Structural features of the metal binding site and dynamics of gallium putidaredoxin, a diamagnetic derivative of a Cys4Fe2S2ferredoxin

The first reconstitution of an Fe₂S₂ferredoxin with a diamagnetic prosthetic group was recently described[Kazanis et al. (1995) J. Am. Chem. Soc., 117, 6625–6626]. Thereplacement of the iron–sulfur cluster of the bacterial ferredoxinputidaredoxin (Pdx) by gallium (Ga³⁺) renders the proteindiamagnetic and permits the use of high-resolution NMR methods to identifyresonances near the metal binding site. We now describe structural featuresof the metal binding site that are not observable by standard NMR methods innative Pdx due to paramagnetic line broadening. These results provide thefirst example of high-resolution NMR-derived structural data concerning themetal binding domain of an Fe₂S₂ ferredoxin, andthe first structural information of any sort for the metal binding site of aferredoxin from this class, which includes adrenodoxin, placental ferredoxinand terpredoxin. Assignments were obtained by applying multidimensional NMRmethods to a series of selectively and nonselectively ¹⁵N- and¹³C/¹⁵N-labeled GaPdx samples. For mostexperiments, a mutant of Pdx was used in which a nonligatingCys⁸⁵ is replaced by serine. All of the major structuralfeatures that were identified in native Pdx are conserved in GaPdx. Theoverall protein dynamics is considerably faster in GaPdx than in the nativeprotein, as reflected by amide proton exchange rates. The C-terminalresidue, Trp¹⁰⁶, also exhibits considerable mobility, asindicated by ¹⁵N{¹H} NOE and ¹⁵NT₁ values of the C-terminal residue of the protein.     

Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin

Combined QM/MM calculations of the active-site of cytochrome P450cam have been performed before and after the binding of P450cam to putidaredoxin. The calculations were carried out for both a 5-coordinated and a 6-coordinated active-site of cytochrome P450cam, with either a water molecule or a carbon monoxide molecule as a 6th distal ligand. An experimentally observed increase in the Fe-S stretching frequency that occurs after cytochrome P450cam binds to putidaredoxin, has been reproduced in our study. Experimentally observed changes in the Fe-C and C-O vibration frequencies that occur after binding of both proteins, have also been reproduced in our study. The computed increase of the Fe-S and Fe-C stretching frequencies is correlated with a corresponding decrease of the Fe-S and Fe-C interatomic distances. According to our calculations, for the active-site with carbon monoxide in the triplet electronic state, the binding process increases the spin densities on the iron and sulfur atoms, which changes the Fe-C and C-O stretching frequencies in opposite directions, in agreement with experimental data.     

An Electrochemical Study of the Factors Responsible for Modulating the Reduction Potential of Putidaredoxin

 The gene coding for putidaredoxin has been synthesized using a combination of chemical and enzymatic methods and subsequently expressed in Escherichia coli. The recombinant protein characterized by electronic spectroscopy, mass spectrometry, and electrochemistry was found to be identical to putidaredoxin obtained from Pseudomonas putida. Polylysine was found to promote the fast and reversible electrochemistry of putidaredoxin at negatively charged electrodes such as indium-doped tin oxide or gold surfaces modified with mercaptoalkanoate groups. The value of the heterogeneous electron transfer rate constant obtained from solutions containing a mixture of putidaredoxin and polylysine (k _s =1.3×10^–3 cm/s) is one order of magnitude larger than the values reported previously at gold electrodes modified with mercaptoethylamine or at antimony-doped tin oxide semiconductor electrodes. It was observed that when the reduction potential of putidaredoxin is measured by cyclic voltammetry, the resultant value is consistently more positive (64 mV) than the reduction potential measured with potentiometric titrations. A comparison between the electrochemical responses of putidaredoxin and spinach ferredoxin, combined with the examination of their corresponding three-dimensional structures, indicates that the positive shift in the reduction potential of putidaredoxin originates from the formation of a transient complex between putidaredoxin and polylysine at the electrode surface. The formation of this transient complex modulates the reduction potential of putidaredoxin by lowering the value of the dielectric constant around its iron-sulfur cluster microenvironment, specifically by neutralizing negative charges surrounding the active site and by excluding water from the solvent exposed iron sulfur cluster. The observed positive shift in E°′, which is induced by complexation with polylysine at the electrode-surface, suggests that similar factors are likely to contribute to the anodic shift in the E°′ of cytochrome P450_cam-bound putidaredoxin (+44 mV) with respect to the E°′ measured for free putidaredoxin. Received: 14 June 1999 / Accepted: 6 August 1999     

