Journal of Biomolecular NMR

, Volume 62, Issue 3, pp 353–371 | Cite as

Information content of long-range NMR data for the characterization of conformational heterogeneity

  • Witold Andrałojć
  • Konstantin Berlin
  • David Fushman
  • Claudio Luchinat
  • Giacomo Parigi
  • Enrico Ravera
  • Luca Sgheri


Long-range NMR data, namely residual dipolar couplings (RDCs) from external alignment and paramagnetic data, are becoming increasingly popular for the characterization of conformational heterogeneity of multidomain biomacromolecules and protein complexes. The question addressed here is how much information is contained in these averaged data. We have analyzed and compared the information content of conformationally averaged RDCs caused by steric alignment and of both RDCs and pseudocontact shifts caused by paramagnetic alignment, and found that, despite the substantial differences, they contain a similar amount of information. Furthermore, using several synthetic tests we find that both sets of data are equally good towards recovering the major state(s) in conformational distributions.


Paramagnetic NMR Residual dipolar couplings Two-domain proteins Protein mobility Conformational variability 



This work has been supported by Ente Cassa di Risparmio di Firenze, MIUR PRIN 2012SK7ASN, NIH Grant GM065334, European Commission projects BioMedBridges No. 284209, pNMR No. 317127, and Instruct, part of the European Strategy Forum on Research Infrastructures (ESFRI) and supported by national member subscriptions. Specifically, we thank the EU ESFRI Instruct Core Centre CERM, Italy.

Conflict of interest

The authors declare that they have no conflict of interest.

Compliance with ethical standard

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

10858_2015_9951_MOESM1_ESM.docx (1.9 mb)
Supplementary material 1 (DOCX 1902 kb)


