Low-temperature optical spectroscopy: metalloprotein structure and dynamics

Cd, Hg, and Pb Compounds of Benzene-1,3-diamidoethanethiol (BDETH(2))

Benzene-1,3-diamidoethanethiol (BDETH2) is an exceptional precipitant for removing soft heavy metals from water. The present work will detail the bonding arrangement of BDETH2 to the metals Cd, Hg, and Pb, along with the full characterization data of the BDET-M compounds. It was found that the Hg compound has a linear S-M-S geometry. The characterization data consisted of Mp, EA, IR, Raman, MS, XANES, EXAFS, and solid-state multinuclear NMR.

Assessing the integrity of designed homomeric parallel three-stranded coiled coils in the presence of metal ions

De novo design of alpha-helical peptides that self-assemble to form helical coiled coils is a powerful tool for studying molecular recognition between peptides/proteins and determining the fundamental forces involved in their folding and structure. These amphipathic helices assemble in aqueous solution to generate the final coiled coil motif, with the hydrophobic residues in the interior and the polar/hydrophilic groups on the exterior. Considerable effort has been devoted to investigate the forces that determine the overall stability and final three-dimensional structure of the coiled coils. One of the major challenges in coiled coil design is the achievement of specificity in terms of the oligomeric state, with respect to number (two, three, four, or higher), nature (homomers vs heteromers), and strand orientation (parallel vs antiparallel). As seen in nature, metal ions play an important role in this self-organization process, and the overall structure of metalloproteins is primarily the result of two driving forces: the metal coordination preference and the fold of the polypeptide backbone. Previous work in our group has shown that metal ions such as As(III) and Hg(II) can be used to enforce different aggregation states in the Cys derivatives of the designed homotrimeric coiled-coil TRI family [Ac-G(LKALEEK)4G-CONH2]. We are now interested in studying the interplay between the metal ion and peptide preferences in controlling the specificity and relative orientation of the alpha-helices in coiled coils. For this objective, two derivatives of the TRI family, TRi L2WL9C and TRi L2WL23C, have been synthesized. Along with those two peptides, two derivatives of Coil-Ser, CSL9C and CSL19C (CS = Ac-EWEALEKKLAALESKLQALEKKLEALEHG-CONH2), a similar de novo designed three-stranded coiled coil that has the potential to form antiparallel coiled coils, have also been used. Circular dichroism, UV-vis, and 199Hg and 113Cd NMR spectroscopy results reveal that the addition of Hg(II) and Cd(II) to the different mixtures of these peptides forms preferentially homotrimeric coiled coils, over a statistical population of heterotrimeric parallel and antiparallel coiled coils.

Interaction of glutathione reductase with heavy metal: the binding of Hg(II) or Cd(II) to the reduced enzyme affects both the redox dithiol pair and the flavin

To determine the inhibition mechanism of yeast glutathione reductase (GR) by heavy metal, we have compared the electronic absorption and resonance Raman (RR) spectra of the enzyme in its oxidized (Eox) and two-electron reduced (EH2) forms, in the absence and the presence of Hg(II) or Cd(II). The spectral data clearly show a redox dependence of the metal binding. The metal ions do not affect the absorption and RR spectra of Eox. On the contrary, the EH2 spectra, generated by addition of NADPH, are strongly modified by the presence of heavy metal. The absorption changes of EH2 are metal-dependent. On the one hand, the main flavin band observed at 450 nm for EH2 is red-shifted at 455 nm for the EH2-Hg(II) complex and at 451 nm for the EH2-Cd(II) complex. On the other hand, the characteristic charge-transfer (CT) band at 540 nm is quenched upon metal binding to EH2. In NADPH excess, a new CT band is observed at 610 nm for the EH2-Hg(II)-NADPH complex and at 590 nm for EH2-Cd(II)-NADPH. The RR spectra of the EH2-metal complexes are not sensitive to the NADPH concentration. With reference to the RR spectra of EH2 in which the frequencies of bands II and III were observed at 1582 and 1547 cm-1, respectively, those of the EH2-metal complexes are detected at 1577 and 1542 cm-1, indicating an increased flavin bending upon metal coordination to EH2. From the frequency shifts of band III, a concomitant weakening of the H-bonding state of the N5 atom is also deduced. Taking into account the different chemical properties of Hg(II) and Cd(II), the coordination number of the bound metal ion was deduced to be different in GR. A mechanism of the GR inhibition is proposed. It proceeds primarily by a specific binding of the metal to the redox thiol/thiolate pair and the catalytic histidine of EH2. The bound metal ion then acts on the bending of the isoalloxazine ring of FAD as well as on the hydrophobicity of its microenvironment.

