Assessment of the Effects of Increased Relaxation Dispersion Data on the Extraction of 3-site Exchange Parameters Characterizing the Unfolding of an SH3 Domain |
| |
Authors: | Philipp Neudecker Dmitry M Korzhnev Lewis E Kay |
| |
Institution: | (1) Departments of Medical Genetics, Biochemistry, and Chemistry, University of Toronto, 1 King’s College Circle, Toronto, M5S 1A8, ON, Canada |
| |
Abstract: | Recently a suite of six CPMG relaxation dispersion experiments has been described for quantifying millisecond time-scale exchange
processes in proteins. The methodology has been applied to study the folding reaction of a G48M Fyn SH3 domain mutant that
exchanges between the native state, and low populated unfolded and intermediate states. A complex non-linear global optimization
protocol allows extraction of the kinetics and thermodynamics of the 3-site exchange process from the experimental data, as
well as reconstruction of the amide group chemical shifts of the excited states. We show here, through a series of Monte-Carlo
simulations on various synthetic data sets, that the 3-site exchange parameters extracted for this system on the basis of
15N single-quantum (SQ) dispersion profiles exclusively, recorded at a single temperature, are significantly in error. While
a temperature dependent 15N study improves the robustness of extracted parameters, as does a combined analysis of 15N and 1H SQ data sets measured at a single temperature, the best agreement is observed in cases where the full complement of six
dispersion profiles per residue is analyzed. |
| |
Keywords: | chemical exchange CPMG NMR relaxation dispersion Monte-Carlo simulation protein folding SH3 domain |
本文献已被 PubMed SpringerLink 等数据库收录! |
|