  1. Al-Hashimi HM, Valafar H, Terrell M, Zartler ER, Eidsness MK, Prestegard JH (2000) Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings. J Magn Reson 143:402–406ADSGoogle Scholar
  2. Allegrozzi M, Bertini I, Janik MBL, Lee Y-M, Liu G, Luchinat C (2000) Lanthanide induced pseudocontact shifts for solution structure refinements of macromolecules in shells up to 40 Å from the metal ion. J Am Chem Soc 122:4154–4161Google Scholar
  3. Andralojc W, Luchinat C, Parigi G, Ravera E (2014) Exploring regions of conformational space occupied by two-domain proteins. J Phys Chem B 118:10576–10587Google Scholar
  4. Balayssac S, Bertini I, Bhaumik A, Lelli M, Luchinat C (2008) Paramagnetic shifts in solid-state NMR of proteins to elicit strucutral information. Proc Natl Acad Sci USA 105:17284–17289ADSGoogle Scholar
  5. Banci L, Bertini I, Bren KL, Cremonini MA, Gray HB, Luchinat C, Turano P (1996) The use of pseudocontact shifts to refine solution structures of paramagnetic metalloproteins: Met80Ala cyano-cytochrome c as an example. J Biol Inorg Chem 1:117–126Google Scholar
  6. Banci L, Bertini I, Gori Savellini G, Romagnoli A, Turano P, Cremonini MA, Luchinat C, Gray HB (1997) Pseudocontact shifts as constraints for energy minimization and molecular dynamic calculations on solution structures of paramagnetic metalloproteins. Proteins Struct Funct Genet 29:68–76Google Scholar
  7. Banci L, Bertini I, Huber JG, Luchinat C, Rosato A (1998) Partial orientation of oxidized and reduced cytochrome b5 at high magnetic fields: magnetic susceptibility anisotropy contributions and consequences for protein solution structure determination. J Am Chem Soc 120:12903–12909Google Scholar
  8. 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 31:5269–5278Google Scholar
  9. Barthelmes K, Reynolds AM, Peisach E, Jonker HRA, DeNunzio NJ, Allen KN, Imperiali B, Schwalbe H (2011) Engineering encodable lanthanide-binding tags into loop regions of proteins. J Am Chem Soc 133:808–819Google Scholar
  10. Bashir Q, Volkov AN, Ullmann GM, Ubbink M (2010) Visualization of the encounter ensemble of the transient electron transfer complex of cytochrome c and cytochrome c peroxidase. J Am Chem Soc 132:241–247Google Scholar
  11. Berlin K, O’Leary DP, Fushman D (2009) Improvement and analysis of computational methods for prediction of residual dipolar couplings. J Magn Reson 201:25–33ADSGoogle Scholar
  12. Berlin K, Castañeda CA, Schneidman-Dohovny D, Sali A, Nava-Tudela A, Fushman D (2013) Recovering a representative conformational ensemble from underdetermined macromolecular structural data. J Am Chem Soc 135:16595–16609Google Scholar
  13. Bernadò P, Mylonas E, Petoukhov MV, Blackledge M, Svergun DI (2007) Structural characterization of flexible proteins using small-angle X-ray scattering. J Am Chem Soc 129:5656–5664Google Scholar
  14. Bertini I, Donaire A, Jiménez B, Luchinat C, Parigi G, Piccioli M, Poggi L (2001a) Paramagnetism-based versus classical constraints: an analysis of the solution structure of Ca Ln calbindin D9k. J Biomol NMR 21:85–98Google Scholar
  15. Bertini I, Janik MBL, Lee Y-M, Luchinat C, Rosato A (2001b) Magnetic susceptibility tensor anisotropies for a lanthanide Ion series in a fixed protein matrix. J Am Chem Soc 123:4181–4188Google Scholar
  16. Bertini I, Janik MBL, Liu G, Luchinat C, Rosato A (2001c) Solution structure calculations through self-orientation in a magnetic field of cerium (III) substituted calcium-binding protein. J Magn Reson 148:23–30ADSGoogle Scholar
  17. Bertini I, Longinetti M, Luchinat C, Parigi G, Sgheri L (2002a) Efficiency of paramagnetism-based constraints to determine the spatial arrangement of α-helical secondary structure elements. J Biomol NMR 22:123–136Google Scholar
  18. Bertini I, Luchinat C, Parigi G (2002b) Magnetic susceptibility in paramagnetic NMR. Prog NMR Spectrosc 40:249–273Google Scholar
  19. Bertini I, Gelis I, Katsaros N, Luchinat C, Provenzani A (2003) Tuning the affinity for lanthanides of calcium binding proteins. Biochemistry 42:8011–8021Google Scholar
  20. Bertini I, Del Bianco C, Gelis I, Katsaros N, Luchinat C, Parigi G, Peana M, Provenzani A, Zoroddu MA (2004a) Experimentally exploring the conformational space sampled by domain reorientation in calmodulin. Proc Natl Acad Sci USA 101:6841–6846ADSGoogle Scholar
