Skip to main content
SpringerLink
Log in

NMR Spectroscopic Studies of the Conformational Ensembles of Intrinsically Disordered Proteins

  • Chapter
  • First Online:
Intrinsically Disordered Proteins Studied by NMR Spectroscopy

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 870))

Abstract

Intrinsically disordered proteins (IDPs) are characterized by substantial conformational flexibility and thus not amenable to conventional structural biology techniques. Given their inherent structural flexibility NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This chapter will summarize key advances in NMR methodology. Despite the availability of efficient (multi-dimensional) NMR experiments for signal assignment of IDPs it is discussed that NMR of larger and more complex IDPs demands spectral simplification strategies capitalizing on specific isotope-labeling strategies. Prototypical applications of isotope labeling-strategies are described. Since IDP-ligand association and dissociation processes frequently occur on time scales that are amenable to NMR spectroscopy we describe in detail the application of CPMG relaxation dispersion techniques to studies of IDP protein binding. Finally, we demonstrate that the complementary usage of NMR and EPR data provide a more comprehensive picture about the conformational states of IDPs and can be employed to analyze the conformational ensembles of IDPs.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Allerhand A, Gutowsky HS (1964) Spin-Echo NMR studies of chemical exchange.1. Some general aspects. J Chem Phys 41:2115

    Google Scholar 

  • Allison JR, Varnai P, Dobson CM et al (2009) Determination of the free energy landscape of α-synuclein using spin label nuclear magnetic resonance measurements. J Am Chem Soc 131:18314–18326

    Article  CAS  PubMed  Google Scholar 

  • Arnaudon L, Assmann R, Billan J et al (1993) Measurement of the mass of the Z-Boson and the energy calibration of lep. Phys Lett B 307:187–193

    Article  CAS  Google Scholar 

  • Baldwin AJ, Kay LE (2009) NMR spectroscopy brings invisible protein states into focus. Nat Chem Biol 5:808–814

    Article  CAS  PubMed  Google Scholar 

  • Bartels T, Choi JG, Selkoe DJ (2011) α-Synuclein occurs physiologically as a helically folded tetramer that resists aggregation. Nature 477:107–110

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Battiste JL, Wagner G (2000) Utilization of site-directed spin labeling and high-resolution heteronuclear nuclear magnetic resonance for global fold determination of large proteins with limited nuclear overhauser effect data. Biochemistry 39:5355–5365

    Article  CAS  PubMed  Google Scholar 

  • Beharry C, Cohen LS, Di J et al (2014) Tau-induced neurodegeneration: mechanisms and targets. Neurosci Bull 30:346–358

    Article  CAS  PubMed  Google Scholar 

  • Berezovsky IN, Trifonov EN (2002) Back to units of protein folding. J Biomol Struct Dyn 20:315–316

    Article  CAS  PubMed  Google Scholar 

  • Berjanskii M, Wishart DS (2006) NMR: prediction of protein flexibility. Nat Protoc 1:683–688

    Article  CAS  PubMed  Google Scholar 

  • Bermel W, Bertini I, Chill J et al (2012) Exclusively heteronuclear 13C-detected amino-acid-selective NMR experiments for the study of intrinsically disordered proteins (IDPs). Chembiochem 13:2425–2432

    Article  CAS  PubMed  Google Scholar 

  • BernadÏŒ P, Blanchard L, Timmins P et al (2005) A structural model for unfolded proteins from residual dipolar couplings and small-angle X-ray scattering. Proc Natl Acad Sci U S A 102:17002–17007

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Bertini I, Felli IC, Gonnelli L et al (2011) High-resolution characterization of intrinsic disorder in proteins: expanding the suite of 13C-detected NMR spectroscopy experiments to determine key observables. Chembiochem 12:2347–2352

    Article  CAS  PubMed  Google Scholar 

  • Bibow S, Ozenne V, Biernat J et al (2011) Structural impact of proline-directed pseudophosphorylation at AT8, AT100, and PHF1 epitopes on 441-residue tau. J Am Chem Soc 133:15842–15845

    Article  CAS  PubMed  Google Scholar 

  • Borg M, Mittag T, Pawson T et al (2007) Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity. Proc Natl Acad Sci U S A 104:9650–9655

