Literature DB >> 10423379

Estimation of dynamic parameters from NMR relaxation data using the Lipari-Szabo model-free approach and Bayesian statistical methods.

M Andrec1, G T Montelione, R M Levy.   

Abstract

In order to analyze NMR relaxation data in terms of parameters which describe internal motion, one must first obtain a description of the overall tumbling of the macromolecule in solution. Methods currently used to estimate these global parameters may not always provide reliable estimates of their values and uncertainties. In this paper, we present a general data analysis formalism based on products of Bayesian marginal probability densities which can be used to efficiently combine the information content from multiple experiments, such as R(1), R(2), and NOE data collected at multiple magnetic field strengths, or data from cross-correlation or rotating frame relaxation dispersion experiments. Our approach allows the estimation of global tumbling and internal dynamical parameters and their uncertainties without some of the assumptions which are made in the commonly-used methods for model-selection and global parameter estimation. Compared to an equivalent classical statistical approach, the Bayesian method not only is more computationally efficient, but also provides greater insight into the information content of the data. We demonstrate that this approach can be used to estimate both the isotropic rotational correlation time in the context of the original and "extended" Lipari-Szabo formalisms [Lipari & Szabo, J. Am. Chem. Soc. 1982, 104, 4546; Clore et al., J. Am. Chem. Soc. 1990, 112, 4989], as well as the rotational diffusion coefficients for axially symmetric anisotropic tumbling. Copyright 1999 Academic Press.

Mesh:

Year:  1999        PMID: 10423379     DOI: 10.1006/jmre.1999.1839

Source DB:  PubMed          Journal:  J Magn Reson        ISSN: 1090-7807            Impact factor:   2.229


  18 in total

1.  Lipari-Szabo mapping: A graphical approach to Lipari-Szabo analysis of NMR relaxation data using reduced spectral density mapping.

Authors:  M Andrec; G T Montelione; R M Levy
Journal:  J Biomol NMR       Date:  2000-10       Impact factor: 2.835

2.  Comparison of (13)C(alpha)H and (15)NH backbone dynamics in protein GB1.

Authors:  Djaudat Idiyatullin; Irina Nesmelova; Vladimir A Daragan; Kevin H Mayo
Journal:  Protein Sci       Date:  2003-05       Impact factor: 6.725

3.  The use of model selection in the model-free analysis of protein dynamics.

Authors:  Edward J d'Auvergne; Paul R Gooley
Journal:  J Biomol NMR       Date:  2003-01       Impact factor: 2.835

4.  Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation.

Authors:  Jianhan Chen; Charles L Brooks; Peter E Wright
Journal:  J Biomol NMR       Date:  2004-07       Impact factor: 2.835

5.  Model-free model elimination: a new step in the model-free dynamic analysis of NMR relaxation data.

Authors:  Edward J d'Auvergne; Paul R Gooley
Journal:  J Biomol NMR       Date:  2006-06-22       Impact factor: 2.835

6.  Quantifying Lipari-Szabo modelfree parameters from 13CO NMR relaxation experiments.

Authors:  Tianzhi Wang; Daniel S Weaver; Sheng Cai; Erik R P Zuiderweg
Journal:  J Biomol NMR       Date:  2006-09-22       Impact factor: 2.835

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

Authors:  Shou-Lin Chang; Andrew P Hinck; Rieko Ishima
Journal:  J Biomol NMR       Date:  2007-06-26       Impact factor: 2.835

8.  Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. II: nuclear magnetic resonance experiments.

Authors:  Vitaly V Vostrikov; Hong Gu; Helgi I Ingólfsson; James F Hinton; Olaf S Andersen; Benoît Roux; Roger E Koeppe
Journal:  J Phys Chem B       Date:  2011-05-16       Impact factor: 2.991

9.  Multilanthanide Systems for Medical Imaging Applications.

Authors:  Jeremiah D Moore; Matthew J Allen
Journal:  Recent Pat Nanomed       Date:  2011-12-01

10.  Dynamics of Ca2+-saturated calmodulin D129N mutant studied by multiple molecular dynamics simulations.

Authors:  Vladimir A Likić; Emanuel E Strehler; Paul R Gooley
Journal:  Protein Sci       Date:  2003-10       Impact factor: 6.725

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