Skip to main content
SpringerLink
Log in

Model-free analysis for large proteins at high magnetic field strengths

  • Article
  • Published:
Journal of Biomolecular NMR Aims and scope Submit manuscript

Abstract

Protein backbone dynamics is often characterized using model-free analysis of three sets of 15N relaxation data: longitudinal relaxation rate (R 1), transverse relaxation rate (R 2), and 15N–{H} NOE values. Since the experimental data is limited, a simplified model-free spectral density function is often used that contains one Lorentzian describing overall rotational correlation but not one describing internal motion. The simplified spectral density function may be also used in estimating the overall rotational correlation time, by making the R 2/R 1 largely insensitive to internal motions, as well as used as one of the choices in the model selection protocol. However, such approximation may not be valid for analysis of relaxation data of large proteins recorded at high magnetic field strengths since the contribution to longitudinal relaxation from the Lorentzian describing the overall rotational diffusion of the molecule is comparably small relative to that describing internal motion. Here, we quantitatively estimate the errors introduced by the use of the simplified spectral density in model-free analysis for large proteins at high magnetic field strength.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Abu-Abed M, Millet O, MacLennan DH, Ikura M (2004) Probing nucleotide-binding effects on backbone dynamics and folding of the nucleotide-binding domain of the sarcoplasmic/endoplasmic-reticulum Ca2+-ATPase. Biochem J 379:235–242

    Article  Google Scholar 

  • Andrec M, Montelione GT, Levy RM (1999) Estimation of dynamic parameters from NMR relaxation data using the Lipari-Szabo model-free approach and Bayesian statistical methods. J Magn Reson 139:408–421

    Article  ADS  Google Scholar 

  • Barchi JJJ, Grasberger B, Gronenborn AM, Clore GM (1994) Investigation of the backbone dynamics of the IgG-binding domain of streptococcal protein G by heteronuclear two-dimensional 1H-15N nuclear magnetic resonance spectroscopy. Protein Sci 3:15–21

    Article  Google Scholar 

  • Bouamr F, Cornilescu CC, Goff SP, Tjandra N, Carter CA (2005) Structural and dynamics studies of the D54A mutant of human T cell leukemia virus-1 capsid protein. J Biol Chem 280:6792–6801

    Article  Google Scholar 

  • Bruschweiler R (2003) New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins. Curr Opin Struct Biol 13:175–183

    Article  Google Scholar 

  • Campbell AP, Spyracopoulos L, Irvin RT, Sykes BD (2000) Backbone dynamics of a bacterially expressed peptide from the receptor binding domain of Pseudomonas aeruginosa pilin strain PAK from heteronuclear 1H-15N NMR spectroscopy. J Biomol NMR 17:239–255

    Article  Google Scholar 

  • Cavanagh J, Fairbrother WJ, Palmer AG, Skelton NJ (1996) Protein NMR spect. Academic Press, San Diego

    Google Scholar 

  • Chandrasekhar I, Clore GM, Szabo A, Gronenborn AM, Brooks BR (1992) A 500 ps molecular dynamics simulation study of interleukin-1 beta in water. Correlation with nuclear magnetic resonance spectroscopy and crystallography. J Mol Biol 226:239–250

    Article  Google Scholar 

  • Chang SL, Tjandra N (2005) Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation. J Magn Reson 174:43–53

    Article  ADS  Google Scholar 

  • Chen J, Brooks CLI, Wright PE (2004) Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation. J Biomol NMR 29:243–257

    Article  Google Scholar 

  • Clore GM, D riscoll PC, Wingfield PT, Gronenborn AM (1990) Analysis of the backbone dynamics of interleukin-1 beta using two-dimensional inverse detected heteronuclear 15N-1H NMR spectroscopy. Biochemistry 29:7387–7401

    Article  Google Scholar 

  • Coles M, Diercks T, Muehlenweg B, Bartsch S, Zoelzer V, Tschesche H, Kessler H (1999) The solution strucuture and dynamics of human neutrophil gelatinase-associated lipocalin. J Mol Biol 289:139–157