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Bytchenkoff D, Pelupessy P, Bodenhausen G (2005) Anisotropic local motions and location of amide protons in proteins. J Am Chem Soc 127:5180–5185

    Article  CAS  PubMed  Google Scholar 

  • Camilloni C, De Simone A, Vranken WF et al (2012) Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts. BioChemistry 51:2224–2231

    Article  CAS  PubMed  Google Scholar 

  • Carlomagno T, Maurer M, Hennig M et al (2000) Ubiquitin backbone motion studied via NHN−C`Cα Dipolar−Dipolar and C`−C`Cα/NHN CSA-dipolar cross-correlated relaxation. J Am Chem Soc 122:5105–5113

    Article  CAS  Google Scholar 

  • Carver JP, Richards RE (1972) General 2-site solution for chemical exchange produced dependence of T2 upon Carr-Purcell pulse separation. J Magn Reson 6:89

    CAS  Google Scholar 

  • Chang SL, Tjandra N (2005) Temperature dependence of protein backbone motion from carbonyl 15C and amide 15N NMR relaxation. J Magn Reson 174:43–53

    Article  CAS  PubMed  Google Scholar 

  • Chiarparin E, Pelupessy P, Ghose R et al (1999) Relaxation of two-spin coherence due to cross-correlated fluctuations of dipole-dipole couplings and anisotropic shifts in NMR of N-15,C-13-labeled biomolecules. J Am Chem Soc 121:6876–6883

    Article  CAS  Google Scholar 

  • Choy WY, Forman-Kay JD (2001) Calculation of ensembles of structures representing the unfolded state of an SH3 domain. J Mol Biol 308:1011–1032

    Article  CAS  PubMed  Google Scholar 

  • Clore GM, Szabo A, Bax A et al (1990) Deviations from the simple 2-parameter model-free approach to the interpretation of N-15 nuclear magnetic-relaxation of proteins. J Am Chem Soc 112:4989–4991

    Article  CAS  Google Scholar 

  • Deribe YL, Pawson T, Dikic I (2010) Post-translational modifications in signal integration. Nat Struct Mol Biol 17:666–672

    Article  CAS  PubMed  Google Scholar 

  • Dill KA (1999) Polymer principles and protein folding. Protein Sci 8:1166–1180

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Dyson HJ, Wright PE (2004) Unfolded proteins and protein folding studied by NMR. Chem Rev 104:3607–3622

    Article  CAS  PubMed  Google Scholar 

  • Errington N, Doig AJ (2005) A phosphoserine-lysine salt bridge within an α-helical peptide, the strongest α-helix side-chain interaction measured to date. Biochemistry 44:7553–7558

    Article  CAS  PubMed  Google Scholar 

  • Fieber W, Schneider ML, Matt T et al (2001) Structure, function, and dynamics of the dimerization and DNA-binding domain of oncogenic transcription factor v-Myc. J Mol Biol 307:1395–1410

    Article  CAS  PubMed  Google Scholar 

  • Fisher CK, Stultz CM (2011) Constructing ensembles for intrinsically disordered proteins. Curr Opin Struct Biol 21:426–431

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Fisher CK, Huang A, Stultz CM (2010) Modeling intrinsically disordered proteins with bayesian statistics. J Am Chem Soc 132:14919–14927

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Fleissner MR, Brustad EM, Kalai T et al (2009) Site-directed spin labeling of a genetically encoded unnatural amino acid. Proc Natl Acad Sci U S A 106:21637–21642

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gans P, Hamelin O, Sounier R et al (2010) Stereospecific isotopic labeling of Methyl groups for NMR spectroscopic studies of high-molecular-weight proteins. Angew Chem Int Edit 49:1958–1962

    Article  CAS  Google Scholar 

  • Geist L, Henen MA, Haiderer S et al (2013) Protonation-dependent conformational variability of intrinsically disordered proteins. Protein Sci 22:1196–1205

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gluck JM, Hoffmann S, Koenig BW et al (2010) Single vector system for efficient N-myristoylation of recombinant proteins in E. coli. PloS ONE 5:e10081

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Goldman M (1984) Interference effects in the relaxation of a pair of unlike spin-1/2 nuclei. J Magn Reson 60:437–452