Genetic attachment of undecane peptides to ovomucoid third domain can suppress the production of specific IgG and IgE antibodies

An undecane peptide (Gly-Ser-Pro-Gly-Ile-Pro-Gly-Ser-Thr-Gly-Met) was genetically attached to the N-terminus of ovomucoid third domain (DIII) to investigate structural characteristics of linear IgE and IgG (B cell) epitopes in DIII with respect to modulation of the immune response towards antigenicity and allergenicity. Balb/c mice were sensitized with native DIII, wild type recombinant DIII, and recombinant modified DIII containing the extra amino acid stretch. The immune responses to the antigens were compared using enzyme-linked immunosorbent assay. Interestingly, specific IgE and IgG levels were suppressed when the modified DIII was used as antigen. This was further confirmed by synthesizing immunodominant IgE and IgG epitopes of DIII on cellulose acetate membrane (SPOTs) and probing them with antibodies raised against DIII antigens. Anti-recombinant wild type DIII anti-serum showed strong binding activities to immunodominant IgE and IgG epitopes, while anti-modified DIII serum did not show any significant binding to the IgE and IgG epitopes. Thus, it is clearly demonstrated that the amino acid stretch in DIII is masking the immune reactive epitope. Genetical attachment of peptides into DIII was found to be effective in reducing the production of specific IgE and IgG antibodies in mice.     

Aromatic stacking as a determinant of the thermal stability of CYP119 from Sulfolobus solfataricus

Two notable features of the thermophilic CYP119, an Arg154-Glu212 salt bridge between the F-G loop and the I helix and an extended aromatic cluster, were studied to determine their contributions to the thermal stability of the enzyme. Site-specific mutants of the salt bridge (Arg154, Glu212) and aromatic cluster (Tyr2, Trp4, Trp231, Tyr250, Trp281) were expressed and purified. The substrate-binding and kinetic constants for lauric acid hydroxylation are little affected in most mutants, but the E212D mutant is inactive and the R154Q mutant has higher K(s),K(m), and k(cat) values. The salt bridge mutants, like wild-type CYP119, melt at 91+/-1 degrees C, whereas mutation of individual residues in the extended aromatic cluster lowers the T(m) by 10-15 degrees C even though no change is observed on mutation of an unrelated aromatic residue. The extended aromatic cluster, but not the Arg154-Glu212 salt bridge, contributes to the thermal stability of CYP119.     

Structural biology of redox partner interactions in P450cam monooxygenase: A fresh look at an old system

The P450cam monooxygenase system consists of three separate proteins: the FAD-containing, NADH-dependent oxidoreductase (putidaredoxin reductase or Pdr), cytochrome P450cam and the 2Fe2S ferredoxin (putidaredoxin or Pdx), which transfers electrons from Pdr to P450cam. Over the past few years our lab has focused on the interaction between these redox components. It has been known for some time that Pdx can serve as an effector in addition to its electron shuttle role. The binding of Pdx to P450cam is thought to induce structural changes in the P450cam active site that couple electron transfer to substrate hydroxylation. The nature of these structural changes has remained unclear until a particular mutant of P450cam (Leu358Pro) was found to exhibit spectral perturbations similar to those observed in wild type P450cam bound to Pdx. The crystal structure of the L358P variant has provided some important insights on what might be happening when Pdx docks. In addition to these studies, many Pdx mutants have been analyzed to identify regions important for electron transfer. Somewhat surprisingly, we found that Pdx residues predicted to be at the P450cam–Pdx interface play different roles in the reduction of ferric P450cam and the ferrous P450–O₂ complex. More recently we have succeeded in obtaining the structure of a chemically cross-linked Pdr–Pdx complex. This fusion protein represents a valid model for the noncovalent Pdr–Pdx complex as it retains the redox activities of native Pdr and Pdx and supports monooxygenase reactions catalyzed by P450cam. The insights gained from these studies will be summarized in this review.