A stable mercury-containing complex of the organomercurial lyase MerB: catalysis, product release, and direct transfer to MerA

Bacteria isolated from organic mercury-contaminated sites have developed a system of two enzymes that allows them to efficiently convert both ionic and organic mercury compounds to the less toxic elemental mercury. Both enzymes are encoded on the mer operon and require sulfhydryl-bound substrates. The first enzyme is an organomercurial lyase (MerB), and the second enzyme is a mercuric ion reductase (MerA). MerB catalyzes the protonolysis of the carbon-mercury bond, resulting in the formation of a reduced carbon compound and inorganic ionic mercury. Of several mercury-containing MerB complexes that we attempted to prepare, the most stable was a complex consisting of the organomercurial lyase (MerB), a mercuric ion, and a molecule of the MerB inhibitor dithiothreitol (DTT). Nuclear magnetic resonance (NMR) spectroscopy and extended X-ray absorption fine structure spectroscopy of the MerB/Hg/DTT complex have shown that the ligands to the mercuric ion in the complex consist of both sulfurs from the DTT molecule and one cysteine ligand, C96, from the protein. The stability of the MerB/Hg/DTT complex, even in the presence of a large excess of competing cysteine, has been demonstrated by NMR and dialysis. We used an enzyme buffering test to determine that the MerB/Hg/DTT complex acts as a substrate for the mercuric reductase MerA. The observed MerA activity is higher than the expected activity assuming free diffusion of the mercuric ion from MerB to MerA. This suggests that the mercuric ion can be transferred between the two enzymes by a direct transfer mechanism.

EPR studies on the photoinduced intermediates of NO complexes in recombinant ferric-Mb trapped at low temperatures

The nitrosyl complex of ferric myoglobin is EPR-silent. Upon photolysis at low temperatures, the photoinduced intermediates trapped in the distal heme cavity exhibit new EPR spectra due to the interaction between the photodissociated NO (S=1/2) and the ferric high spin heme (S=5/2). In order to elucidate the effect of distal E7 (His64) and E11 (Val68) mutations upon the electronic structure of the metal center, its immediate environment, and its interaction with the photodissociated NO, EPR spectra of the photoproducts of the NO complexes of recombinant ferric Mb mutants were measured at 5 K. EPR spectra of the photoproducts were closely related to the size and/or the polarity of the distal pocket residues. The distal pocket of the E7 mutants seemed to be sterically crowded, even decreasing the side chain volume or changing its hydrophobicity by replacing amino acid at position 64. We have found that the mobility of the photodissociated NO molecule in the distal heme pocket was strongly governed by the nature of the amino acid residue at E11 position.