    CAS  Google Scholar 

  • Goto NK, Gardner KH, Mueller GA et al (1999) A robust and cost-effective method for the production of Val, Leu, Ile (delta 1) methyl-protonated N-15-, C-13-, H-2-labeled proteins. J Biomol NMR 13:369–374

    Article  CAS  PubMed  Google Scholar 

  • Gruschus JM, Yap TL, Pistolesi S et al. (2013) NMR structure of calmodulin complexed to an N-terminally acetylated α-synuclein peptide. Biochemistry 52(20):3436–3445

    Article  CAS  PubMed  Google Scholar 

  • Guo RT, Chou LJ, Chen YC et al (2001) Expression in Pichia pastoris and characterization by circular dichroism and NMR of rhodostomin. Proteins 43:499–508

    Article  CAS  PubMed  Google Scholar 

  • Guo CY, Geng C, Tugarinov V (2009) Selective backbone labeling of proteins using {1,2-C-13(2)}-pyruvate as carbon source. J Biomol NMR 44:167–173

    Article  CAS  PubMed  Google Scholar 

  • Holt C, Sawyer L (1993) Caseins as rheomorphic proteins—interpretation of primary and secondary structures of the α-S1-Caseins, β-Caseins and κ-Caseins. J Chem Soc Faraday T 89:2683–2692

    Article  CAS  Google Scholar 

  • Hunter GK (2013) Role of osteopontin in modulation of hydroxyapatite formation. Calcif Tissue Int 93:348–354

    Article  CAS  PubMed  Google Scholar 

  • Ishima R, Torchia DA (1999) Estimating the time scale of chemical exchange of proteins from measurements of transverse relaxation rates in solution. J Biomol NMR 14:369–372

    Article  CAS  PubMed  Google Scholar 

  • Ishima R, Torchia DA (2006) Accuracy of optimized chemical-exchange parameters derived by fitting CPMG R2 dispersion profiles when R2 0a ≠ R2 0b. J Biomol NMR 34:209–219

    Article  CAS  PubMed  Google Scholar 

  • Johnson M, Coulton AT, Geeves MA et al (2010) Targeted amino-terminal acetylation of recombinant proteins in E. coli. PloS ONE 5:e15801

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kay LE, Keifer P, Saarinen T (1992) Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity. J Am Chem Soc 114:10663–10665

    Article  CAS  Google Scholar 

  • Kazanecki CC, Uzwiak DJ, Denhardt DT (2007) Control of osteopontin signaling and function by post-translational phosphorylation and protein folding. J Cell Biochem 102:912–924

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Kazimierczuk K, Stanek J, Zawadzka-Kazimierczuk A et al (2010a) Random sampling in multidimensional NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 57:420–434

    Article  CAS  PubMed  Google Scholar 

  • Kazimierczuk K, Zawadzka-Kazimierczuk A, Kozminski W (2010b) Non-uniform frequency domain for optimal exploitation of non-uniform sampling. J Magn Reson 205:286–292

    Article  CAS  PubMed  Google Scholar 

  • Kehoe JW, Bertozzi CR (2000) Tyrosine sulfation: a modulator of extracellular protein-protein interactions. Chem Biol 7:R57–R61

    Article  CAS  PubMed  Google Scholar 

  • Khoury GA, Baliban RC, Floudas CA (2011) Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database. Scientific reports 1

    Google Scholar 

  • Kim JH, Peng D, Schlebach JP et al. (2014) Modest effects of lipid modifications on the Structure of Caveolin-3. Biochemistry 53(27):4320–4322

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kloiber K, Konrat R (2000) Measurement of the protein backbone dihedral angle phi based on quantification of remote CSA/DD interference in inter-residue 13C'(i-1)-13Cα(i) multiple-quantum coherences. J Biomol NMR 17:265–268

    Article  CAS  PubMed  Google Scholar 

  • Kloiber K, Schuler W, Konrat R (2002) Automated NMR determination of protein backbone dihedral angles from cross-correlated spin relaxation. J Biomol NMR 22:349–363

    Article  CAS  PubMed  Google Scholar 

  • Kloiber K, Spitzer R, Tollinger M et al (2011) Probing RNA dynamics via longitudinal exchange and CPMG relaxation dispersion NMR spectroscopy using a sensitive C-13-methyl label. Nucleic Acids Res 39:4340–4351

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Konrat R (2009) The protein meta-structure: a novel concept for chemical and molecular biology. Cell Mol Life Sci 66:3625–3639

