A Theory of Protein Dynamics to Predict NMR Relaxation

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Presentation transcript:

A Theory of Protein Dynamics to Predict NMR Relaxation Esther Caballero-Manrique, Jenelle K. Bray, William A. Deutschman, Frederick W. Dahlquist, Marina G. Guenza Biophysical Journal Volume 93, Issue 12, Pages 4128-4140 (December 2007) DOI: 10.1529/biophysj.107.111849 Copyright © 2007 The Biophysical Society Terms and Conditions

Figure 1 Time correlation function M1(t), for the first Cα-Cα bond, calculated using different forms of the hydrodynamic matrix. Hydrodynamic interaction from Eq. 2.4 produces an unphysical, diverging correlation function (dotted-dashed line), whereas Eq. 2.7 leads to a function (solid line) in reasonable agreement with simulation data (dashed line). Biophysical Journal 2007 93, 4128-4140DOI: (10.1529/biophysj.107.111849) Copyright © 2007 The Biophysical Society Terms and Conditions

Figure 2 Square difference of the bond time correlation function calculated from theory and from simulations as a function of protein sequence at a fixed time interval. From top to bottom panels, data are reported at increasing time intervals (500, 1000, and 1500 ps) for the rotamer CheYa of the signal transduction protein CheY. Biophysical Journal 2007 93, 4128-4140DOI: (10.1529/biophysj.107.111849) Copyright © 2007 The Biophysical Society Terms and Conditions

Figure 3 Dihedral angle distribution from simulations (top) and bond time correlation functions for each bond participating to the dihedral angle (bottom). In the bottom plots theoretical predictions (solid line) are compared with simulations (dashed line). Biophysical Journal 2007 93, 4128-4140DOI: (10.1529/biophysj.107.111849) Copyright © 2007 The Biophysical Society Terms and Conditions

Figure 4 Comparison between theoretical predictions (circles) and experiments (squares) of spin-lattice relaxation time (T1), spin-spin relaxation time (T2), and NOE of E. coli signal regulator protein CheY, for a 50% mixture of CheYa and CheYb rotamers. Splines interpolate theory (black lines) and experiments (white lines). Biophysical Journal 2007 93, 4128-4140DOI: (10.1529/biophysj.107.111849) Copyright © 2007 The Biophysical Society Terms and Conditions

Figure 5 Comparison between theoretical predictions (solid line) and experiments (dashed line) of NMR order parameter (top panel) and x-ray temperature factors (bottom panel) of E. coli signal regulator protein CheY, for a 50% mixture of CheYa and CheYb rotamers. Biophysical Journal 2007 93, 4128-4140DOI: (10.1529/biophysj.107.111849) Copyright © 2007 The Biophysical Society Terms and Conditions