Electron spin-lattice relaxation rates for high-spin Fe(III) complexes in glassy solvents at temperatures between 6 and 298 K

The temperature dependence of spin-lattice relaxation rates was analyzed for four high-spin nonheme iron proteins between 5 and 20 K, for three high-spin iron porphyrins between 5 and 118 K, and for four high-spin heme proteins between 5 and 150 to 298 K. For the nonheme proteins the zero-field splittings, D, are less than 0.7 cm(-1), and the relaxation is dominated by the Orbach and Raman processes. For the iron porphyrins and heme proteins D is between 4 and 12 cm(-1) and the relaxation is dominated by the Orbach process between about 5 and 100 K and by a local mode at higher temperatures. The relaxation rates for the heme proteins in glassy matrices extrapolated to values at room temperature that are similar to values obtained by NMR relaxivity in fluid solution. This similarity suggests that for high-spin Fe(III) heme proteins with effective intramolecular spin-lattice relaxation processes, the additional motional freedom gained when a relatively large protein goes from glassy solid to liquid solution at room temperature has little impact on spin-lattice relaxation.

UVRR Spectroscopy and Vibrational Analysis of Mercury Thiolate Compounds Resembling d(10) Metal Binding Sites in Proteins

Raman, ultraviolet resonance Raman (UVRR) and far-IR spectra are reported for the mercury-cysteamine complex, Hg(SCH(2)CH(2)NH(2))(2). Band assignments are made for Hg(SCH(2)CH(2)NH(2))(2), and also for [Hg(SBu(t))(3)](-) and [Hg(SMe)(3)](-) on the basis of ab initio calculations with the effective core potential approximation and also on the basis of comparison with vibrational data of corresponding thiols. The calculations show that geometry-optimized [Hg(SBu(t))(3)](-) and [Hg(SMe)(3)](-) have virtually the same Hg-S bond lengths, but very different nu(s) HgS frequencies, 196 and 268 cm(-)(1), in good agreement with the experimental data. The exceptionally low HgS frequency for [Hg(SBu(t))(3)](-) compared to [Hg(SMe)(3)](-) and to the Hg-MerR protein results from kinematic interactions of the Hg-S stretching and S-C-C bending coordinates when all three substituents at C(alpha) are carbon atoms. For Hg(SCH(2)CH(2)NH(2))(2), the HgS stretching coordinate is distributed over three modes, at 339, 273, and 217 cm(-)(1), all of which exhibit UVRR enhancement. The other contributors to these modes are angle bending and torsional coordinates of the chelate rings. Involvement of the CCN bending coordinates is supported by observed and calculated frequency shifts in D(2)O. The excitation profiles track the main UV absorption band, associated with S-->Hg charge transfer. Enhancement is attributable to the weakening of the Hg-S bonds in the excited state, and probably to changes in the SCC bond angle. Also enhanced, albeit weakly, is the nu(CS) mode at 658 cm(-)(1), reflecting C-S bond shortening in the excited state. The mingling of metal-sulfur and internal ligand coordinates is reminiscent of the mingling seen in RR spectra of type 1 Cu proteins. In both cases the phenomenon may be associated with elevated torsional contributions associated with the rigidity of the ligands.

The core metal-recognition domain of MerR

MerR, the metalloregulatory protein of the mercury-resistance operon (mer) has unusually high affinity and specificity for ionic mercury, Hg(II). Prior genetic and biochemical evidence suggested that the protein has a structure consisting of an N-terminal DNA binding domain, a C-terminal Hg(II)-binding domain, and an intervening region involved with communication between these two domains. We have characterized a series of MerR deletion mutants and found that as little as 30% of the protein (residues 80-128) forms a stable dimer and retains high affinity for Hg(II). Biophysical measures indicate that this minimal Hg(II)-binding domain assumes the structural characteristics of the wild-type full-length protein both in the Hg(II) center itself and in an immediately adjacent helical protein domain. Our observations are consistent with the core Hg(II)-binding domain of the MerR dimer being constituted by a pair of antiparallel helices (possibly in a coiled-coil conformation) comprised of residues cysteine 82 through cysteine 117 from each monomer followed by a flexible loop through residue cysteine 126. These antiparallel helices would have a potential Hg(II)-binding site at each end. However, just as in the full-length protein, only one of these potential binding sites in the deleted proteins actually binds Hg(II).