    Article  CAS  PubMed  Google Scholar 

  • Konrat R (2014) NMR contributions to structural dynamics studies of intrinsically disordered proteins. J Magn Reson 241:74–85

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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 41:442–451

    Article  CAS  PubMed  Google Scholar 

  • Korzhnev DM, Salvatella X, Vendruscolo M et al (2004a) Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR. Nature 430:586–590

    Article  CAS  PubMed  Google Scholar 

  • Korzhnev DM, Kloiber K, Kay LE (2004b) Multiple-quantum relaxation dispersion NMR spectroscopy probing millisecond time-scale dynamics in proteins: theory and application. J Am Chem Soc 126:7320–7329

    Article  CAS  PubMed  Google Scholar 

  • Kosen PA (1989) Spin labeling of proteins. Methods Enzymol 177:86–121

    Article  CAS  PubMed  Google Scholar 

  • Kragelj J, Ozenne V, Blackledge M et al (2013) Conformational propensities of intrinsically disordered proteins from NMR chemical shifts. ChemPhysChem 14:3034–3045

    Article  CAS  PubMed  Google Scholar 

  • Kurzbach D, Platzer G, Schwarz TC et al (2013) Cooperative unfolding of compact conformations of the intrinsically disordered protein osteopontin. Biochemistry 52:5167–5175

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kurzbach D, Schwarz TC, Platzer G et al (2014) Compensatory adaptations of structural dynamics in an intrinsically disordered protein complex. Angew Chem Int Ed 53:3840–3843

    Article  CAS  Google Scholar 

  • Landrieu I, Lacosse L, Leroy A et al (2006) NMR analysis of a Tau phosphorylation pattern. J Am Chem Soc 128:3575–3583

    Article  CAS  PubMed  Google Scholar 

  • Latham JA, Dent SY (2007) Cross-regulation of histone modifications. Nat Struct Mol Biol 14:1017–1024

    Article  CAS  PubMed  Google Scholar 

  • Levitt M, Chothia C (1976) Structural patterns in globular proteins. Nature 261:552–558

    Article  CAS  PubMed  Google Scholar 

  • Lichtenecker R, Ludwiczek ML, Schmid W et al (2004) Simplification of protein NOESY spectra using bioorganic precursor synthesis and NMR spectral editing. J Am Chem Soc 126:5348–5349

    Article  CAS  PubMed  Google Scholar 

  • Lichtenecker RJ, Coudevylle N, Konrat R et al (2013a) Selective isotope labelling of leucine residues by using α-ketoacid precursor compounds. ChemBioChem 14:818–821

    Article  CAS  PubMed  Google Scholar 

  • Lichtenecker RJ, Weinhaupl K, Reuther L et al (2013b) Independent valine and leucine isotope labeling in Escherichia coli protein overexpression systems. J Biomol NMR 57:205–209

    Article  CAS  PubMed  Google Scholar 

  • Lichtenecker RJ, Weinhaupl K, Schmid W et al (2013c) α-Ketoacids as precursors for phenylalanine and tyrosine labelling in cell-based protein overexpression. J Biomol NMR 57:327–331

    Article  CAS  PubMed  Google Scholar 

  • Lindorff-Larsen K, Kristjansdottir S, Teilum K et al (2004) Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme A binding protein. J Am Chem Soc 126:3291–3299

    Article  CAS  PubMed  Google Scholar 

  • Liokatis S, Dose A, Schwarzer D et al (2010) Simultaneous detection of protein phosphorylation and acetylation by high-resolution NMR spectroscopy. J Am Chem Soc 132:14704–14705

    Article  CAS  PubMed  Google Scholar 

  • Lipari G, Szabo A (1981a) A model-free approach to the interpretation of NMR relaxation in macromolecules. Biophys J 33:A307–A307

    Google Scholar 

  • Lipari G, Szabo A (1981b) Pade approximants to correlation-functions for restricted rotational diffusion. J Chem Phys 75:2971–2976

    Article  CAS  Google Scholar 

  • Liu CC, Cellitti SE, Geierstanger BH et al (2009) Efficient expression of tyrosine-sulfated proteins in E. coli using an expanded genetic code. Nat Protoc 4:1784–1789