  21. Bertini I, Fragai M, Lee Y-M, Luchinat C, Terni B (2004b) Paramagnetic metal ions in ligand screening: the CoII matrix metalloproteinase 12. Angew Chem Int Ed 43:2254–2256Google Scholar
  22. Bertini I, Luchinat C, Parigi G, Pierattelli R (2005) NMR of paramagnetic metalloproteins. ChemBioChem 6:1536–1549Google Scholar
  23. Bertini I, Gupta YK, Luchinat C, Parigi G, Peana M, Sgheri L, Yuan J (2007) Paramagnetism-based NMR restraints provide maximum allowed probabilities for the different conformations of partially independent protein domains. J Am Chem Soc 129:12786–12794Google Scholar
  24. Bertini I, Luchinat C, Parigi G, Pierattelli R (2008) Perspectives in NMR of paramagnetic proteins. Dalton Trans 2008:3782–3790Google Scholar
  25. 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 131:5134–5144Google Scholar
  26. 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 132:1032–1040Google Scholar
  27. Bertini I, Giachetti A, Luchinat C, Parigi G, Petoukhov MV, Pierattelli R, Ravera E, Svergun DI (2010b) Conformational space of flexible biological macromolecules from average data. J Am Chem Soc 132:13553–13558Google Scholar
  28. Bertini I, Calderone V, Cerofolini L, Fragai M, Geraldes CFGC, Hermann P, Luchinat C, Parigi G, Teixeira JMC (2012a) The catalytic domain of MMP-1 studied through tagged lanthanides. Dedicated to Prof. A.V. Xavier. FEBS Lett 586:557–567Google Scholar
  29. Bertini I, Ferella L, Luchinat C, Parigi G, Petoukhov MV, Ravera E, Rosato A, Svergun DI (2012b) MaxOcc: a web portal for maximum occurence analysis. J Biomol NMR 53:271–280Google Scholar
  30. Bertini I, Luchinat C, Nagulapalli M, Parigi G, Ravera E (2012c) Paramagnetic relaxation enhancements for the characterization of the conformational heterogeneity in two-domain proteins. Phys Chem Chem Phys 14:9149–9156Google Scholar
  31. Blackledge M (2005) Recent progress in the study of biomolecular structure and dynamics in solution from residual dipolar couplings. Prog NMR Spectrosc 46:23–61Google Scholar
  32. Boehr DD, McElheny D, Dyson HJ, Wright PE (2006) The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313:1638–1642ADSGoogle Scholar
  33. Boehr DD, Nussinov R, Wright PE (2009) The role of dynamic conformational ensembles in biomolecular recognition (vol 5, pg 789, 2009). Nat Chem Biol 5:954Google Scholar
  34. Bonvin AM, Brunger AT (1996) Do NOE distances contain enough information to assess the relative populations of multi-conformer structures? J Biomol NMR 7:72–76Google Scholar
  35. Bothe JR, Nikolova EN, Eichhorn CD, Chugh J, Hansen AL, Al Hashimi HM (2011) Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy. Nat Methods 8:919–931Google Scholar
  36. Burgi R, Pitera J, Van Gunsteren WF (2001) Assessing the effect of conformational averaging on the measured values of observables. J Biomol NMR 19:305–320Google Scholar
  37. Camilloni C, Vendruscolo M (2015) A tensor-free method for the structural and dynamical refinement of proteins using residual dipolar couplings. J Phys Chem B 119:653–661Google Scholar
  38. Cerofolini L, Fields GB, Fragai M, Geraldes CFGC, Luchinat C, Parigi G, Ravera E, Svergun DI, Teixeira JMC (2013) Examination of matrix metalloproteinase-1 (MMP-1) in solution: a preference for the pre-collagenolysis state. J Biol Chem 288:30659–30671Google Scholar
  39. Chen Y, Campbell SL, Dokholyan NV (2007) Deciphering protein dynamics from NMR data using explicit structure sampling and selection. Biophys J 93:2300–2306Google Scholar
  40. 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 8:990–997Google Scholar
  41. Choy W-Y, Forman-Kay JD (2001) Calculation of ensembles of structures representing the unfolded state of an SH3 domain. J Mol Biol 308:1011–1032Google Scholar
  42. Chuang GY, Mehra-Chaudhary R, Ngan CH, Zerbe BS, Kozakov D, Vajda S, Beamer LJ (2010) Domain motion and interdomain hot spots in a multidomain enzyme. Protein Sci 19:1662–1672Google Scholar
  43. Clore GM, Schwieters CD (2004) How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation? J Am Chem Soc 126:2923–2938Google Scholar
