Journal of the American Chemical Society, Vol.129, No.6, 1826-1835, 2007
Oxygen as a paramagnetic probe of clustering and solvent exposure in folded and unfolded states of an SH3 domain
The N-terminal SH3 domain of the Drosophila modular protein Drk undergoes slow exchange between a folded (F-exch) and highly populated unfolded (U-exch) state under nondenaturing buffer conditions, enabling both F-exch and U-exch states to be simultaneously monitored. The addition of dissolved oxygen, equilibrated to a partial pressure of either 30 atm or 60 atm, provides the means to study solvent exposure with atomic resolution via C-13 NMR paramagnetic shifts in H-1,C-13 HSQC (heteronuclear single quantum coherence) spectra. Absolute differences in these paramagnetic shifts between the F-exch and U-exch states allow the discrimination of regions of the protein which undergo change in solvent exposure upon unfolding. Contact with dissolved oxygen for both the F-exch and U-exch states could also be assessed through C-13 paramagnetic shifts which were normalized based on the corresponding paramagnetic shifts seen in the free amino acids. In the F-exch state, the C-13 nuclei belonging to the hydrophobic core of the protein exhibited very weak normalized paramagnetic shifts while those with greater solvent accessible surface area exhibited significantly larger normalized shifts. The U-exch state displayed less varied C-13 paramagnetic shifts although distinct regions of protection from solvent exposure could be identified by a lack of such shifts. These regions, which included Phe9, Thr12, Ala13, Lys21, Thr22, Ile24, Ile27, and Arg38, overlapped with those found to have residual nativelike and non-native structures in previous studies and in some cases provided novel information. Thus, the paramagnetic shifts from dissolved oxygen are highly useful in the study of a transient structure or clustering in disordered systems, where conventional NMR measurements (couplings, chemical shift deviations from random coil values, and NOEs) may give little information.