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Luz Z, Meiboom S (1963) Nuclear magnetic resonance study of the protolysis of trimethylammonium ion in aqueous solution-order of the reaction with respect to solvent. J Chem Phys 39:366–370

    Article  CAS  Google Scholar 

  • Maekawa S, Murofushi H, Nakamura S (1994) Inhibitory effect of calmodulin on phosphorylation of NAP-22 with protein kinase C. J Biol Chem 269:19462–19465

    CAS  PubMed  Google Scholar 

  • Maltsev AS, Ying J, Bax A (2012) Impact of N-terminal acetylation of α-synuclein on its random coil and lipid binding properties. Biochemistry 51:5004–5013

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mao AH, Crick SL, Vitalis A et al (2010) Net charge per residue modulates conformational ensembles of intrinsically disordered proteins. Proc Natl Acad Sci U S A 107:8183–8188

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Marion D, Ikura M, Tschudin R et al (1989) Rapid recording of 2D NMR-spectra without phase cycling—application to the study of hydrogen-exchange in proteins. J Magn Reson 85:393–399

    CAS  Google Scholar 

  • Marsh JA, Forman-Kay JD (2011) Ensemble modeling of protein disordered states: Experimental restraint contributions and validation. Proteins 80(20):556–572

    PubMed  Google Scholar 

  • Marsh JA, Singh VK, Jia Z et al (2006) Sensitivity of secondary structure propensities to sequence differences between α- and γ-synuclein: implications for fibrillation. Protein Sci 15:2795–2804

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Matsubara M, Nakatsu T, Kato H et al (2004) Crystal structure of a myristoylated CAP-23/NAP-22 N-terminal domain complexed with Ca2+/calmodulin. EMBO J 23:712–718

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mayer C, Slater L, Erat MC et al (2012) Structural analysis of the plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) intracellular domain reveals a conserved interaction epitope. J Biol Chem 287:7182–7189

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Means GE, Feeney RE (1968) Reductive alkylation of amino groups in proteins. Biochemistry 7:2192–2201

    Article  CAS  PubMed  Google Scholar 

  • Meyer B, Möller H (2007) Conformation of glycopeptides and glycoproteins. Top Curr Chem 267:187–251

    Article  CAS  Google Scholar 

  • Mittag T, Forman-Kay JD (2007) Atomic-level characterization of disordered protein ensembles. Curr Opin Struct Biol 17:3–14

    Article  CAS  PubMed  Google Scholar 

  • Mittag T, Orlicky S, Choy WY et al (2008) Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor. Proc Natl Acad Sci U S A 105:17772–17777

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mittag T, Marsh J, Grishaev A et al (2010) Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. Structure 18:494–506

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mohana-Borges R, Goto NK, Kroon GJ et al (2004) Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings. J Mol Biol 340:1131–1142

    Article  CAS  PubMed  Google Scholar 

  • Motackova V, Novacek J, Zawadzka-Kazimierczuk A et al (2010) Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments. J Biomol NMR 48:169–177

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Nair SK, Burley SK (2003) X-ray structures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by proto-oncogenic transcription factors. Cell 112:193–205

    Article  CAS  PubMed  Google Scholar 

  • Neudecker P, Zarrine-Afsar A, Choy WY et al (2006) Identification of a collapsed intermediate with non-native long-range interactions on the folding pathway of a pair of Fyn SH3 domain mutants by NMR relaxation dispersion spectroscopy. J Mol Biol 363:958–976

    Article  CAS  PubMed  Google Scholar 

  • Neumann H, Peak-Chew SY, Chin JW (2008) Genetically encoding N(epsilon)-acetyllysine in recombinant proteins. Nat Chem Biol 4:232–234

    Article  CAS  PubMed  Google Scholar 

  • Nguyen DP, Garcia Alai MM, Virdee S et al (2010) Genetically directing varepsilon-N, N-dimethyl-L-lysine in recombinant histones. Chem Biol 17:1072–1076

    Article  CAS  PubMed  Google Scholar 

  • Novacek J, Zawadzka-Kazimierczuk A, Papouskova V et al (2011) 5D 13C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion. J Biomol NMR 50:1–11

    Article  CAS  PubMed  Google Scholar 

  • Orekhov VY, Korzhnev DM, Kay LE (2004) Double- and zero-quantum NMR relaxation dispersion experiments sampling millisecond time scale dynamics in proteins. J Am Chem Soc 126:1886–1891

