The rubredoxin from Clostridium pasteurianum (CpRd) provides an excellent system for investigating how the protein sequence modulates the reduction potential of the active site in an iron-sulfur protein. 15 N NMR spectroscopy has allowed us to determine with unprecedented accuracy the strengths of all six key hydrogen bonds between protein backbone amides and the sulfur atoms of the four cysteine residues that ligate the iron in the oxidized (Fe III ) and reduced (Fe II ) forms of wild-type CpRd and nine mutants (V44G, V44A, V44I, V44L, V8G, V8A, V8I, V8L, and V8G͞V44G). The length (or strength) of each hydrogen bond was inferred from the magnitude of electron spin delocalized across the hydrogen bond from the iron atom onto the nitrogen. The aggregate lengths of these six hydrogen bonds are shorter in both oxidation states in variants with higher reduction potential than in those with lower reduction potential. Differences in aggregate hydrogen bonding upon reduction correlate linearly with the published reduction potentials for the 10 CpRd variants, which span 126 mV. Sequence effects on the reduction potential can be explained fully by their influence on hydrogen-bond strengths.iron-sulfur protein ͉ reduction potential tuning ͉ 15 N NMR ͉ paramagnetic NMR

The two heme-copper terminal oxidases of Thermus thermophilus have been shown to catalyze the two-electron reduction of nitric oxide (NO) to nitrous oxide (N2O) [Giuffre, A.; Stubauer, G.; Sarti, P.; Brunori, M.; Zumft, W. G.; Buse, G.; Soulimane, T. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 14718-14723]. While it is well-established that NO binds to the reduced heme a3 to form a low-spin heme {FeNO}7 species, the role CuB plays in the binding of the second NO remains unclear. Here we present low-temperature FTIR photolysis experiments carried out on the NO complex formed by addition of NO to fully reduced cytochrome ba3. Low-temperature UV-vis, EPR, and RR spectroscopies confirm the binding of NO to the heme a3 and the efficiency of the photolysis at 30 K. The nu(NO) modes from the light-induced FTIR difference spectra are isolated from other perturbed vibrations using 15NO and 15N18O. The nu(N-O)a3 is observed at 1622 cm-1, and upon photolysis, it is replaced by a new nu(N-O) at 1589 cm-1 assigned to a CuB-nitrosyl complex. This N-O stretching frequency is more than 100 cm-1 lower than those reported for Cu-NO models with three N-ligands and for CuB+-NO in bovine aa3. Because the UV-vis and RR data do not support a bridging configuration between CuB and heme a3 for the photolyzed NO, we assign the exceptionally low nu(NO) to an O-bound (eta1-O) or a side-on (eta2-NO) CuB-nitrosyl complex. From this study, we propose that, after binding of a first NO molecule to the heme a3 of fully reduced Tt ba3, the formation of an N-bound {CuNO}11 is prevented, and the addition of a second NO produces an O-bond CuB-hyponitrite species bridging CuB and Fea3. In contrast, bovine cytochrome c oxidase is believed to form an N-bound CuB-NO species; the [{FeNO}7{CuNO}11] complex is suggested here to be an inhibitory complex.

A unique feature of Rieske proteins is the pH dependence of their reduction potentials. It has been proposed that protonation of the Nepsilon2 atoms of the two histidine rings ligated to the iron-sulfur cluster is coupled with cluster reduction (electron transfer). We have incorporated [15Ndelta1, 15Nepsilon2]-histidine into the Rieske protein from Thermus thermophilis and have used 15N NMR spectroscopy to determine the pKa values of the histidine residues in the oxidized state of the protein. As expected from studies of a Rieske-type ferredoxin, the signals from the 15Ndelta1 atoms directly bound to iron were too broad to be detected, but broad signals could be detected from the 15Nepsilon2 atom of each of the ligated histidine rings. We measured the chemical shifts of these signals as a function of pH between pH 6 and pH 12 and fitted them to theoretical titration curves. The results yielded well-separated pKa values for the two histidines (7.46 and 9.24), with Hill coefficients close to unity. The pKa values are in excellent agreement with values predicted from the pH dependence of the reduction potentials (7.85 and 9.65).

15N NMR hyperfine-shift data were collected for wild-type and site-specific mutant (V44I, V44A, and V44G) Clostridium pasteurianum rubredoxins in the oxidized state. Whereas most of the (15)N NMR signals did not exhibit large systematic changes upon mutation of residue 44, the signal from the backbone nitrogen of residue 44 itself (arrows) shifted by approximately 400 ppm. These shifts were used to determine the lengths of the hydrogen bond between the backbone amide of residue 44 and the side-chain sulfur of cysteine-44, which is covalently ligated to the iron of the metal center. The results, which demonstrated that this hydrogen bond is shorter in mutants with higher reduction potential, point to the importance of hydrogen bonds in modulating the reduction potential of iron-sulfur proteins.

Stable isotope-labeling methods, coupled with novel techniques for detecting fast-relaxing NMR signals, now permit detailed investigations of paramagnetic centers of metalloproteins. We have utilized these advances to carry out comprehensive assignments of the hyperfine-shifted 13C and 15N signals of the rubredoxin from Clostridium pasteurianum (CpRd) in both its oxidized and reduced states. We used residue-specific labeling (by chemical synthesis) and residue-type-selective labeling (by biosynthesis) to assign signals detected by one-dimensional 15N NMR spectroscopy, to nitrogen atoms near the iron center. We refined and extended these 15N assignments to the adjacent carbonyl carbons by means of one-dimensional 13C[15N] decoupling difference experiments. We collected paramagnetic-optimized SuperWEFT 13C[13C] constant time COSY (SW-CT-COSY) data to complete the assignment of 13C signals of reduced CpRd. By following these 13C signals as the protein was gradually oxidized, we transferred these assignments to carbons in the oxidized state. We have compared these assignments with hyperfine chemical shifts calculated from available X-ray structures of CpRd in its oxidized and reduced forms. The results allow the evaluation of the X-ray structural models as representative of the solution structure of the protein, and they provide a framework for future investigation of the active site of this protein. The methods developed here should be applicable to other proteins that contain a paramagnetic center with high spin and slow electron exchange.