural basis for signal‐sequence recognition by the translocase motor SecA as determined by NMR. Cell 131:756‐769.
   Ginzinger, S.W., Skocibusic, M., and Heun, V. 2009. CheckShift improved: Fast chemical shift reference correction with high accuracy. J. Biomol. NMR 44:207‐211.
   Golovanov, A., Hautbergue, G., Wilson, S., and Lian, L. 2004. A simple method for improving protein solubility and long‐term stability. J. Am. Chem. Soc. 126:8933‐8939.
   Goto, N.K., Gardner, K.H., Mueller, G.A., Willis, R.C., and Kay, L.E. 1999. A robust and cost‐effective method for the production of Val, Leu, Ile (delta 1) methyl‐protonated 15N‐, 13C‐, 2H‐labeled proteins. J. Biomol. NMR 13:369‐374.
   Graslund, S., Nordlund, P., Weigelt, J., Bray, J., Hallberg, B.M., Gileadi, O., Knapp, S., Oppermann, U., Arrowsmith, C., Hui, R., Ming, J., dhe‐Paganon, S., Park, H.‐w., Savchenko, A., Yee, A., Edwards, A., Vincentelli, R., Cambillau, C., Kim, R., Kim, S.‐H., Rao, Z., Shi, Y., Terwilliger, T.C., Kim, C.‐Y., Hung, L.‐W., Waldo, G.S., Peleg, Y., Albeck, S., Unger, T., Dym, O., Prilusky, J., Sussman, J.L., Stevens, R.C., Lesley, S.A., Wilson, I.A., Joachimiak, A., Collart, F., Dementieva, I., Donnelly, M.I., Eschenfeldt, W.H., Kim, Y., Stols, L., Wu, R., Zhou, M., Burley, S.K., Emtage, J.S., Sauder, J.M., Thompson, D., Bain, K., Luz, J., Gheyi, T., Zhang, F., Atwell, S., Almo, S.C., Bonanno, J.B., Fiser, A., Swaminathan, S., Studier, F.W., Chance, M.R., Sali, A., Acton, T.B., Xiao, R., Zhao, L., Ma, L.C., Hunt, J.F., Tong, L., Cunningham, K., Inouye, M., Anderson, S., Janjua, H., Shastry, R., Ho, C.K., Wang, D., Wang, H., Jiang, M., Montelione, G.T., Stuart, D.I., Owens, R.J., Daenke, S., Schutz, A., Heinemann, U., Yokoyama, S., Bussow, K., and Gunsalus, K.C. 2008. Protein production and purification. Nat. Methods 5:135‐146.
   Grishaev, A., Wu, J., Trewhella, J., and Bax, A. 2005. Refinement of multidomain protein structures by combination of solution small‐angle X‐ray scattering and NMR data. J. Am. Chem. Soc. 127:16621‐16628.
   Grishaev, A., Tugarinov, V., Kay, L.E., Trewhella, J., and Bax, A. 2008. Refined solution structure of the 82‐kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints. J. Biomol. NMR 40:95‐106.
   Grzesiek, S. and Bax, A. 1993. Amino‐acid type determination in the sequential assignment procedure of uniformly c‐13/n‐15‐enriched proteins. J. Biomol. NMR 3:185‐204.
   Güntert, P. 2009. Automated structure determination from NMR spectra. Eur. Biophys. J. Biophy. 38:129‐143.
   Güntert, P., Mumenthaler, C., and Wüthrich, K. 1997. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273:283‐298.
   Harris, R., Becker, E., de Menezes, S., Goodfellow, R., and Granger, P. 2002. NMR nomenclature: Nuclear spin properties and conventions for chemical shifts: IUPAC recommendations 2001 (Reprinted from Pure Appl. Chem. 73:1795‐1818, 2001). Solid State Nucl. Mag. 22:458‐483.
   Henzler‐Wildman, K.A., Lei, M., Thai, V., Kerns, S.J., Karplus, M., and Kern, D. 2007. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450:913‐916.
   Hoch, J. and Stern, A. 2001. Maximum entropy reconstruction, spectrum analysis and deconvolution in multidimensional nuclear magnetic resonance. Methods Enzymol. 338:159‐178.