    Article  CAS  PubMed  Google Scholar 

  • Otting G (2010) Protein NMR using paramagnetic ions. Annu Rev Biophys 39:387–405

    Article  CAS  PubMed  Google Scholar 

  • Ozenne V, Bauer F, Salmon L et al (2012) Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables. Bioinformatics 28:1463–1470

    Article  CAS  PubMed  Google Scholar 

  • Pang Y, Buck M, Zuiderweg ER (2002) Backbone dynamics of the ribonuclease binase active site area using multinuclear (15N and 13CO) NMR relaxation and computational molecular dynamics. BioChemistry 41:2655–2666

    Article  CAS  PubMed  Google Scholar 

  • Parra RG, Espada R, Sanchez IE et al (2013) Detecting repetitions and periodicities in proteins by tiling the structural space. J Phys Chem B 117:12887–12897

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Pelupessy P, Chiarparin E, Ghose R et al (1999) Efficient determination of angles subtended by Cα-Hα and N-H(N) vectors in proteins via dipole-dipole cross-correlation. J Biomol NMR 13:375–380

    Article  CAS  PubMed  Google Scholar 

  • Pelupessy P, Espallargas GM, Bodenhausen G (2003a) Symmetrical reconversion: measuring cross-correlation rates with enhanced accuracy. J Magn Reson 161:258–264

    Article  CAS  PubMed  Google Scholar 

  • Pelupessy P, Ravindranathan S, Bodenhausen G (2003b) Correlated motions of successive amide N-H bonds in proteins. J Biomol NMR 25:265–280

    Article  CAS  PubMed  Google Scholar 

  • Pervushin K, Riek R, Wider G et al (1997) Attenuated T2 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Pinheiro AS, Marsh JA, Forman-Kay JD et al (2011) Structural signature of the MYPT1-PP1 interaction. J Am Chem Soc 133:73–80

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Platzer G, Schedlbauer A, Chemelli A et al (2011) The metastasis-associated extracellular matrix protein osteopontin forms transient structure in ligand interaction sites. Biochemistry 50:6113–6124

    Article  CAS  PubMed  Google Scholar 

  • Reif B, Hennig M, Griesinger C (1997) Direct measurement of angles between bond vectors in high-resolution NMR. Science 276:1230–1233

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Rose GD, Fleming PJ, Banavar JR et al (2006) A backbone-based theory of protein folding. Proc Natl Acad Sci U S A 103:16623–16633

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Rule GS, Hitchens TK (2006) Fundamentals of protein NMR spectroscopy. Springer, Dordrecht

    Google Scholar 

  • Salmon L, Nodet G, Ozenne V et al (2010) NMR characterization of long-range order in intrinsically disordered proteins. J Am Chem Soc 132:8407–8418

    Article  CAS  PubMed  Google Scholar 

  • Salzmann M, Pervushin K, Wider G et al (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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sára T, Schwarz TC, Kurzbach D et al. (2014) Magnetic resonance access to transiently formed protein complexes. ChemistryOpen 3(3):115–123

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Sauve S, Tremblay L, Lavigne P (2004) The NMR solution structure of a mutant of the max b/HLH/LZ free of DNA: insights into the specific and reversible DNA binding mechanism of dimeric transcription factors. J Mol Biol 342:813–832

    Article  CAS  PubMed  Google Scholar 

  • Schanda P, Van Melckebeke H, Brutscher B (2006) Speeding up three-dimensional protein NMR experiments to a few minutes. J Am Chem Soc 128:9042–9043

    Article  CAS  PubMed  Google Scholar 

  • Schanda P, Brutscher B, Konrat R et al (2008) Folding of the KIX domain: characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. J Mol Biol 380:726–741

    Article  CAS  PubMed  Google Scholar 

  • Schwalbe H, Carlomagno T, Hennig M et al (2001) Cross-correlated relaxation for measurement of angles between tensorial interactions. Methods Enzymol 338:35–81

    Article  CAS  PubMed  Google Scholar 

  • Selenko P, Frueh DP, Elsaesser SJ et al. (2008) In situ observation of protein phosphorylation by high-resolution NMR spectroscopy. Nat Struct Mol Biol 15:321–329