    Article  Google Scholar 

  • d’Auvergne EJ, Gooley PR (2003) The use of model selection in the model-free analysis of protein dynamics. J Biomol NMR 25:25–39

    Article  Google Scholar 

  • Dayie KT, W agner G, Lefevre JF (1996) Theory and practice of nuclear spin relaxation in proteins. Annu Rev Phys Chem 47:243–282

    Article  ADS  Google Scholar 

  • Ding Z, Lee GI, Liang X, Gallazzi F, Arunima A, Van Doren SR (2005) PhosphoThr peptide binding globally rigidifies much of the FHA domain from Arabidopsis receptor kinase-associated protein phosphatase. Biochemistry 44:10119–10134

    Article  Google Scholar 

  • Farrow NA, Muhandiram R, Singer AU, Pascal SM, Kay CM, Gish G, Shoelson SE, Pawson T, Forman-Kay JD, Kay LE (1994) Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry 33:5984–6003

    Article  Google Scholar 

  • Fausti S, Weiler S, Cuniberti C, Hwang KJ, No KT, Gruschus JM, Perico A, Nirenberg M, Ferretti JA (2001) Backbone dynamics for the wild type and a double H52R/T56W mutant of the vnd/NK-2 homeodomain from Drosophila melanogaster. Biochemistry 40:12004–12023

    Article  Google Scholar 

  • Fushman D, Cowburn D (2001) Nuclear magnetic resonance relaxation in determination of residue-specific N-15 chemical shift tensors in proteins in solution: protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy. Nuclear Magnet Reson Biol Macromol Pt B:109–126

    Google Scholar 

  • Fushman D, Tjandra N, Cowburn D (1999) An approach to direct determination of protein dynamics from N-15 NMR relaxation at multiple fields, independent of variable N-15 chemical shift anisotropy and chemical exchange contributions. J Am Chem Soc 121:8577–8582

    Article  Google Scholar 

  • Fushman D, Weisemann R, Thuring H, Ruterjans H (1994) Backbone dynamics of ribonuclease-T1 and its complex with BA 2’GMP studied by 2-dimensional heteronuclear NMR-spectroscopy S. J Biomol NMR 4:61–78

    Article  Google Scholar 

  • Garcia FL, Szyperski T, Dyer JH, Choinowski T, Seedorf U, Hauser H, Wuthrich K (2000) NMR structure of the sterol carrier protein-2: implications for the biological role. J Mol Biol 295:595–603

    Article  Google Scholar 

  • Gong Q, Ishima R (2007) 15N-{1H} NOE experiment at high magnetic field strengths. J Biomol NMR 37:147–157

    Article  Google Scholar 

  • Grzesiek S, Bax A (1993) The importance of not saturating H2O in protein NMR – application to sensitivity enhancement and NOE measurements. J Am Chem Soc 115:12593

    Article  Google Scholar 

  • Idiyatullin D, Daragan VA, Mayo KH (2003) (NH)-N-15 backbone dynamics of protein GB1: comparison of order parameters and correlation times derived using various “model-free" approaches. J Phys Chem B 107:2602–2609

    Article  Google Scholar 

  • Igumenova TI, Frederick KK, Wand AJ (2006) Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem Rev 106:1672–1699

    Article  Google Scholar 

  • Ilangovan U, Ding W, Zhong Y, Wilson CL, Groppe JC, Trbovich JT, Zuniga J, Demeler B, Tang Q, Gao G, Mulder KM, Hinck AP (2005) Structure and dynamics of the homodimeric dynein light chain km23. J Mol Biol 352:338–354

    Article  Google Scholar 

  • Ishima R, Nagayama K (1995) Protein backbone dynamics revealed by quasi spectral density function analysis of amide N-15 nuclei. Biochemistry 34:3162–3171

    Article  Google Scholar 

  • Ishima R, Torchia DA (2000) Protein dynamics from NMR. Nat Struct Biol 7:740–743

    Article  Google Scholar 

  • Jarymowycz VA, Stone MJ (2006) Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences. Chem Rev 106:1624–1671

