An introduction to NMR-based approaches for measuring protein dynamics.
Biochim Biophys Acta. 2010 Nov 5;
Authors: Kleckner IR, Foster MP
Proteins are inherently flexible at ambient temperature. At equilibrium, they are characterized by a set of conformations that undergo continuous exchange within a hierarchy of spatial and temporal scales ranging from nanometers to micrometers and femtoseconds to hours. Dynamic properties of proteins are essential for describing the structural bases of their biological functions including catalysis, binding, regulation and cellular structure. Nuclear magnetic resonance (NMR) spectroscopy represents a powerful technique for measuring these essential features of proteins. Here we provide an introduction to NMR-based approaches for studying protein dynamics, highlighting eight distinct methods with recent examples, contextualized within a common experimental and analytical framework. The selected methods are (1) Real-time NMR, (2) Exchange spectroscopy, (3) Lineshape analysis, (4) CPMG relaxation dispersion, (5) Rotating frame relaxation dispersion, (6) Nuclear spin relaxation, (7) Residual dipolar coupling, (8) Paramagnetic relaxation enhancement.
PMID: 21059410 [PubMed - as supplied by publisher]
Measuring (1)H (N) temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy.
Measuring (1)H (N) temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy.
Measuring (1)H (N) temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy.
J Biomol NMR. 2011 Mar 18;
Authors: Bouvignies G, Vallurupalli P, Cordes MH, Hansen DF, Kay LE
A method based on the Carr-Purcell-Meiboom-Gill relaxation dispersion experiment is presented for measuring the temperature coefficients of amide proton chemical shifts of low populated 'invisible' protein states that exchange...
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Measuring 1HN temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy
Measuring 1HN temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy
Abstract A method based on the Carr-Purcell-Meiboom-Gill relaxation dispersion experiment is presented for measuring the temperature coefficients of amide proton chemical shifts of low populated â??invisibleâ?? protein states that exchange with a â??visibleâ?? ground state on the millisecond time-scale. The utility of the approach is demonstrated with an application to an I58D mutant of the Pfl6 Cro protein that undergoes exchange between the native, folded state and a cold...
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[NMR paper] Measuring pK(a) values in protein folding transition state ensembles by NMR spectrosc
Measuring pK(a) values in protein folding transition state ensembles by NMR spectroscopy.
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J Am Chem Soc. 2005 Jun 29;127(25):8904-5
Authors: Tollinger M, Kay LE, Forman-Kay JD
Protein folding kinetic data have been obtained for the marginally stable N-terminal SH3 domain of the Drosophila protein drk as a function of pH in order to investigate the electrostatic properties of Asp8 in the folding transition state ensemble. The slow exchange...
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11-25-2010 08:21 PM
[NMR paper] Leveraging structural approaches: applications of NMR-based screening and X-ray cryst
Leveraging structural approaches: applications of NMR-based screening and X-ray crystallography for inhibitor design.
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J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):97-100
Authors: Moore J, Abdul-Manan N, Fejzo J, Jacobs M, Lepre C, Peng J, Xie X
In the last several years, NMR strategies in drug discovery have evolved from a primarily structural focus to a set of technologies that are non-structural in nature but...
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11-24-2010 09:16 PM
[NMR paper] Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study
Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study of delta131delta.
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J Am Chem Soc. 2003 Feb 19;125(7):1748-58
Authors: Choy WY, Shortle D, Kay LE
NMR relaxation data on disordered proteins can provide insight into both structural and dynamic properties of these molecules. Because of chemical shift degeneracy in correlation spectra, detailed site-specific analyses of side chain dynamics...
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11-24-2010 09:01 PM
[NMR paper] Protein dynamics measurements by TROSY-based NMR experiments.
Protein dynamics measurements by TROSY-based NMR experiments.
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J Magn Reson. 2000 Apr;143(2):423-6
Authors: Zhu G, Xia Y, Nicholson LK, Sze KH
The described TROSY-based experiments for investigating backbone dynamics of proteins make it possible to elucidate internal motions in large proteins via measurements of T(1), T(2), and NOE of backbone (15)N nuclei. In our proposed sequences, the INEPT sequence is eliminated and the PEP sequence is replaced by the ST2-PT...
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11-18-2010 09:15 PM
[NMR paper] Structure-based analysis of protein dynamics: comparison of theoretical results for h
Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data.
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Proteins. 1999 Dec 1;37(4):654-67
Authors: Haliloglu T, Bahar I
An analytical approach based on Gaussian network model (GNM) is proposed for predicting the rotational dynamics of proteins. The method, previously shown to successfully...
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[NMR paper] Measuring protein self-association using pulsed-field-gradient NMR spectroscopy: appl
Measuring protein self-association using pulsed-field-gradient NMR spectroscopy: application to myosin light chain 2.
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J Biomol NMR. 1995 Nov;6(3):321-8
Authors: Dingley AJ, Mackay JP, Chapman BE, Morris MB, Kuchel PW, Hambly BD, King GF
At the millimolar concentrations required for structural studies, NMR spectra of the calcium-binding protein myosin light chain 2 (MLC2) showed resonance line widths indicative...
An introduction to NMR-based approaches for measuring protein dynamics.
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