No abstract

NMR spin relaxation experiments are used to characterize the dynamics of the backbone of ubiquitin. Chemical exchange processes affecting residues Ile 23, Asn 25, Thr 55, and Val 70 are characterized using on-and off-resonance rotating-frame 15 N R 1 relaxation experiments to have a kinetic exchange rate constant of 25,000 sec −1 at 280 K. The exchange process affecting residues 23, 25, and 55 appears to result from disruption of N-cap hydrogen bonds of the ␣-helix and possibly from repacking of the side chain of Ile 23. Chemical exchange processes affecting other residues on the surface of ubiquitin are identified using 1 H-15 N multiple quantum relaxation experiments. These residues are located near or at the regions known to interact with various enzymes of the ubiquitin-dependent protein degradation pathway.

NMR spin relaxation in the rotating frame (R(1 rho)) is one of few methods available to characterize chemical exchange kinetic processes occurring on micros-ms time scales. R(1 rho) measurements for heteronuclei in biological macromolecules generally require decoupling of (1)H scalar coupling interactions and suppression of cross-relaxation processes. Korzhnev and co-workers demonstrated that applying conventional (1)H decoupling schemes while the heteronuclei are spin-locked by a radio frequency (rf) field results in imperfect decoupling [Korzhnev, Skrynnikov, Millet, Torchia, Kay. J. Am. Chem. Soc. 2002, 124, 10743-10753]. Experimental NMR pulse sequences were presented that provide accurate measurements of R(1 rho) rate constants for radio frequency field strengths > 1000 Hz. This paper presents new two-dimensional NMR experiments that allow the use of weak rf fields, between 150 and 1000 Hz, in R(1 rho) experiments. Fourier decomposition and average Hamiltonian theory are employed to analyze the spin-lock sequence and provide a guide for the development of improved experiments. The new pulse sequences are validated using ubiquitin and basic pancreatic trypsin inhibitor (BPTI). The use of weak spin-lock fields in R(1 rho) experiments allows the study of the chemical exchange process on a wider range of time scales, bridging the gap that currently exists between Carr-Purcell-Meiboom-Gill and conventional R(1 rho) experiments. The new experiments also extend the capability of the R(1 rho) technique to study exchange processes outside the fast exchange limit.