   Hooft, R., Vriend, G., Sander, C., and Abola, E. 1996. Errors in protein structures. Nature 381:272‐272.
   Huang, Y., Powers, R., and Montelione, G. 2005. Protein NMR recall, precision, and F‐measure scores (RPF scores): Structure quality assessment measures based on information retrieval statistics. J. Am. Chem. Soc. 127:1665‐1674.
   Huth, J.R., Bewley, C.A., Jackson, B.M., Hinnebusch, A.G., Clore, G.M., and Gronenborn, A.M. 1997. Design of an expression system for detecting folded protein domains and mapping macromolecular interactions by NMR. Protein Sci. 6:2359‐2364.
   Ikura, M., Kay, L.E., and Bax, A. 1990. A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: Heteronuclear triple‐resonance three‐dimensional NMR spectroscopy. Application to calmodulin. Biochemistry 29:4659‐4667.
   Isaacson, R.L., Simpson, P.J., Liu, M., Cota, E., Zhang, X., Freemont, P., and Matthews, S. 2007. A new labeling method for methyl transverse relaxation‐optimized spectroscopy NMR spectra of alanine residues. J. Am. Chem. Soc. 129:15428‐15429.
   Ishima, R. and Torchia, D.A. 2000. Protein dynamics from NMR. Nat. Struct. Biol. 7:740‐743.
   Ito, T. and Wagner, G. 2004. Using codon optimization, chaperone co‐expression, and rational mutagenesis for production and NMR assignments of human eIF2 alpha. J. Biomol. NMR 28:357‐367.
   Jeener, J. 1971. Two‐dimensional Fourier Transform NMR. Presented at Ampère Summer School, Basko Polje, Yugoslavia.
   Joachimiak, A. 2009. High‐throughput crystallography for structural genomics. Curr. Opin. Struct. Biol. 19:573‐584.
   Jung, Y. and Zweckstetter, M. 2004. Mars: Robust automatic backbone assignment of proteins. J. Biomol. NMR 30:11‐23.
   Kainosho, M., Torizawa, T., Iwashita, Y., Terauchi, T., Mei Ono, A., and Güntert, P. 2006. Optimal isotope labelling for NMR protein structure determinations. Nature 440:52‐57.
   Karplus, M. 1959. Contact electron‐spin coupling of nuclear magnetic moments. J. Chem. Phys. 30:11‐15.
   Karplus, M. 1963. Vicinal proton coupling in nuclear magnetic resonance. J. Am. Chem. Soc. 85:2870‐2871.
   Kay, L.E. 1998. Protein dynamics from NMR. Nat. Struct. Biol. 5:513‐517.
   Kay, L.E., Torchia, D.A., and Bax, A. 1989. Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: Application to staphylococcal nuclease. Biochemistry 28:8972‐8979.
   Kay, L.E., Clore, G., Bax, A., and Gronenborn, A. 1990a. 4‐dimensional heteronuclear triple‐resonance nmr‐spectroscopy of interleukin‐1‐beta in solution. Science 249:411‐414.
   Kay, L.E., Ikura, M., Tschudin, R., and Bax, A. 1990b. 3‐Dimensional triple‐resonance nmr‐spectroscopy of isotopically enriched proteins. J. Magn. Reson. 89:496‐514.
   Kazimierczuk, K., Kozminski, W., and Zhukov, I. 2006. Two‐dimensional Fourier transform of arbitrarily sampled NMR data sets. J. Magn. Reson. 179:323‐328.
   Kelly, A.E., Ou, H.D., Withers, R., and Dötsch, V. 2002. Low‐conductivity buffers for high‐sensitivity NMR measurements. J. Am. Chem. Soc. 124:12013‐12019.
   Kim, H.J., Howell, S.C., Van Horn, W.D., Jeon, Y.H., and Sanders, C.R. 2009. Recent advances in the application of solution NMR spectroscopy to multi‐span integral membrane proteins. Prog. Nucl. Mag. Res. Sp. 55:335‐360.
