Gel-Based NMR Method for Observing Submicrosecond Protein Dynamics at Atomic Resolution

NMR spectroscopy is uniquely suitable of observing functionally important protein motions at atomic resolution under near-physiological conditions in solution. Longitudinal and transverse spin relaxation experiments report about fast subnanosecond and low nanosecond motions, but they are insensitive to slower motions. The recently introduced nanoparticle assisted spin relaxation (NASR) method increases the observation window into the submicrosecond range by measuring the increase in transverse relaxation by the presence of silica nanoparticles. It is demonstrated here how a similar effect can be observed via the transverse relaxation enhancement ΔR₂ due to the presence of polyacrylamide and agarose gel. While compressed or stretched polyacrylamide gels are commonly used in protein NMR for residual dipolar coupling measurements, the gel-induced transverse relaxation enhancement, for both compressed and uncompressed gel, directly provides complementary dynamics information with the change in R₂ proportional to the site-specific model-free S² order parameter encompassing dynamics on the submicrosecond range. This generalized NASR approach is demonstrated for K-Ras and other proteins exhibiting internal dynamics with variable amplitudes on a wide range of time scales.