A Structural Mode-Coupling Approach to ¹⁵N NMR Relaxation in Proteins

Abstract

The two-body Slowly Relaxing Local Structure (SRLS) model was applied to (15)N NMR spin relaxation in proteins and compared with the commonly used original and extended model-free (MF) approaches. In MF, the dynamic modes are assumed to be decoupled, local ordering at the N-H sites is represented by generalized order parameters, and internal motions are described by effective correlation times. SRLS accounts for dynamical coupling between the global diffusion of the protein and the internal motion of the N-H bond vector. The local ordering associated with the coupling potential and the internal N-H diffusion are tensors with orientations that may be tilted relative to the global diffusion and magnetic frames. SRLS generates spectral density functions that differ from the MF formulas. The MF spectral densities can be regarded as limiting cases of the SRLS spectral density. SRLS-based model-fitting and model-selection schemes similar to the currently used MF-based ones were devised, and a correspondence between analogous SRLS and model-free parameters was established. It was found that experimental NMR data are sensitive to the presence of mixed modes. Our results showed that MF can significantly overestimate order parameters and underestimate local motion correlation times in proteins. The extent of these digressions in the derived microdynamic parameters is estimated in the various parameter ranges, and correlated with the time scale separation between local and global motions. The SRLS-based analysis was tested extensively on (15)N relaxation data from several isotropically tumbling proteins. The results of SRLS-based fitting are illustrated with RNase H from E. coli, a protein extensively studied previously with MF.

An Improved Picture of Methyl Dynamics in Proteins from Slowly Relaxing Local Structure Analysis of 2H Spin Relaxation

“…[16][17][18][19][20][21][22][23] Two rotators, representing the global motion of the protein, R C , and the local motion of the probe (C-D bond in this case), R L , are treated. The motions of the protein and the probe are coupled by a local potential, U(Ω C'M ), where C' denotes the local director fixed in the protein, and M the local ordering/local diffusion frame fixed in the probe.…”

“…[16][17][18][19][20][21][22][23] This has been accomplished by applying to NMR spin relaxation in proteins 16 the Slowly Relaxing Local Structure (SRLS) approach of Freed and co-workers. [24][25][26] SRLS can be considered the generalization of MF, yielding the latter in asymptotic limits.…”

“…It features explicitly local motional modes parallel and perpendicular to the methyl rotation axis. [16][17][18][19][20][21][22][23]25,26 and accounts rigorously for the tilt between a rhombic local ordering frame, M, and the magnetic frame, Q. The Euler angles Ω C'M , which relate the M frame to a local director frame, C' (e.g., the equilibrium C-CH 3 orientation), are governed by the coupling/ ordering potential.…”

“…For a M frame tilted relative to the Q frame the spectral density, J QQ (ω) (QQ denotes quadrupolar auto-correlated relaxation), comprises three generic spectral density functions, j K (ω), with K = 0, 1, 2 (refs. 16,25,26 ), by analogy with J(ω) for axial global diffusion of a rigid protein comprising three Lorentzian functions with K = 0, 1, 2. Yet, the MF spectral density consists of a single function which represents the K = 0 contribution.…”

PhosphoThr Peptide Binding Globally Rigidifies Much of the FHA Domain from Arabidopsis Receptor Kinase-Associated Protein Phosphatase,

“…These suggest that phosphoThr binding results in enhanced overall rigidity on psec to nsec scale. Model-free τ e values (Figure 4c 74,75). The relaxation data and model-free results for KI-FHA, free and bound to CLV1 pT868, were deposited under BMRB accession codes 5841 and 6474, respectively, at www.bmrb.wisc.edu.…”