   Kiyoshi, T., Otsuka, A., Kosuge, M., Yuyama, M., Nagai, H., and Matsumoto, F. 2006. Generation of high magnetic fields using superconducting magnets. Fusion Eng. Des. 81:2411‐2415.
   Kobashigawa, Y., Kumeta, H., Ogura, K., and Inagaki, F. 2009. Attachment of an NMR‐invisible solubility enhancement tag using a sortase‐mediated protein ligation method. J. Biomol. NMR 43:145‐150.
   Kochendoerfer, G., Jones, D., Lee, S., Oblatt‐Montal, M., Opella, S., and Montal, M. 2004. Functional characterization and NMR Spectroscopy on full‐length Vpu from HIV‐1 prepared by total chemical synthesis. J. Am. Chem. Soc. 126:2439‐2446.
   Konrat, R., Yang, D., and Kay, L.E. 1999. A 4D TROSY‐based pulse scheme for correlating (HNi)‐H‐1,Ni‐15,C‐13(i)alpha,C‐13 '(i‐1) chemical shifts in high molecular weight, N‐15,C‐13, H‐2 labeled proteins. J. Biomol. NMR 15:309‐313.
   Koradi, R., Billeter, M., and Wüthrich, K. 1996. MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14:51‐55.
   Korzhnev, D.M., Religa, T.L., Banachewicz, W., Fersht, A.R., and Kay, L.E. 2010. A transient and low‐populated protein‐folding intermediate at atomic resolution. Science 329:1312‐1316.
   Laskowski, R., Rullmann, J., and MacArthur, M. 1996. AQUA and PROCHECK‐NMR: Programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8:477‐486.
   Lee, A.L., Urbauer, J.L., and Wand, A.J. 1997. Improved labeling strategy for 13C relaxation measurements of methyl groups in proteins. J. Biomol. NMR 9:437‐440.
   LeMaster, D.M. and Richards, F.M. 1988. NMR sequential assignment of Escherichia coli thioredoxin utilizing random fractional deuteriation. Biochemistry 27:142‐150.
   Lepre, C.A. and Moore, J.M. 1998. Microdrop screening: A rapid method to optimize solvent conditions for NMR spectroscopy of proteins. J. Biomol. NMR 12:493‐499.
   Lescop, E. and Brutscher, B. 2009. Highly automated protein backbone resonance assignment within a few hours: The ((BATCH)) strategy and software package. J. Biomol. NMR 44:43‐57.
   Leutner, M., Gschwind, R., Liermann, J., Schwarz, C., Gemmecker, G., and Kessler, H. 1998. Automated backbone assignment of labeled proteins using the threshold accepting algorithm. J. Biomol. NMR 11:31‐43.
   Levitt, M.H. 2008. Spin Dynamics: Basics of Nuclear Magnetic Resonance, 2nd ed, Wiley‐Blackwell, Hoboken, N.J.
   Li, K. and Sanctuary, B. 1997a. Automated resonance assignment of proteins using heteronuclear 3D NMR: Backbone spin systems extraction and creation of polypeptides. J. Chem. Inf. Comp. Sci. 37:359‐366.
   Li, K. and Sanctuary, B. 1997b. Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence‐specific assignment. J. Chem. Inf. Comp. Sci. 37:467‐477.
   Linge, J.P., Williams, M.A., Spronk, C.A., Bonvin, A.M., and Nilges, M. 2003. Refinement of protein structures in explicit solvent. Proteins 50:496‐506.
   Lipari, G. and Szabo, A. 1982. Model‐free approach to the interpretation of nuclear magnetic‐resonance relaxation in macromolecules. 2. Analysis of experimental results. J. Am. Chem. Soc. 104:4559‐4570.
   Lukin, J., Gove, A., Talukdar, S., and Ho, C. 1997. Automated probabilistic method for assigning backbone resonances of (C‐13,N‐15)‐labeled proteins. J. Biomol. NMR 9:151‐166.
   Mandel, A.M., Akke, M., and Palmer, A.G. 1995. Backbone dynamics of Escherichia coli ribonuclease hi: Correlations with structure and function in an active enzyme. J. Mol. Biol. 246:144‐163.
