Accuracy of optimized chemical-exchange parameters derived by fitting CPMG R2 dispersion profiles when R2(0a) not = R2(0b).

Journal of Biomolecular NMR
Rieko Ishima, D A Torchia

Abstract

The transverse relaxation rate, R2, measured as a function of the effective field (R2 dispersion) using a Carr-Purcell-Meiboom-Gill (CPMG) pulse train, is well suited to detect conformational exchange in proteins. The dispersion data are commonly fitted by a two-site (sites a and b) exchange model with four parameters: the relative population, pa, the difference in chemical shifts of the two sites, deltaomega, the correlation time for exchange, tau(ex), and the intrinsic relaxation rate (i.e., transverse relaxation rate in the absence of chemical exchange), R2(0). Although the intrinsic relaxation rates of the two sites, R2(0a) and R2(0b), can differ, they are normally assumed to be the same (i.e., R2(0a) = R2(0b) = R2(0)) when fitting dispersion data. The purpose of this investigation is to determine the magnitudes of the errors in the optimized exchange parameters that are introduced by the assumption that R2(0a) = R2(0b). In order to accomplish this goal, we first generated synthetic constant-time CPMG R2 dispersion data assuming two-site exchange with R2(0a) not equal R2(0b), and then fitted the synthetic data assuming two-site exchange with R2(0) = R2(0a) = R2(0b). Although all the synthetic data generated assuming R2(0a) ...Continue Reading

References

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Citations

Dec 14, 2011·Journal of Biomolecular NMR·Ian R Kleckner, Mark P Foster
Nov 3, 2012·The Journal of Physical Chemistry. B·Janarthanan KrishnamoorthyAyyalusamy Ramamoorthy
Nov 10, 2010·Biochimica Et Biophysica Acta·Ian R Kleckner, Mark P Foster
Mar 25, 2014·Journal of Magnetic Resonance·Arthur G Palmer
Nov 23, 2010·Journal of Molecular Biology·Patrick J Farber, Anthony Mittermaier
May 24, 2014·Journal of Magnetic Resonance·Andrew J Baldwin
Feb 14, 2015·The Journal of Physical Chemistry. B·Gennady Khirich, J Patrick Loria
Apr 10, 2010·Journal of the American Chemical Society·Patrick FarberAnthony Mittermaier
Aug 19, 2009·Journal of the American Chemical Society·D Flemming HansenLewis E Kay
Jun 1, 2015·Biophysics Reviews·Patrick J Farber, Anthony Mittermaier
Dec 26, 2017·Journal of the American Chemical Society·Elise DelaforgeMalene Ringkjøbing Jensen

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