    Article  CAS  PubMed  Google Scholar 

  • Solyom Z, Schwarten M, Geist L et al (2013) BEST-TROSY experiments for time-efficient sequential resonance assignment of large disordered proteins. J Biomol NMR 55:311–321

    Article  CAS  PubMed  Google Scholar 

  • Stanek J, Saxena S, Geist L et al (2013) Probing local backbone geometries in intrinsically disordered proteins by cross-correlated NMR relaxation. Angew Chem Int Ed Engl 52:4604–4606

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sugase K, Lansing JC, Dyson HJ et al. (2007) Tailoring relaxation dispersion experiments for fast-associating protein complexes. J Am Chem Soc 129:13406

    Google Scholar 

  • Tamiola K, Mulder FA (2012) Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins. Biochem Soc Trans 40:1014–1020

    Article  CAS  PubMed  Google Scholar 

  • Tejero-Diez P, Rodriguez-Sanchez P, Martin-Cofreces NB et al (2000) bFGF stimulates GAP-43 phosphorylation at ser41 and modifies its intracellular localization in cultured hippocampal neurons. Mol Cell Neurosci 16:766–780

    Article  CAS  PubMed  Google Scholar 

  • Theillet FX, Liokatis S, Jost JO et al (2012) Site-specific mapping and time-resolved monitoring of lysine methylation by high-resolution NMR spectroscopy. J Am Chem Soc 134:7616–7619

    Article  CAS  PubMed  Google Scholar 

  • Theillet FX, Rose HM, Liokatis S et al (2013) Site-specific NMR mapping and time-resolved monitoring of serine and threonine phosphorylation in reconstituted kinase reactions and mammalian cell extracts. Nat Protoc 8:1416–1432

    Article  PubMed  CAS  Google Scholar 

  • Theillet FX, Binolfi A, Frembgen-Kesner T et al. (2014) Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs). Chem Rev 114(13):6661–6714

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Tjandra N, Bax A (1997) Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278:1111–1114

    Article  CAS  PubMed  Google Scholar 

  • Tjandra N, Szabo A, Bax A (1996) Protein backbone dynamics and N-15 chemical shift anisotropy from quantitative measurement of relaxation interference effects. J Am Chem Soc 118:6986–6991

    Article  CAS  Google Scholar 

  • Tollinger M, Skrynnikov NR, Mulder FAA et al (2001) Slow dynamics in folded and unfolded states of an SH3 domain. J Am Chem Soc 123:11341–11352

    Article  CAS  PubMed  Google Scholar 

  • Tollinger M, Kloiber K, Agoston B et al (2006) An isolated helix persists in a sparsely populated form of KIX under native conditions. Biochemistry 45:8885–8893

    Article  CAS  PubMed  Google Scholar 

  • Trifonov EN, Frenkel ZM (2009) Evolution of protein modularity. Curr Opin Struct Biol 19:335–340

    Article  CAS  PubMed  Google Scholar 

  • Tugarinov V, Kay LE (2004a) 1H, 13C-1H, 1H dipolar cross-correlated spin relaxation in methyl groups. J Biomol NMR 29:369–376

    Article  CAS  PubMed  Google Scholar 

  • Tugarinov V, Kay LE (2004b) An isotope labeling strategy for methyl TROSY spectroscopy. J Biomol NMR 28:165–172

    Article  CAS  PubMed  Google Scholar 

  • Tugarinov V, Hwang PM, Ollerenshaw JE et al (2003) Cross-correlated relaxation enhanced 1H(bond)13C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes. J Am Chem Soc 125:10420–10428

    Article  CAS  PubMed  Google Scholar 

  • Tugarinov V, Sprangers R, Kay LE (2004) Line narrowing in methyl-TROSY using zero-quantum 1H-13C NMR spectroscopy. J Am Chem Soc 126:4921–4925

    Article  CAS  PubMed  Google Scholar 

  • Veit M (2000) Palmitoylation of the 25-kDa synaptosomal protein (SNAP-25) in vitro occurs in the absence of an enzyme, but is stimulated by binding to syntaxin. Biochem J 345(Pt 1):145–151

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Vogeli B, Yao L (2009) Correlated dynamics between protein HN and HC bonds observed by NMR cross relaxation. J Am Chem Soc 131:3668–3678