  44. Das Gupta S, Hu X, Keizers PHJ, Liu W-M, Luchinat C, Nagulapalli M, Overhand M, Parigi G, Sgheri L, Ubbink M (2011) Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains. J Biomol NMR 51:253–263Google Scholar
  45. Diaz-Moreno I, Diaz-Quintana A, De la Rosa MA, Ubbink M (2005) Structure of the complex between plastocyanin and cytochrome f from the cyanobacterium nostoc Sp. PCC 7119 as determined by paramagnetic NMR. J Biol Chem 280:18908–18915Google Scholar
  46. Fisher CK, Stultz CM (2011) Constructing ensembles for instrinsically disordered proteins. Curr Opin Struct Biol 21:426–431Google Scholar
  47. Fisher CK, Huang A, Stultz CM (2010) Modeling intrinsically disordered proteins with bayesian statistics. J Am Chem Soc 132:14919–14927Google Scholar
  48. Fragai M, Luchinat C, Parigi G (2006) “Four-dimensional” protein structures: examples from metalloproteins. Acc Chem Res 39:909–917Google Scholar
  49. Gaponenko V, Sarma SP, Altieri AS, Horita DA, Li J, Byrd RA (2004) Improving the accuracy of NMR structures of large proteins using pseudocontact shifts as long/range restraints. J Biomol NMR 28:205–212Google Scholar
  50. Gardner RJ, Longinetti M, Sgheri L (2005) Reconstruction of orientations of a moving protein domain from paramagnetic data. Inverse Probl 21:879–898MathSciNetADSGoogle Scholar
  51. Gempf KL, Butler SJ, Funk AM, Parker D (2013) Direct and selective tagging of cysteine residues in peptides and proteins with 4-nitropyridyl lanthanide complexes. Chem Commun (Camb) 49:9104–9106Google Scholar
  52. Gochin M, Roder H (1995a) Protein structure refinement based on paramagnetic NMR shifts: applications to wild-type and mutants forms of cytochrome c. Protein Sci 4:296–305Google Scholar
  53. Gochin M, Roder H (1995b) Use of pseudocontact shifts as a structural constraint for macromolecules in solution. Bull Magn Reson 17:1–4Google Scholar
  54. Guerry P, Salmon L, Mollica L, Ortega Roldan JL, Markwick P, van Nuland NA, McCammon JA, Blackledge M (2013) Mapping the population of protein conformational energy sub-states from NMR dipolar couplings. Angew Chem Int Ed Engl 52:3181–3185Google Scholar
  55. Hansen MR, Mueller L, Pardi A (1998) Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nat Struct Biol 5:1065–1074Google Scholar
  56. Hass MAS, Keizers PHJ, Blok A, Hiruma Y, Ubbink M (2010) Validation of a lanthanide tag for the analysis of protein dynamics by paramagnetic NMR spectroscopy. J Am Chem Soc 132:9952–9953Google Scholar
  57. Häussinger D, Huang J, Grzesiek S (2009) DOTA-M8: an extremely rigid, high-affinity lanthanide chelating tag for PCS NMR spectroscopy. J Am Chem Soc 131:14761–14767Google Scholar
  58. Huang J, Grzesiek S (2010) Ensemble calculations of unstructured proteins constrained by RDC and PRE data: a case study of urea-denatured ubiquitin. J Am Chem Soc 132:694–705Google Scholar
  59. Hulsker R, Baranova MV, Bullerjahn GS, Ubbink M (2008) Dynamics in the transient complex of plastocyanin-cytochrome f from Prochlorothrix hollandica. J Am Chem Soc 130:1985–1991Google Scholar
  60. Iwahara J, Schwieters CD, Clore GM (2004) Ensemble approach for NMR structure refinement against H-1 paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule. J Am Chem Soc 126:5879–5896Google Scholar
  61. Jensen MR, Hansen DF, Ayna U, Dagil R, Hass MA, Christensen HE, Led JJ (2006) On the use of pseudocontact shifts in the structure determination of metalloproteins. Magn Reson Chem 44:294–301Google Scholar
  62. John M, Otting G (2007) Strategies for measurements of pseudocontact shifts in protein NMR spectroscopy. ChemPhysChem 8:2309–2313Google Scholar
  63. Jones E, Oliphant E, Peterson P et al (2001) SciPy: Open source scientific tools for PythonGoogle Scholar
  64. Keizers PHJ, Saragliadis A, Hiruma Y, Overhand M, Ubbink M (2008) Design, synthesis, and evaluation of a lanthanide chelating protein probe: CLaNP-5 yields predictable paramagnetic effects independent of environment. J Am Chem Soc 130:14802–14812Google Scholar
  65. Kobashigawa Y, Saio T, Ushio M, Sekiguchi M, Yokochi M, Ogura K, Inagaki F (2012) Convenient method for resolving degeneracies due to symmetry of the magnetic susceptibility tensor and its application to pseudo contact shift-based protein-protein complex structure determination. J Biomol NMR 53:53–63Google Scholar