    Article  Google Scholar 

  • Kay LE (2005) NMR studies of protein structure and dynamics. J Magn Reson 173:193–207

    Article  ADS  Google Scholar 

  • Kay LE, Torchia DA, Bax A (1989) Backbone dynamics of proteins as studied by nitrogen-15 inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. Biochemistry 28:8972–8979

    Article  Google Scholar 

  • Korchuganov DS, Gagnidze IE, Tkach EN, Schulga AA, Kirpichnikov MP, Arseniev AS (2004) Determination of protein rotational correlation time from NMR relaxation data at various solvent viscosities. J Biomol NMR 30:431–442

    Article  Google Scholar 

  • Korzhnev DM, Orekhov VY, Arseniev AS (1997) Model-free approach beyond the borders of its applicability. J Biomol NMR 127:184–191

    Google Scholar 

  • Kroenke CD, Loria JP, Lee LK, Rance M, Palmer AG (1998) Longitudinal and transverse H-1-N-15 dipolar N-15 chemical shift anisotropy relaxation interference: unambiguous determination of rotational diffusion tensors and chemical exchange effects in biological macromolecules. J Am Chem Soc 120:7905–7915

    Article  Google Scholar 

  • Lee AL, Wand AJ (1999) Assessing potential bias in the determination of rotational correlations times of proteins by NMR. J Biomol NMR 13:101–112

    Google Scholar 

  • Lee LK, Rance M, Chazin WJ, Palmer AGr (1997) Rotational diffusion anisotropy of proteins from simultaneous analysis of 15N and 13C alpha nuclear spin relaxation. J Biomol NMR 9:287–298

    Article  Google Scholar 

  • Lefevre JF, Dayie KT, Peng JW, Wagner G (1996). Internal mobility in the partially folded DNA binding and dimerization domains of GAL4: NMR analysis of the N-H spectral density functions. Biochemistry 35:2674–2686

    Article  Google Scholar 

  • Li YC, Montelione GT (1994) Overcoming solvent saturation-transfer artifacts in protein Nmr at neutral Ph – application of pulsed-field gradients in measurements of H-1 N-15 overhauser effects. J Magnet Reson Ser B 105:45–51

    Article  Google Scholar 

  • Lipari G, Szabo A (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 104:4546–4559

    Article  Google Scholar 

  • Mandel AM, Akke M, Palmer AG (1995) Backbone dynamics of Escherichia coli ribonuclease Hi – correlations with structure and function in an active enzyme. J Mol Biol 246:144–163

    Article  Google Scholar 

  • Meirovitch E, Shapiro YE, Liang ZC, Freed JH (2003) Mode-coupling SRLS versus mode-decoupled model-free N-H bond dynamics: mode-mixing and renormalization. J Phys Chem B 107:9898–9904

    Article  Google Scholar 

  • Palmer AG 3rd (2001) Nmr probes of molecular dynamics: overview and comparison with other. Annu Rev Biophys Biomol Struct 30:129–155

    Article  Google Scholar 

  • Palmer AG, Rance M, Wright PE (1991) Intramolecular motions of a zinc finger DNA-binding domain from Xfin characterized by proton-detected natural abundance 13C heteronuclear NMR spectroscopy. J Am Chem Soc 113:4371–4380

    Article  Google Scholar 

  • Pawley NH, Wang C, Koide S, Nicholson LK (2001) An improved method for distinguishing between anisotropic tumbling and chemical exchange in analysis of 15N relaxation parameters. J Biomol NMR 20:149–165

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Peng JW, Wagner G (1995) Frequency spectrum of NH bonds in eglin c from spectral density mapping at multiple fields. Biochemistry 34:16733–16752

    Article  Google Scholar 

  • Pfeiffer S, Fushman D, Cowburn D (2001) Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for βARK1 PH domain. J Am Chem Soc 123:3021–3026

    Article  Google Scholar 

  • Philippopoulos M, Mandel AM, Palmer AGr, Lim C (1997) Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics. Proteins 28:481–493