   Marion, D., Driscoll, P.C., Kay, L.E., Wingfield, P.T., Bax, A., Gronenborn, A.M., and Clore, G.M. 1989. Overcoming the overlap problem in the assignment of 1H NMR spectra of larger proteins by use of three‐dimensional heteronuclear 1H‐15N Hartmann‐Hahn‐multiple quantum coherence and nuclear Overhauser‐multiple quantum coherence spectroscopy: application to interleukin 1 beta. Biochemistry 28:6150‐6156.
   Markley, J.L., Ulrich, E.L., Berman, H.M., Henrick, K., Nakamura, H., and Akutsu, H. 2008. BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): New policies affecting biomolecular NMR depositions. J. Biomol. NMR 40:153‐155.
   McDermott, A. 2009. Structure and dynamics of membrane proteins by magic angle spinning solid‐state NMR. Ann. Rev. Biophys. 38:385‐403.
   Millet, O., Muhandiram, D., Skrynnikov, N., and Kay, L.E. 2002. Deuterium spin probes of side‐chain dynamics in proteins. 1. Measurement of five relaxation rates per deuteron in C‐13‐labeled and fractionally H‐2‐enriched proteins in solution. J. Am. Chem. Soc. 124:6439‐6448.
   Mittermaier, A. and Kay, L.E. 2006. Review: New tools provide new insights in NMR studies of protein dynamics. Science 312:224‐228.
   Modig, K., Jürgensen, V.W., Lindorff‐Larsen, K., Fieber, W., Bohr, H.G., and Poulsen, F.M. 2007. Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis. FEBS Lett. 581:4965‐4971.
   Mulder, F.A. and Filatov, M. 2010. NMR chemical shift data and ab initio shielding calculations: Emerging tools for protein structure determination. Chem. Soc. Rev. 39:578‐590.
   Muona, M., Aranko, A.S., Raulinaitis, V., and Iwai, H. 2010. Segmental isotopic labeling of multi‐domain and fusion proteins by protein trans‐splicing in vivo and in vitro. Nat. Protoc. 5:574‐587.
   Nabuurs, S.M. and Van Mierlo, C.P.M. 2010. Interrupted hydrogen/deuterium exchange reveals the stable core of the remarkably helical molten globule of alpha‐beta parallel protein flavodoxin. J. Biol. Chem. 285:4165‐4172.
   Nabuurs, S.B., Spronk, C.A., Krieger, E., Maassen, H., Vriend, G., and Vuister, G.W. 2003. Quantitative evaluation of experimental NMR restraints. J. Am. Chem. Soc. 125:12026‐12034.
   Nabuurs, S.B., Nederveen, A.J., Vranken, W., Doreleijers, J.F., Bonvin, A.M., Vuister, G.W., Vriend, G., and Spronk, C.A. 2004. DRESS: A database of REfined solution NMR structures. Proteins 55:483‐486.
   Nabuurs, S.B., Krieger, E., Spronk, C.A., Nederveen, A.J., Vriend, G., and Vuister, G.W. 2005. Definition of a new information‐based per‐residue quality parameter. J. Biomol. NMR 33:123‐134.
   Nabuurs, S.B., Spronk, C.A., Vuister, G.W., and Vriend, G. 2006. Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLoS Comput. Biol. 2:e9.
   Nabuurs, S.M., Westphal, A.H., and Van Mierlo, C.P.M. 2008. Extensive formation of off‐pathway species during folding of an α−β parallel protein is due to docking of (non)native structure elements in unfolded molecules. J. Am. Chem. Soc. 130:16914‐16920.
   Nabuurs, S.M., Westphal, A.H., and Van Mierlo, C.P.M. 2009. Noncooperative formation of the off‐pathway molten globule during folding of the α−β parallel protein apoflavodoxin. J. Am. Chem. Soc. 131:2739‐2746.
   Nabuurs, S.M., de Kort, B.J., Westphal, A.H., and Van Mierlo, C.P. 2010. Non‐native hydrophobic interactions detected in unfolded apoflavodoxin by paramagnetic relaxation enhancement. Eur. Biophys. J. Biophys. 39:689‐698.
