Skip to main content
SpringerLink
Log in
Book cover

Structural Biology pp 289–310Cite as

Protein Dynamics

  • Chapter
  • First Online:

  • 3103 Accesses

Abstract

High-resolution NMR spectroscopy has become a unique and powerful approach with atomic resolution not only for determining structures of biological macromolecules but also for characterizing the overall and internal rotational motions in proteins. The dynamic behavior of proteins at different timescales can be monitored experimentally by different methods because it is difficult, if not impossible, to completely characterize all motional processes by a single approach. Nuclear spin relaxation measurement provides information on fast motions on the timescales of picosecond to nanosecond (laboratory frame nuclear spin relaxation experiments), and slow motions on the timescales of microsecond to millisecond (rotating frame nuclear spin relaxation measurements), whereas magnetization exchange spectroscopy deals with motions on the timescales of millisecond to second. This chapter focuses on the experiments and data analysis for heteronuclear spin relaxation approaches used to characterize the dynamic processes of proteins in solution.

This is a preview of subscription content, 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   39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   54.99
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

Learn about institutional subscriptions

References

  • Abragam A (1961) Principles of nuclear magnetism. Clarendon Press, Oxford

    Google Scholar 

  • Akke M, Palmer G (1996) Monitoring macromolecular motions on microsecond to millisecond time scales by R1ρ−R1 constant relaxation time NMR spectroscopy. J Am Chem Soc 118:911–912

    Article  CAS  Google Scholar 

  • Brüschweiler R, Liao X, Wright PE (1995) Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling. Science 268:886–889

    Article  PubMed  Google Scholar 

  • Bull TE (1992) Relaxation in the rotating frame in liquids. Prog Nucl Magn Reson Spectrosc 24:377–410

    Article  CAS  Google Scholar 

  • Carr HY, Purcell EM (1954) Effects of diffusion on free precession in nuclear magnetic resonance experiments. Phys Rev 94:630–638

    Article  CAS  Google Scholar 

  • Clore GM, Szabo A, Bax A, Kay LE, Driscoll PC, Gronenborn AM (1990a) Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J Am Chem Soc 112:4989–4991

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Dellwo MJ, Wand AJ (1989) Model-independent and model-dependent analysis of the global and internal dynamics of cyclosporin A. J Am Chem Soc 111:4571–4578

    Article  CAS  Google Scholar 

  • Desvaux H, Berthault P (1999) Study of dynamic processes in liquids using off-resonance rf irradiation. Prog Nucl Magn Reson Spectrosc 35:295–340

    Article  CAS  Google Scholar 

  • Farrow NA, Zhang O, Szabo A, Torchoia DA, Kay LE (1995) Spectral density function mapping using 15N relaxation data exclusively. J Biomol NMR 6:153–162

    Article  PubMed  CAS  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 a phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry 33:5984–6003

    Article  PubMed  CAS  Google Scholar 

  • Flynn PF, Bieber Urbauer RJ, Zhang H, Lee AL, Wand AJ (2001) Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2. Biochemistry 40:6559–6569

    Article  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 

  • Hiyama Y, Niu C, Silverton JV, Bavoso A, Torchia DA (1988) Determination of 15N chemical shift tensor via 15N-2H dipolar coupling in Boc-glycylglycyl[15N glycine]benzyl ester. J Am Chem Soc 110:2378–2383

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Ishima R, Nagayama K (1995b) Quasi-spectral-density function analysis for nitrogen-15 nuclei in proteins. J Magn Reson B108:73–76

    Google Scholar 

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

    Article  PubMed  CAS  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 

  • Kroenke CD, Rance M, Palmer AG III (1999) Variability of the 15N chemical shift anisotropy in Escherichia coli Ribonuclease H in solution. J Am Chem Soc 121:10119–10125

    Article  CAS  Google Scholar 

  • Lipari G, Szabo A (1982a) 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  CAS  Google Scholar 

  • Lipari G, Szabo A (1982b) 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

    Article  CAS  Google Scholar 

  • London RE (1980) Intramolecular dynamics of proteins and peptides as monitored by nuclear magnetic relaxation experiments. in Magnetic Resonance in Biology, J.S. Cohen (ed.), Wiley, New York, pp. 1–69