    Article  Google Scholar 

  • Redfield C (2004) Using nuclear magnetic resonance spectroscopy to study molten globule states of proteins. Methods Mol Biol 34:121–132

    Google Scholar 

  • Renner C, Schleicher M, Moroder L, Holak TA (2002) Practical aspects of the 2D N-15-{H-1}-NOE experiment. J Biomol NMR 23:23–33

    Article  Google Scholar 

  • Savard PY, Gagne SM (2006) Backbone dynamics of TEM-1 determined by NMR: evidence for a highly ordered protein. Biochemistry 45:11414–11424

    Article  Google Scholar 

  • Schneider DM, Dellwo MJ, Wand AJ (1992) Fast internal main-chain dynamics of human ubiquitin. Biochemistry 31:3645–3652

    Article  Google Scholar 

  • Schramm HJ, Nakashima H, Schramm W, Wakayama H, Yamamoto N (1991) HIV-1 reproduction is inhibited by peptides derived from the N- and C-termini. Biochem Biophys Res Commun 179:847–851

    Article  Google Scholar 

  • Sheinerman FB, Brooks CLr (1997) A molecular dynamics simulation study of segment B1 of protein G. Proteins 29:193–202

    Article  Google Scholar 

  • Skelton NJ, Palmer AG, Akke M, Kordel J, Rance M, Chazin WJ (1993) Practical aspects of 2-dimensional proton-detected N-15 spin relaxation measurements. J Magnet Reson Ser B 102:253–264

    Article  Google Scholar 

  • Spyracopoulos L (2006) A suite of mathematica notebooks for the analysis of protein main chain (15)N NMR relaxation data. J Biomol NMR 36:215–224

    Article  Google Scholar 

  • Stone M, Chandrasekhar K, Holmgren A, Wright PE, Dyson HJ (1993) Abstract comparison of backbone and tryptophan side-chain dynamics of reduced and oxidized Escherichia coli thioredoxin using 15N NMR relaxation measurements. Biochemistry 32:426–435

    Google Scholar 

  • Tjandra N, Kuboniwa H, Ren H, Bax A (1995) Rotational dynamics of calcium-free calmodulin studied by 15N-NMR relaxation measurements. Eur J Biochem 230:1014–1024

    Article  Google Scholar 

  • Yuan P, Marshall VP, Petzold GL, Poorman RA, Stockman BJ (1999) Dynamics of stromelysin/inhibitor interactions studied by 15N NMR relaxation measurements: comparison of ligand binding to the S1-S3 and S1-S3 subsites. J Biomol NMR 15:55–64

    Article  Google Scholar 

  • Zhuravleva AV, Korzhnev DM, Kupce E, Arseniev AS, Billeter M, Orekhov VYY (2004) Gated electron transfers and electron pathways in azurin: a NMR dynamic study at multiple fields and temperatures. J Mol Biol 342:1599–1611

    Article  Google Scholar 

Download references

Acknowledgements

We thank Dennis Torchia and Nico Tjandra for critical reading of the manuscript. Financial support for this work was provided by University of Pittsburgh to R.I., and the NIH and the Robert A. Welch Foundation to A.H.

Author information

Authors and Affiliations

  1. Institute of Bioinformatics and Structural Biology, Department of Life Science, National Tsing Hua University, HsinChu, 30055, Taiwan

    Shou-Lin Chang

  2. Department of Biochemistry, MC 7760, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229-3900, USA

    Andrew P. Hinck

  3. Department of Structural Biology, School of Medicine, University of Pittsburgh, Rm 1037, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA, 15260, USA

    Rieko Ishima

Authors
  1. Shou-Lin Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Andrew P. Hinck
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rieko Ishima
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rieko Ishima.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chang, SL., Hinck, A.P. & Ishima, R. Model-free analysis for large proteins at high magnetic field strengths. J Biomol NMR 38, 315–324 (2007). https://doi.org/10.1007/s10858-007-9171-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10858-007-9171-9

Keywords

Search

Navigation