O₂ Penetration and Proton Burial Depth in Proteins:  Applicability to Fold Family Recognition

Abstract

Paramagnetically induced relaxation effects of O2 and the nitroxide 4-hydroxy TEMPO were measured for the amide protons of perdeuterated rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus and the mesophilic bacterium Clostridium pasteurianum. For both O2 and the impermeant nitroxide, the induced relaxation at the static solvent inaccessible amide sites is dominated by long-range interactions with the paramagnetic species in the bulk aqueous phase. The upper bound of O2 solubility in the internal matrix of the rubredoxins is one-tenth that of the bulk aqueous phase. Furthermore, the difference between the oxygen solubilities inside the two rubredoxins is at most 1% that of bulk water O2 solubility, suggesting that there are only modest differences in this measure of fluidity for the mesophile vs hyperthermophile protein interiors. Calculations based on the assumption of a paramagnet uniformly distributed on the protein exterior yield accurate predictions at nearly all amide sites for the minimum relaxation value observed from either the O2 or nitroxide data. Model calculations indicate that the readily obtained paramagnetically induced relaxation effects should prove effective in recognition of structural homology for proteins that are too widely diverged for sequence-based recognition.

Molecular oxygen as a paramagnetic NMR probe of protein solvent exposure and topology

“…Thus, R 1p is acutely sensitive to local topology (i.e., f and b above). Note that since the paramagnetic rates depend on the square of the gyromagnetic ratio, relatively large (relaxation) effects may be seen on 1 H and 19 F nuclei (8,11,12,(18)(19)(20) …”

Chromium(III) complexes as intermolecular probes

“…The presence or absence of a first coordination sphere water molecule makes no difference when the metal ion complex is used as a paramagnetic relaxation agent for molecules other than the solvent water. However, it is important to recognize the potential contribution of first coordination sphere water to the water proton relaxivity in cases where it may be convenient to normalize solute relaxation rate constants to the water proton relaxation rate constant [35,13].…”

Spatial distribution of dielectric shielding in the interior of Pyrococcus furiosus rubredoxin as sampled in the subnanosecond timeframe by hydrogen exchange

“…Ionic radii of 0.7 Å and 0.6 Å were used for Zn(II) and Ga(III), respectively. The 1.1 Å resolution structure of Pf rubredoxin does not contain any internal cavities large enough to contain a water molecule [25] for potential inclusion in the PoissonBoltzmann calculations. The grid size was 167 with a 50% filling factor.…”