   Neal, S., Nip, A., Zhang, H., and Wishart, D. 2003. Rapid and accurate calculation of protein H‐1, C‐13 and N‐15 chemical shifts. J. Biomol. NMR 26:215‐240.
   Nietlispach, D., Clowes, R., Broadhurst, R., Ito, Y., Keeler, J., Kelly, M., Ashurst, J., Oschkinat, H., Domaille, P., and Laue, E. 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.
   Nilges, M., Clore, G., and Gronenborn, A. 1988. Determination of three‐dimensional structures of proteins from interproton distance data by hybrid distance geometry‐dynamical simulated annealing calculations. FEBS Lett. 229:317‐324.
   Nilges, M., Macias, M.J., O'Donoghue, S.I., and Oschkinat, H. 1997. Automated NOESY interpretation with ambiguous distance restraints: The refined NMR solution structure of the pleckstrin homology domain from beta‐spectrin. J. Mol. Biol. 269:408‐422.
   Nishimura, C. 2005. Enhanced picture of protein‐folding intermediates using organic solvents in H/D exchange and quench‐flow experiments. Proc. Natl. Acad. Sci. U.S.A. 102:4765‐4770.
   O'Connell, M.R., Gamsjaeger, R., and Mackay, J.P. 2009. The structural analysis of protein‐protein interactions by NMR spectroscopy. Proteomics 9:5224‐5232.
   Olejniczak, E., Xu, R., and Fesik, S. 1992. A 4D‐HCCH‐TOCSY experiment for assigning the side‐chain h‐1‐resonance and c‐13‐resonance of proteins. J. Biomol. NMR 2:655‐659.
   Ollerenshaw, J., Tugarinov, V., and Kay, L.E. 2003. Methyl TROSY: Explanation and experimental verification. Magn. Reson. Chem. 41:843‐852.
   Otten, R., Chu, B., Krewulak, K.D., Vogel, H.J., and Mulder, F.A.A. 2010. Comprehensive and cost‐effective NMR spectroscopy of methyl groups in large proteins. J. Am. Chem. Soc. 132:2952‐2960.
   Palmer, A.G. 1997. Probing molecular motion by NMR. Curr. Opin. Struct. Biol. 7:732‐737.
   Palmer, A.G. 2004. NMR characterization of the dynamics of biomacromolecules. Chem. Rev. 104:3623‐3640.
   Palmer, A.G., Rance, M., and Wright, P. 1991. Intramolecular motions of a zinc finger dna‐binding domain from xfin characterized by proton‐detected natural abundance c‐12 heteronuclear nmr‐spectroscopy. J. Am. Chem. Soc. 113:4371‐4380.
   Palmer, A.G., Kroenke, C.D., and Loria, J.P. 2001. Nuclear magnetic resonance methods for quantifying microsecond‐to‐millisecond motions in biological macromolecules. Meth. Enzymol. 339:204‐238.
   Pervushin, K., Riek, R., Wider, G., and Wüthrich, K. 1997. Attenuated T‐2 relaxation by mutual cancellation of dipole‐dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc. Natl. Acad. Sci. U.S.A. 94:12366‐12371.
   Pervushin, K., Riek, R., Wider, G., and Wüthrich, K. 1998. Transverse relaxation‐optimized spectroscopy (TROSY) for NMR studies of aromatic spin systems in C‐13‐labeled proteins. J. Am. Chem. Soc. 120:6394‐6400.
   Pervushin, K., Vogeli, B., and Eletsky, A. 2002. Longitudinal H‐1 relaxation optimization in TROSY NMR spectroscopy. J. Am. Chem. Soc. 124:12898‐12902.
   Prestegard, J., Bougault, C., and Kishore, A. 2004. Residual dipolar couplings in structure determination of biomolecules. Chem. Rev. 104:3519‐3540.
   Rieping, W. and Vranken, W.F. 2010. Validation of archived chemical shifts through atomic coordinates. Proteins 78:2482‐2489.
   Rieping, W., Habeck, M., Bardiaux, B., Bernard, A., Malliavin, T.E., and Nilges, M. 2007. ARIA2: Automated NOE assignment and data integration in NMR structure calculation. Bioinformatics 23:381‐382.