Structures of the reduced and mercury-bound forms of MerP, the periplasmic protein from the bacterial mercury detoxification system

Bacteria carrying plasmids with the mer operon, which encodes the proteins responsible for the bacterial mercury detoxification system, have the ability to transport Hg(II) across the cell membrane into the cytoplasm where it is reduced to Hg(0). This is significant because metallic mercury is relatively nontoxic and volatile and thus can be passively eliminated. The structures of the reduced and mercury-bound forms of merP, the periplasmic protein, which binds Hg(II) and transfers it to the membrane transport protein merT, have been determined in aqueous solution by multidimensional NMR spectroscopy. The 72-residue merP protein has a betaalpha betabeta alphabeta fold with the two alpha helices overlaying a four-strand antiparallel beta sheet. Structural differences between the reduced and mercury-bound forms of merP are localized to the metal binding loop containing the consensus sequence GMTCXXC. The structure of the mercury-bound form of merP shows that Hg(II) is bicoordinate with the Cys side chain ligands, and this is confirmed by the chemical shift frequency of the 199Hg resonance.

Global mapping of structural solutions provided by the extended X-ray absorption fine structure ab initio code FEFF 6.01: structure of the cryogenic photoproduct of the myoglobin-carbon monoxide complex

X-ray methods based on synchrotron technology have the promise of providing time-resolved structural data based on the high flux and brightness of the X-ray beams. One of the most closely examined problems in this area of time-resolved structure determination has been the examination of intermediates in ligand binding to myoglobin. Recent crystallographic experiments using synchrotron radiation have identified the protein tertiary and heme structural changes that occur upon photolysis of the myoglobin--carbon monoxide complex at cryogenic temperatures [Schlichting, I., Berendzen, J., Phillips, G., & Sweet, R. (1994) Nature 371, 808--812]. However, the precision of protein crystallographic data (approximately 0.2 A) is insufficient to provide precise metrical details of the iron--ligand bond lengths. Since bond length changes on this scale can trigger reactivity changes of several orders of magnitude, such detail is critical to a full understanding of metalloprotein structure--function relationships. Extended X-ray absorption fine structure (EXAFS) spectroscopy has the potential for analyzing bond distances to a precision of 0.02 A but is hampered by its relative insensitivity to the geometry of the backscattering atoms. Thus, it is often unable to provide a unique solution to the structure without ancillary structural information. We have developed a suite of computer programs that incorporate this ancillary structural information and compute the expected experimental spectra for a wide ranging series of Cartesian coordinate sets (global mapping). The programs systematically increment the distance of the metal to various coordinating ligands (along with their associated higher shells). Then, utilizing the ab initio EXAFS code FEFF 6.01, simulated spectra are generated and compared to the actual experimental spectra, and the differences are computed. Finally, the results for hundreds of simulations can be displayed (and compared) in a single plot. The power of this approach is demonstrated in the examination of high signal to noise EXAFS data from a photolyzed solution sample of the myoglobin--carbon monoxide complex at 10 K. Evaluation of these data using our global mapping procedures placed the iron to pyrrole nitrogen average distances close to the value for deoxymyoglobin (2.05 +/- 0.01 A), while the distance from iron to the proximal histidine nitrogen is seen to be 2.20 +/- 0.04 A. It is also shown that one cannot uniquely position the CO ligand on the basis of the EXAFS data alone, as a number of reasonable minima (from the perspective of the EXAFS) are observed. This provides a reasonable explanation for the multiplicity of solutions that have been previously reported. The results presented here are seen to be in complete agreement with the crystallographic results of Schlichting et al. (1994) within the respective errors of the two techniques; however, the extended X-ray absorption fine structure data allow the iron--ligand bond lengths to be precisely defined. An examination of the available spectroscopic data, including EXAFS, shows that the crystallographic results of Schlichting et al. (1994) are highly relevant to the physiological solution state and must be taken into account in any attempt to understand the incomplete relaxation process of the heme iron for the Mb*CO photoproduct at low temperature.