Faithful estimation of dynamics parameters from CPMG relaxation dispersion measurements.

This work examines the robustness of fitting of parameters describing conformational exchange (k(ex), p(a/b), and Deltaomega) processes from CPMG relaxation dispersion data. We have analyzed the equations describing conformational exchange processes for the intrinsic inter-dependence of their parameters that leads to the existence of multiple equivalent solutions, which equally satisfy the experimental data. We have used Monte-Carlo simulations and fitting to the synthetic data sets as well as the direct 3-D mapping of the parameter space of k(ex), p(a/b), and Deltaomega to quantitatively assess the degree of the parameter inter-dependence. The demonstrated high correlation between parameters can preclude accurate dynamics parameter estimation from NMR spin-relaxation data obtained at a single static magnetic field. The strong parameter inter-dependence can readily be overcome through acquisition of spin-relaxation data at more than one static magnetic field thereby allowing accurate assessment of conformational exchange properties.

[1]  Christopher D. Kroenke,et al.  The Static Magnetic Field Dependence of Chemical Exchange Linebroadening Defines the NMR Chemical Shift Time Scale , 2000 .

[2]  J. Brender,et al.  Functional dynamics in the active site of the ribonuclease binase , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Frederick W. Dahlquist,et al.  Studying excited states of proteins by NMR spectroscopy , 2001, Nature Structural Biology.

[4]  J. Jen Chemical exchange and nmr T2 relaxation—The multisite case , 1978 .

[5]  W. DeGrado,et al.  Molecular Motions and Protein Folding: Characterization of the Backbone Dynamics and Folding Equilibrium of α2D Using13C NMR Spin Relaxation , 2000 .

[6]  D. Woessner,et al.  Nuclear Transfer Effects in Nuclear Magnetic Resonance Pulse Experiments , 1961 .

[7]  A. Palmer,et al.  Mapping chemical exchange in proteins with MW > 50 kD. , 2003, Journal of the American Chemical Society.

[8]  J. P. Loria,et al.  Evidence for flexibility in the function of ribonuclease A. , 2002, Biochemistry.

[9]  A. Palmer,et al.  Solution NMR spin relaxation methods for characterizing chemical exchange in high-molecular-weight systems. , 2005, Methods in enzymology.

[10]  C. Dobson,et al.  Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR , 2004, Nature.

[11]  A. Palmer,et al.  Disulfide bond isomerization in basic pancreatic trypsin inhibitor: multisite chemical exchange quantified by CPMG relaxation dispersion and chemical shift modeling. , 2003, Journal of the American Chemical Society.

[12]  J. Baum,et al.  Characterization of millisecond time-scale dynamics in the molten globule state of alpha-lactalbumin by NMR. , 1999, Journal of molecular biology.

[13]  D. Torchia,et al.  Using Amide 1H and 15N Transverse Relaxation To Detect Millisecond Time-Scale Motions in Perdeuterated Proteins: Application to HIV-1 Protease , 1998 .

[14]  D. Torchia,et al.  Estimating the time scale of chemical exchange of proteins from measurements of transverse relaxation rates in solution , 1999, Journal of biomolecular NMR.

[15]  Mikael Akke,et al.  NMR methods for characterizing microsecond to millisecond dynamics in recognition and catalysis. , 2002, Current opinion in structural biology.

[16]  L. Kay,et al.  Slow dynamics in folded and unfolded states of an SH3 domain. , 2001, Journal of the American Chemical Society.

[17]  R. Richards,et al.  A general two-site solution for the chemical exchange produced dependence of T2 upon the carr-Purcell pulse separation , 1972 .

[18]  S. Meiboom,et al.  Nuclear Magnetic Resonance Study of the Protolysis of Trimethylammonium Ion in Aqueous Solution—Order of the Reaction with Respect to Solvent , 1963 .

[19]  J. P. Loria,et al.  Conservation of mus-ms enzyme motions in the apo- and substrate-mimicked state. , 2005, Journal of the American Chemical Society.

[20]  D. A. Bosco,et al.  Enzyme Dynamics During Catalysis , 2002, Science.

[21]  H. S. Gutowsky,et al.  Nuclear magnetic resonance methods for determining chemical-exchange rates. , 1966, Journal of the American Chemical Society.

[22]  H. S. Gutowsky,et al.  SPIN-ECHO STUDIES OF CHEMICAL EXCHANGE. II. CLOSED FORMULAS FOR TWO SITES. , 1965, The Journal of chemical physics.

[23]  D. G. Davis,et al.  Direct measurements of the dissociation-rate constant for inhibitor-enzyme complexes via the T1 rho and T2 (CPMG) methods. , 1994, Journal of magnetic resonance. Series B.

[24]  A. Kristina Downing,et al.  Protein NMR techniques , 2004 .

[25]  P E Wright,et al.  Backbone dynamics in dihydrofolate reductase complexes: role of loop flexibility in the catalytic mechanism. , 2001, Biochemistry.