Dynamic 15N{1H} NOE measurements: a tool for studying protein dynamics

Abstract

Intramolecular motions in proteins are one of the important factors that determine their biological activity and interactions with molecules of biological importance. Magnetic relaxation of 15N amide nuclei allows one to monitor motions of protein backbone over a wide range of time scales. 15N{1H} nuclear Overhauser effect is essential for the identification of fast backbone motions in proteins. Therefore, exact measurements of NOE values and their accuracies are critical for determining the picosecond time scale of protein backbone. Measurement of dynamic NOE allows for the determination of NOE values and their probable errors defined by any sound criterion of nonlinear regression methods. The dynamic NOE measurements can be readily applied for non-deuterated or deuterated proteins in both HSQC and TROSY-type experiments. Comparison of the dynamic NOE method with commonly implied steady-state NOE is presented in measurements performed at three magnetic field strengths. It is also shown that improperly set NOE measurement cannot be restored with correction factors reported in the literature.

Increased slow dynamics defines ligandability of BTB domains

“…Residues with the complete set of 15 N-R 1 , 15 N-R 2 , and { 1 H}- 15 N NOE parameters from two fields were subjected to model-free analysis (MFA). The dynamics interpretation based on the collected 15 N spin relaxation data was performed according to our previous approaches 54,64,65 . In short: a fully anisotropic model of motion was applied for all proteins, with the assumption of C2 symmetry for each homo-dimer resulting in four global parameters, D 1 , D 2 , D 3 and γ Euler angle (while α = β = 0 o ).…”

Binding Specificity of ASHH2 CW Domain Toward H3K4me1 Ligand Is Coupled to Its Structural Stability Through Its α1-Helix

“…Overall, the average hetNOE values for the domain bound to the peptides were around 0.8, indicating moderate local protein motions on the picosecond timescale ( Kharchenko et al, 2020 ), except in the η1-loop, which remained quite flexible with hetNOE values as low as 0.5–0.7 ( Figure 3 ). Generally, the binding of the H3K4me1 peptide results in movement restriction of the unstructured C-terminal I921-Q923 region.…”

“…Early characterization of ASHH2 CW domain binding behavior was performed by Hoppmann et al (2011) and later expanded with the structures of the bound state by Liu and Huang (2018) and Dobrovolska et al (2020) . The latter study and ligand titration experiments indicated that the CW domain sampled a range of conformations across the ns–ms timescale at equilibrium ( Kharchenko et al, 2020 ). Relaxation–dispersion experiments were then used to verify that some residues exhibited exchange on the timescales (i.e., up to ms) associated with conformational selection, a binding mode where ligands bind the correct conformation from a continuum of existing conformations ( Farber and Mittermaier, 2015 ; Dobrovolska et al, 2020 ).…”

Structure and DNA binding analysis of AT‐rich interaction domain present in human BAF‐B specific subunit BAF250b

“…We recorded a steady‐state backbone { 1 H}‐ 15 N heteronuclear NOE (het‐NOE) experiment on BAF250b ARID. The backbone { 1 H}‐ 15 N heteronuclear NOE experiment provides information on the motion of individual N‐H bond vectors 42 . Those that undergo motion faster than the overall tumbling of the molecules (in ps to ns timescale) show a decreased het‐NOE intensity relative to the average observed for most of the residues.…”

“…The backbone { 1 H}- 15 N heteronuclear NOE experiment provides information on the motion of individual N-H bond vectors. 42 Those that undergo motion faster than the overall tumbling of the molecules (in ps to ns timescale) show a decreased het-NOE intensity relative to the average observed for most of the residues. For instance, decreased het-NOE values are observed for the residues at the N-and C-terminal ends and flexible loop regions of the protein compared to the ordered and rigid regions that show positive heteronuclear NOE values of ~0.8.…”