  66. Korzhnev DM, Kay LE (2008) Probing invisible, low-populated states of protein molecules by relaxation dispersion NMR spectroscopy: an application to protein folding. Acc Chem Res 41:442–451Google Scholar
  67. Kuffner JJ (2004) Effective sampling and distance metrics for 3D rigid body path planning. In: Proceedings IEEE international conference on Robotics and Automation (ICRA), vol 4, p 3993Google Scholar
  68. Kukic P, Camilloni C, Cavalli A, Vendruscolo M (2014) Determination of the individual roles of the linker residues in the interdomain motions of calmodulin using NMR chemical shifts. J Mol Biol 426:1826–1838Google Scholar
  69. Kurland RJ, McGarvey BR (1970) Isotropic NMR shifts in transition metal complexes: calculation of the Fermi contact and pseudocontact terms. J Magn Reson 2:286–301ADSGoogle Scholar
  70. Lakomek NA, Walter KF, Fares C, Lange OF, de Groot BL, Grubmuller H, Bruschweiler R, Munk A, Becker S, Meiler J, Griesinger C (2008) Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics. J Biomol NMR 41:139–155Google Scholar
  71. Lange OF, Lakomek N-A, Farès C, Schröder GF, Walter KFA, Becker S, Meiler J, Grubmüller H, Griesinger C, de Groot BL (2008) Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 320:1471–1475ADSGoogle Scholar
  72. Latham MP, Hanson P, Brown DJ, Pardi A (2008) Comparison of alignment tensors generated for native tRNA(Val) using magnetic fields and liquid crystalline media. J Biomol NMR 40:83–94Google Scholar
  73. Lindorff-Larsen K, Best RB, DePristo MA, Dobson CM, Vendruscolo M (2005) Simultaneous determination of protein structure and dynamics. Nature 433:128–132ADSGoogle Scholar
  74. Liu WM, Keizers PH, Hass MA, Blok A, Timmer M, Sarris AJ, Overhand M, Ubbink M (2012) A pH-sensitive, colorful, lanthanide-chelating paramagnetic NMR probe. J Am Chem Soc 134:17306–17313Google Scholar
  75. Loh CT, Ozawa K, Tuck KL, Barlow N, Huber T, Otting G, Graham B (2013) Lanthanide tags for site-specific ligation to an unnatural amino acid and generation of pseudocontact shifts in proteins. Bioconjug Chem 24:260–268Google Scholar
  76. Lohman JAB, Maclean C (1978) Alignment effects on high resolution NMR spectra induced by the magnetic field. Chem Phys 35:269–274ADSGoogle Scholar
  77. Longinetti M, Luchinat C, Parigi G, Sgheri L (2006) Efficient determination of the most favored orientations of protein domains from paramagnetic NMR data. Inverse Probl 22:1485–1502MathSciNetADSGoogle Scholar
  78. Losonczi JA, Prestegard JH (1998) Improved dilute bicelle solutions for high-resolution NMR of biological macromolecules. J Biomol NMR 12:447–451Google Scholar
  79. Losonczi JA, Andrec M, Fischer MW, Prestegard JH (1999) Order matrix analysis of residual dipolar couplings using singular value decomposition. J Magn Reson 138:334–342ADSGoogle Scholar
  80. Luchinat C, Nagulapalli M, Parigi G, Sgheri L (2012a) Maximum occurence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins. J Magn Reson 215:85–93ADSGoogle Scholar
  81. Luchinat C, Parigi G, Ravera E, Rinaldelli M (2012b) Solid state NMR crystallography through paramagnetic restraints. J Am Chem Soc 134:5006–5009Google Scholar
  82. Maltsev AS, Grishaev A, Roche J, Zasloff M, Bax A (2014) Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase. J Am Chem Soc 136:3752–3755Google Scholar
  83. Man B, Su XC, Liang H, Simonsen S, Huber T, Messerle BA, Otting G (2010) 3-Mercapto-2,6-pyridinedicarboxylic acid: a small lanthanide-binding tag for protein studies by NMR spectroscopy. Chem Eur J 16:3827–3832Google Scholar
  84. Montalvao R, Camilloni C, De SA, Vendruscolo M (2014) New opportunities for tensor-free calculations of residual dipolar couplings for the study of protein dynamics. J Biomol NMR 58:233–238Google Scholar
  85. Musiani F, Rossetti G, Capece L, Gerger TM, Micheletti C, Varani G, Carloni P (2014) Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 transactivation responsive RNA. J Am Chem Soc 136:15631–15637Google Scholar
  86. Nesterov Y (2012) Efficiency of coordinate descent methods on huge-scale optimization problems. SIAM J Optim 22:341–362MathSciNetGoogle Scholar