   Rosen, M., Gardner, K., Willis, R., Parris, W., Pawson, T., and Kay, L.E. 1996. Selective methyl group protonation of perdeuterated proteins. J. Mol. Biol. 263:627‐636.
   Salzmann, M., Pervushin, K., Wider, G., Senn, H., and Wüthrich, K. 1998. TROSY in triple‐resonance experiments: New perspectives for sequential NMR assignment of large proteins. Proc. Natl. Acad. Sci. U.S.A. 95:13585‐13590.
   Salzmann, M., Wider, G., Pervushin, K., Senn, H., and Wüthrich, K. 1999. TROSY‐type triple‐resonance experiments for sequential NMR assignments of large proteins. J. Am. Chem. Soc. 121:844‐848.
   Sattler, M., Schleucher, J., and Griesinger, C. 1999. Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog. Nucl. Mag. Res. Sp. 34:93‐158.
   Schanda, P., Kupce, E., and Brutscher, B. 2005. SOFAST‐HMQC experiments for recording two‐dimensional heteronuclear correlation spectra of proteins within a few seconds. J. Biomol. NMR 33:199‐211.
   Schmidt, P.G. and Kuntz, I.D. 1984. Distance measurements in spin‐labeled lysozyme. Biochemistry 23:4261‐4266.
   Schneider‐Muntau, H. 1997. High field NMR magnets. Solid State Nucl. Mag. 9:61‐71.
   Schulman, B.A., Kim, P.S., Dobson, C.M., and Redfield, C. 1997. A residue‐specific NMR view of the non‐cooperative unfolding of a molten globule. Nat. Struct. Biol. 4:630‐634.
   Schwieters, C., Kuszewski, J., Tjandra, N., and Clore, G. 2003. The Xplor‐NIH NMR molecular structure determination package. J. Magn. Reson. 160:65‐73.
   Selenko, P. and Wagner, G. 2007. Looking into live cells with in‐cell NMR spectroscopy. J. Struct. Biol. 158:244‐253.
   Shekhtman, A., Ghose, R., Goger, M., and Cowburn, D. 2002. NMR structure determination and investigation using a reduced proton (REDPRO) labeling strategy for proteins. FEBS Lett. 524:177‐182.
   Shen, Y., Lange, O., Delaglio, F., Rossi, P., Aramini, J., Liu, G., Eletsky, A., Wu, Y., Singarapu, K., Lemak, A., Ignatchenko, A., Arrowsmith, C., Szyperski, T., Montelione, G., Baker, D., and Bax, A. 2008. Consistent blind protein structure generation from NMR chemical shift data. Proc. Natl. Acad. Sci. U.S.A. 105:4685‐4690
   Shen, Y., Delaglio, F., Cornilescu, G., and Bax, A. 2009. TALOS+: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J. Biomol. NMR 44:213‐223.
   Simon, B., Madl, T., Mackereth, C.D., Nilges, M., and Sattler, M. 2010. An efficient protocol for NMR‐spectroscopy‐based structure determination of protein complexes in solution. Angew. Chem. Int. Ed. 49:1967‐1970.
   Skrisovska, L., Schubert, M., and Allain, F.H.‐T. 2010. Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins. J. Biomol. NMR 46:51‐65.
   Skrynnikov, N., Millet, O., and Kay, L.E. 2002. Deuterium spin probes of side‐chain dynamics in proteins. 2. Spectral density mapping and identification of nanosecond time‐scale side‐chain motions. J. Am. Chem. Soc. 124:6449‐6460.
   Smith, D.B. and Johnson, K.S. 1988. Single‐step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S‐transferase. Gene 67:31‐40.
   Snyder, D.A. and Montelione, G.T. 2005. Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. Proteins 59:673‐686.
   Spronk, C., Linge, J., Hilbers, C., and Vuister, G. 2002. Improving the quality of protein structures derived by NMR spectroscopy. J. Biomol. NMR 22:281‐289.
   Spronk, C.A., Nabuurs, S.B., Krieger, E., Vriend, G., and Vuister, G.W. 2004. Validation of protein structures derived by NMR spectroscopy. Prog. Nucl. Mag. Res. Sp. 45:315‐337.