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wang T, Frederick KK, Igumenova TI et al (2005) Changes in calmodulin main-chain dynamics upon ligand binding revealed by cross-correlated NMR relaxation measurements. J Am Chem Soc 127:828–829

    Article  CAS  PubMed  Google Scholar 

  • Wang T, Weaver DS, Cai S et al (2006) Quantifying Lipari-Szabo modelfree parameters from 13CO NMR relaxation experiments. J Biomol NMR 36:79–102

    Article  CAS  PubMed  Google Scholar 

  • Wells M, Tidow H, Rutherford TJ et al (2008) Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain. Proc Natl Acad Sci U S A 105:5762–5767

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wolynes PG (1996) Symmetry and the energy landscapes of biomolecules. Proc Natl Acad Sci U S A 93:14249–14255

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wood MJ, Komives EA (1999) Production of large quantities of isotopically labeled protein in Pichia pastoris by fermentation. J Biomol NMR 13:149–159

    Article  CAS  PubMed  Google Scholar 

  • Yang DW, Konrat R, Kay LE (1997) A multidimensional NMR experiment for measurement of the protein dihedral angle psi based on cross-correlated relaxation between (H α-13C α)-H-1 dipolar and 13C' (carbonyl) chemical shift anisotropy mechanisms. J Am Chem Soc 119:11938–11940

    Article  CAS  Google Scholar 

  • Yang D, Gardner KH, Kay LE (1998) A sensitive pulse scheme for measuring the backbone dihedral angle psi based on cross-correlation between 13C α- 1H α dipolar and carbonyl chemical shift anisotropy relaxation interactions. J Biomol NMR 11:213–220

    Article  CAS  PubMed  Google Scholar 

  • Young TS, Schultz PG (2010) Beyond the canonical 20 amino acids: expanding the genetic lexicon. J Biol Chem 285:11039–11044

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zakharov VV, Capony JP, Derancourt J et al (2003) Natural N-terminal fragments of brain abundant myristoylated protein BASP1. Biochim Biophys Acta 1622:14–19

    Article  CAS  PubMed  Google Scholar 

  • Zawadzka-Kazimierczuk A, Kozminski W, Sanderova H et al (2012) High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins. J Biomol NMR 52:329–337

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zeng L, Fischer MW, Zuiderweg ER (1996) Study of protein dynamics in solution by measurement of 13C α- 13CO NOE and 13CO longitudinal relaxation. J Biomol NMR 7:157–162

    CAS  PubMed  Google Scholar 

  • Zintsmaster JS, Wilson BD, Peng JW (2008) Dynamics of ligand binding from C-13 NMR relaxation dispersion at natural abundance. J Am Chem Soc 130(43):14060–14061

    Google Scholar 

Download references

Acknowledgments

The work of the author was supported in part by the FWF (P20549-N19 and W-1221-B03). The authors are grateful to all members of the group for providing experimental data, figures, valuable discussions and comments to the manuscript. The fruitful cooperations with Wiktor Kozminski (University of Warsaw), Bernhard Brutscher (ISB Grenoble) and Phil Selenko (FMP Berlin) and colleagues are also gratefully acknowledged.

Author information

Authors and Affiliations

  1. Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria

    Dennis Kurzbach, Georg Kontaxis, Nicolas Coudevylle & Robert Konrat

Authors
  1. Dennis Kurzbach
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Georg Kontaxis
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nicolas Coudevylle
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Robert Konrat
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Robert Konrat .

Editor information

Editors and Affiliations

  1. CERM and Department of Chemistry, "Ugo Schiff" University of Florence, Florence, Italy

    Isabella C. Felli

  2. CERM and Department of Chemistry, "Ugo Schiff" University of Florence, Florence, Italy

    Roberta Pierattelli

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Kurzbach, D., Kontaxis, G., Coudevylle, N., Konrat, R. (2015). NMR Spectroscopic Studies of the Conformational Ensembles of Intrinsically Disordered Proteins. In: Felli, I., Pierattelli, R. (eds) Intrinsically Disordered Proteins Studied by NMR Spectroscopy. Advances in Experimental Medicine and Biology, vol 870. Springer, Cham. https://doi.org/10.1007/978-3-319-20164-1_5

Download citation

Publish with us

Policies and ethics

Search

Navigation