  87. Nodet L, Salmon L, Ozenne V, Meier S, Jensen MR, Blackledge M (2009) Quantitative description of backbone conformational sampling of unfolded proteins at amino acid resolution from NMR residual dipolar couplings. J Am Chem Soc 131:17908–17918Google Scholar
  88. O’Leary DP (2009) Scientific computing with case studies. SIAM, BangkokGoogle Scholar
  89. Pickford AR, Campbell ID (2004) NMR studies of modular protein structures and their interactions. Chem Rev 104:3557–3566Google Scholar
  90. Pintacuda G, John M, Su XC, Otting G (2007) NMR structure determination of protein-ligand complexes by lanthanide labeling. Acc Chem Res 40:206–212Google Scholar
  91. Prestegard JH, Al-Hashimi HM, Tolman JR (2000) NMR structures of biomolecules using field oriented media and residual dipolar couplings. Q Rev Biophys 33:371–424Google Scholar
  92. Ramirez BE, Bax A (1998) Modulation of the alignment tensor of macromolecules dissolved in a dilute liquid crystalline medium. J Am Chem Soc 120:9106–9107Google Scholar
  93. Ravera E, Salmon L, Fragai M, Parigi G, Al-Hashimi HM, Luchinat C (2014) Insights into domain-domain motions in proteins and RNA from solution NMR. Acc Chem Res 47:3118–3126Google Scholar
  94. Rinnenthal J, Buck J, Ferner J, Wacker A, Furtig B, Schwalbe H (2011) Mapping the landscape of RNA dynamics with NMR spectroscopy. Acc Chem Res 44:1292–1301Google Scholar
  95. Rodriguez-Castañeda F, Haberz P, Leonov A, Griesinger C (2006) Paramagnetic tagging of diamagnetic proteins for solution NMR. Magn Reson Chem 44:S10–S16Google Scholar
  96. Russo L, Maestre-Martinez M, Wolff S, Becker S, Griesinger C (2013) Interdomain dynamics explored by paramagnetic NMR. J Am Chem Soc 135:17111–17120Google Scholar
  97. Ryabov YE, Fushman D (2006) Analysis of interdomain dynamics in a two-domain protein using residual dipolar couplings together with 15 N relaxation data. Magn Reson Chem 44:S143–S151Google Scholar
  98. Ryabov YE, Fushman D (2007) A model of Interdomain mobility in a multidomain protein. J Am Chem Soc 129:3315–3327Google Scholar
  99. Saio T, Ogura K, Shimizu K, Yokochi M, Burke TR Jr, Inagaki F (2011) An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe. J Biomol NMR 51:395–408Google Scholar
  100. Schmitz C, Vernon R, Otting G, Baker D, Huber T (2012) Protein structure determination from pseudocontact shifts using ROSETTA. J Mol Biol 416:668–677Google Scholar
  101. Schroeder R, Barta A, Semrad K (2004) Strategies for RNA folding and assembly. Nat Rev Mol Cell Biol 5:908–919Google Scholar
  102. Sgheri L (2010a) Conformational freedom of proteins and the maximal probability of sets of orientations. Inverse Probl 26:035003-1–035003-19Google Scholar
  103. Sgheri L (2010b) Joining RDC data from flexible protein domains. Inverse Probl 26:115021-1–115021-12Google Scholar
  104. Sicheri F, Kuriyan J (1997) Structures of Src-family tyrosine kinases. Curr Opin Struct Biol 7:777–785Google Scholar
  105. Simin M, Irausquin S, Cole CA, Valafar H (2014) Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings. J Biomol NMR 60:241–264Google Scholar
  106. Stelzer AC, Frank AT, Bailor MH, Andricioaei I, Al Hashimi HM (2009) Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs. Methods 49:167–173Google Scholar
  107. Su XC, Otting G (2010) Paramagnetic labelling of proteins and oligonucleotides for NMR. J Biomol NMR 46:101–112Google Scholar
  108. Su XC, Huber T, Dixon NE, Otting G (2006) Site-specific labelling of proteins with a rigid lanthanide-binding tag. ChemBioChem 7:1599–1604Google Scholar
  109. Su XC, Man B, Beeren S, Liang H, Simonsen S, Schmitz C, Huber T, Messerle BA, Otting G (2008a) A dipicolinic acid tag for rigid lanthanide tagging of proteins and paramagnetic NMR spectroscopy. J Am Chem Soc 130:10486–10487Google Scholar
  110. Su XC, McAndrew K, Huber T, Otting G (2008b) Lanthanide-binding peptides for NMR measurements of residual dipolar couplings and paramagnetic effects from multiple angles. J Am Chem Soc 130:1681–1687Google Scholar
  111. Svergun DI, Petoukhov MV, Koch MHJ (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys J 80:2946–2953Google Scholar
  112. Swarbrick JD, Ung P, Chhabra S, Graham B (2011a) An iminodiacetic acid based lanthanide binding tag for paramagnetic exchange NMR spectroscopy. Angew Chem Int Ed Engl 50:4403–4406Google Scholar