   Sunnerhagen, M., Olah, G., Stenflo, J., Forsen, S., Drakenberg, T., and Trewhella, J. 1996. The relative orientation of Gla and EGF domains in coagulation factor X is altered by Ca2+ binding to the first EGF domain. A combined NMR small angle X‐ray scattering study. Biochemistry 35:11547‐11559.
   Terwilliger, T.C., Stuart, D., and Yokoyama, S. 2009. Lessons from structural genomics. Ann. Rev. Biophys. 38:371‐383.
   Tjandra, N. and Bax, A. 1997. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278:1111‐1114.
   Tollinger, M., Skrynnikov, N.R., Mulder, F.A., Forman‐Kay, J.D., and Kay, L.E. 2001. Slow dynamics in folded and unfolded states of an SH3 domain. J. Am. Chem. Soc. 123:11341‐11352.
   Tolman, J.R., Flanagan, J.M., Kennedy, M.A., and Prestegard, J.H. 1995. Nuclear magnetic dipole interactions in field‐oriented proteins: Information for structure determination in solution. Proc. Natl. Acad. Sci. U.S.A. 92:9279‐9283.
   Tugarinov, V., Sprangers, R., and Kay, L.E. 2004. Line narrowing in methyl‐TROSY using zero‐quantum H‐1‐C‐13 NMR spectroscopy. J. Am. Chem. Soc. 126:4921‐4925.
   Tugarinov, V., Choy, W., Orekhov, V., and Kay, L.E. 2005. Solution NMR‐derived global fold of a monomeric 82‐kDa enzyme. Proc. Natl. Acad. Sci. U.S.A. 102:622‐627.
   Tycko, R. 2006. Characterization of amyloid structures at the molecular level by solid state nuclear magnetic resonance spectroscopy. Methods Enzymol. 413:103‐122.
   Ulrich, E.L., Akutsu, H., Doreleijers, J.F., Harano, Y., Ioannidis, Y.E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z., Nakatani, E., Schulte, C.F., Tolmie, D.E., Wenger, R.K., Yao, H., and Markley, J.L. 2008. BioMagResBank. Nucleic Acids Res. 36:D402‐D408.
   Valafar, H. and Prestegard, J. 2004. REDCAT: A residual dipolar coupling analysis tool. J. Magn. Reson. 167:228‐241.
   Vallurupalli, P., Hansen, D.F., and Kay, L.E. 2008. Probing structure in invisible protein states with anisotropic NMR chemical shifts. J. Am. Chem. Soc. 130:2734‐2735.
   Van Zijl, P., Sukumar, S., Johnson, M., Webb, P., and Hurd, R. 1994. Optimized shimming for high‐resolution nmr using 3‐dimensional image‐based field‐mapping. J. Magn. Reson. Ser. A 111:203‐207.
   Vranken, W., Boucher, W., Stevens, T., Fogh, R., Pajon, A., Llinas, P., Ulrich, E., Markley, J., Ionides, J., and Laue, E. 2005. The CCPN data model for NMR spectroscopy: Development of a software pipeline. Proteins 59:687‐696.
   Vriend, G. 1990. WHAT IF: A molecular modeling and drug design program. J. Mol. Graph. 8:52‐56.
   Vuister, G.W., Clore, G., Gronenborn, A.M., Powers, R., Garrett, D., Tschudin, R., and Bax, A. 1993. Increased resolution and Improved spectral quality in 4‐dimensional C‐13/C‐13‐separated HMQC‐NOESY‐HMQC spectra using pulsed field gradients. J. Magn. Reson. Ser. B 101:210‐213.
   Vuister, G.W., Tessari, M., Karimi‐Nejad, Y., and Whitehead, B. 1999. Pulse sequences for measuring coupling constants. Biol. Magn. Reson. 16:195‐257.
   Wang, B., Wang, Y., and Wishart, D.S. 2010. A probabilistic approach for validating protein NMR chemical shift assignments. J. Biomol. NMR 47:85‐99.