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Mayo KH, Daragan VA, Idiyatullin D, Nesmelova I (2000) Peptide internal motions on nanosecond time scale derived from direct fitting of 13C and 15N NMR spectral density functions. J Magn Reson 146:188–195

    Article  PubMed  CAS  Google Scholar 

  • Meiboom S, Gill D (1958) Modified spin‐echo method for measuring nuclear relaxation times. Rev Sci Instrum 29:688–691

    Article  CAS  Google Scholar 

  • Meiboom S (1961) Nuclear magnetic resonance study of the proton transfer in water. J Chem Phys 34:375–388

    Article  CAS  Google Scholar 

  • Messerlie BA, Wider G, Otting G, Weber C, Wuthrich K (1989) Solvent suppression using a spin lock in 2D and 3D NMR spectroscopy with H2O solutions. J Magn Reson 85:608–613

    Google Scholar 

  • Mulder FAA, de Graaf RA, Kaptein R, Boelens R (1998) An off-resonance rotating frame relaxation experiment for the investigation of macromolecular dynamics using adiabatic rotations. J Magn Reson 131:351–357

    Article  PubMed  CAS  Google Scholar 

  • Nicholson LK, Kay LE, Baldisseri DM, Arango J, Young PE, Torchia DA (1992) Dynamics of methyl groups in proteins as studied by proton-detected carbon-13 NMR spectroscopy. Application to the leucine residues of staphylococcal nuclease. Biochemistry 31:5253–5263

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Peng JW, Wagner G (1994) Protein Mobility from Multiple 15N relaxation Parameters in Tycko R (ed.) Nuclear Magnetic Resonance Probes of Molecular Dynamics. Kluwer, Dordrecht, pp. 373–454

    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  PubMed  CAS  Google Scholar 

  • Peng JW, Thanabal V, Wagner G (1991) 2D heteronuclear NMR measurements of spin–lattice relaxation times in the rotating frame of X nuclei in heteronuclear HX spin systems. J Magn Reson 94:82–100

    CAS  Google Scholar 

  • Phan IQ, Boyd J, Campbell ID (1996) Dynamic studies of a fibronectin type I module pair at three frequencies: anisotropic modelling and direct determination of conformational exchange. J Biomol NMR 8:369–378

    Article  PubMed  CAS  Google Scholar 

  • Szyperski T, Luginbul P, Otting G, Guntert P, Wuthrich K (1993) Protein dynamics studied by rotating frame 15N spin relaxation times. J Biomol NMR 3:151–164

    PubMed  CAS  Google Scholar 

  • Wittebort R, Szabo A (1978) Theory of NMR relaxation in macromolecules: restricted diffusion and jump models for multiple internal rotations in amino acid side chains. J Chem Phys 69:1722–1736

    Article  CAS  Google Scholar 

  • Yamazaki T, Muhandiram R, Kay LE (1994) NMR experiments for the measurement of carbon relaxation properties in highly enriched, uniformly 13C, 15N-labeled proteins: application to 13Cα carbons. J Am Chem Soc 116:8266–8278

    Article  CAS  Google Scholar 

  • Ye C, Fu R, Hu J, Hou L, Ding S (1993) Carbon-13 chemical shift anisotropies of solid amino acids. Magn Reson Chem 31:699–704

    Article  CAS  Google Scholar 

  • Zinn-Justin S, Berthault P, Guenneuges M, Desvaux H (1997) Off-resonance rf fields in heteronuclear NMR: application to the study of slow motions. J Biomol NMR 10:363–372

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Pharmaceutical and Biomedical Sciences College of Pharmacy, University of Georgia, Athens, GA, USA

    Quincy Teng

Authors
  1. Quincy Teng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Quincy Teng .

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this chapter

Cite this chapter

Teng, Q. (2013). Protein Dynamics. In: Structural Biology. Springer, Boston, MA. https://doi.org/10.1007/978-1-4614-3964-6_8

Download citation

Publish with us

Policies and ethics

Search

Navigation