  113. Swarbrick JD, Ung P, Su XC, Maleckis A, Chhabra S, Huber T, Otting G, Graham B (2011b) Engineering of a bis-chelator motif into a protein alpha-helix for rigid lanthanide binding and paramagnetic NMR spectroscopy. Chem Commun (Camb) 47:7368–7370Google Scholar
  114. Tjandra N, Bax A (1997) Direct measurement of distances and angles in biomolecules by NMR in a diluite liquid crystalline medium. Science 278:1111–1114ADSGoogle Scholar
  115. Tjandra N, Kuboniwa H, Ren H, Bax A (1995) Rotational dynamics of calcium-free calmodulin studied by 15N-NMR relaxation measurements. Eur J Biochem 230:1014–1024Google Scholar
  116. Tolman JR (2001) Dipolar couplings as a probe of molecular dynamics and structure in solution. Curr Opin Struct Biol 11:532–539Google Scholar
  117. Tolman JR, Ruan K (2006) NMR residual dipolar couplings as probes of biomolecular dynamics. Chem Rev 106:1720–1736Google Scholar
  118. Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH (1995) Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution. Proc Natl Acad Sci USA 92:9279–9283ADSGoogle Scholar
  119. Tonks NK (2006) Protein tyrosine phosphatases: from genes, to function, to disease. Nat Rev Mol Cell Biol 7:833–846Google Scholar
  120. Torchia DA (2015) NMR studies of dynamic biomolecular conformational ensembles. Prog Nucl Magn Reson Spectrosc 84–85:14–32Google Scholar
  121. Valafar H, Prestegard JH (2004) REDCAT: a residual dipolar coupling analysis tool. J Magn Reson 167:228–241ADSGoogle Scholar
  122. Wang H, Eberstadt M, Olejniczak ET, Meadows RP, Fesik SW (1998) A liquid crystalline medium for measuring residual dipolar couplings over a wide range of temperatures. J Biomol NMR 12:443–446Google Scholar
  123. Wöhnert J, Franz KJ, Nitz M, Imperiali B, Schwalbe H (2003) Protein alignment by a coexpressed lanthanide-binding tag for the measurement of residual dipolar couplings. J Am Chem Soc 125:13338–13339Google Scholar
  124. Yagi H, Maleckis A, Otting G (2013a) A systematic study of labelling an alpha-helix in a protein with a lanthanide using IDA-SH or NTA-SH tags. J Biomol NMR 55:157–166Google Scholar
  125. Yagi H, Pilla KB, Maleckis A, Graham B, Huber T, Otting G (2013b) Three-dimensional protein fold determination from backbone amide pseudocontact shifts generated by lanthanide tags at multiple sites. Structure 21:883–890Google Scholar
  126. Zhang Y, Zuiderweg ER (2004) The 70-kDa heat shock protein chaperone nucleotide-binding domain in solution unveiled as a molecular machine that can reorient its functional subdomains. Proc Natl Acad Sci USA 101:10272–10277ADSGoogle Scholar
  127. Zhang Q, Throolin R, Pitt SW, Serganov A, Al Hashimi HM (2003) Probing motions between equivalent RNA domains using magnetic field induced residual dipolar couplings: accounting for correlations between motions and alignment. J Am Chem Soc 125:10530–10531Google Scholar
  128. Zhuang T, Lee HS, Imperiali B, Prestegard JH (2008) Structure determination of a Galectin-3-carbohydrate complex using paramagnetism-based NMR constraints. Protein Sci 17:1220–1231Google Scholar
  129. Zweckstetter M (2008) NMR: prediction of molecular alignment from structure using the PALES software. Nat Protoc 3:679–690Google Scholar
  130. Zweckstetter M, 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 122:3791–3792Google Scholar
  131. Zweckstetter M, Bax A (2001) Characterization of molecular alignment in aqueous suspensions of Pf1 bacteriophage. J Biomol NMR 20:365–377Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Witold Andrałojć
    • 1
  • Konstantin Berlin
    • 2
  • David Fushman
    • 2
  • Claudio Luchinat
    • 1
    • 3
  • Giacomo Parigi
    • 1
    • 3
  • Enrico Ravera
    • 1
    • 3
  • Luca Sgheri
    • 4
  1. 1.Center for Magnetic Resonance (CERM)University of FlorenceSesto FiorentinoItaly
  2. 2.Department of Chemistry and Biochemistry, Center for Biomolecular Structure and OrganizationUniversity of MarylandCollege ParkUSA
  3. 3.Department of Chemistry “Ugo Schiff”University of FlorenceSesto FiorentinoItaly
  4. 4.Istituto per le Applicazioni del Calcolo, Sezione di FirenzeCNRSesto FiorentinoItaly

Personalised recommendations