   Wang, J., Zuo, X., Yu, P., Byeon, I.‐J. L., Jung, J., Wang, X., Dyba, M., Seifert, S., Schwieters, C.D., Qin, J., Gronenborn, A.M., and Wang, Y.‐X. 2009. Determination of multicomponent protein structures in solution using global orientation and shape restraints. J. Am. Chem. Soc. 131:10507‐10515.
   Wang, L. and Markley, J.L. 2009. Empirical correlation between protein backbone N‐15 and C‐13 secondary chemical shifts and its application to nitrogen chemical shift re‐referencing. J. Biomol. NMR 44:95‐99.
   Williamson, M.P. and Craven, C.J. 2009. Automated protein structure calculation from NMR data. J. Biomol. NMR 43:131‐143.
   Wishart, D.S., Sykes, B.D., and Richards, F.M. 1992. The chemical shift index: A fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31:1647‐1651.
   Wishart, D.S., Bigam, C.G., Yao, J., Abildgaard, F., Dyson, H.J., Oldfield, E., Markley, J.L., and Sykes, B.D. 1995. 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J. Biomol. NMR 6:135‐140.
   Wu, B., Petersen, M., Girard, F., Tessari, M., and Wijmenga, S. 2006. Prediction of molecular alignment of nucleic acids in aligned media. J. Biomol. NMR 35:103‐115.
   Wüthrich, K. 2003. NMR studies of structure and function of biological macromolecules (Nobel Lecture). Angew. Chem. Int. Ed. 42:3340‐3363.
   Yanagisawa, Y., Nakagome, H., Hosono, M., Hamada, M., Kiyoshi, T., Hobo, F., Takahashi, M., Yamazaki, T., and Maeda, H. 2008. Towards beyond‐1 GHz solution NMR: Internal H‐2 lock operation in an external current mode. J. Magn. Reson. 192:329‐337.
   Yang, D. and Kay, L.E. 1999. TROSY triple‐resonance four‐dimensional NMR spectroscopy of a 46 ns tumbling protein. J. Am. Chem. Soc. 121:2571‐2575.
   Yao, J., Chung, J., Eliezer, D., Wright, P.E., and Dyson, H.J. 2001. NMR structural and dynamic characterization of the acid‐unfolded state of apomyoglobin provides insights into the early events in protein folding. Biochemistry 40:3561‐3571.
   Yee, A., Gutmanas, A., and Arrowsmith, C.H. 2006. Solution NMR in structural genomics. Curr. Opin. Struct. Biol. 16:611‐617.
   Zhou, M.M., Ravichandran, K.S., Olejniczak, E.F., Petros, A.M., Meadows, R.P., Sattler, M., Harlan, J.E., Wade, W.S., Burakoff, S.J., and Fesik, S.W. 1995. Structure and ligand recognition of the phosphotyrosine binding domain of Shc. Nature 378:584‐592.
   Zhou, P. and Wagner, G. 2010. Overcoming the solubility limit with solubility‐enhancement tags: Successful applications in biomolecular NMR studies. J. Biomol. NMR 46:23‐31.
   Zhou, P., Lugovskoy, A.A., and Wagner, G. 2001. A solubility‐enhancement tag (SET) for NMR studies of poorly behaving proteins. J. Biomol. NMR 20:11‐14.
   Zimmerman, D., Kulikowski, C., Huang, Y., Feng, W., Tashiro, M., Shimotakahara, S., Chien, C., Powers, R., and Montelione, G. 1997. Automated analysis of protein NMR assignments using methods from artificial intelligence. J. Mol. Biol. 269:592‐610.
   Züger, S. and Iwai, H. 2005. Intein‐based biosynthetic incorporation of unlabeled protein tags into isotopically labeled proteins for NMR studies. Nat. Biotechnol. 23:736‐740.
   Zuiderweg, E.R. and Fesik, S.W. 1989. Heteronuclear three‐dimensional NMR spectroscopy of the inflammatory protein C5a. Biochemistry 28:2387‐2391.
   Zweckstetter, M. 2008. NMR: Prediction of molecular alignment from structure using the PALES software. Nat. Protoc. 3:679‐690.
   Zweckstetter, M. and Bax, A. 2000. Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR. J. Am. Chem. Soc. 122:3791‐3792.
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