Rubredoxin from Desulfovibrio gigas. A molecular model of the oxidized form at 1.4 A resolution

Multifrequency EPR study of Fe3+ and Co2+ in the active site of desulforedoxin

The understanding of the electronic structure of S > 1/2 transition-metal sites that show a large zero-field splitting (ZFS) of the magnetic sublevels benefits greatly from study by electron-paramagnetic-resonance (EPR) spectroscopy at frequencies above the standard 9.5 GHz. However, high-frequency EPR spectroscopy is technically challenging and still developing. Particularly the sensitivity of high-frequency EPR spectrometers is often too low to apply the technique in the study of transition-metal sites in proteins and enzymes. Here we report a multifrequency EPR study (at 9.5, 94.9, and 275.7 GHz) of the active site of the protein desulforedoxin, both in its natural Fe(3+) form and substituted with Co(2+). The 275.7 GHz EPR spectra made it possible to determine the ZFS parameters of the Fe(3+) site with high precision. No 275.7 GHz spectrum could be observed of the Co(2+) site, but based on 9.5 GHz spectra, its ZFS parameters could be estimated. We find that the typical variation in the geometry of the active site of a protein or enzyme, referred to as conformational strain, does not only make the detection of EPR spectra challenging, but also their analysis. Comparison of the EPR results on the active site of desulforedoxin to those of the closely related active site of rubredoxin illustrates the necessity of explicit quantum-chemical calculations in order to interrelate the electronic and geometric structure of biological transition-metal sites.

Continuous-wave EPR at 275GHz: application to high-spin Fe(3+) systems

The 275GHz electron-paramagnetic-resonance spectrometer we reported on in 2004 has been equipped with a new probe head, which contains a cavity especially designed for operation in continuous-wave mode. The sensitivity and signal stability that is achieved with this new probe head is illustrated with 275GHz continuous-wave spectra of a 1mM frozen solution of the complex Fe(III)-ethylenediamine tetra-acetic acid and of 10mM frozen solutions of the protein rubredoxin, which contains Fe(3+) in its active site, from three different organisms. The high quality of the spectra of the rubredoxins allows the determination of the zero-field-splitting parameters with an accuracy of 0.5GHz. The success of our approach results partially from the enhanced absolute sensitivity, which can be reached using a single-mode cavity. At least as important is the signal stability that we were able to achieve with the new probe head.

Crystal structure of the electron transfer complex rubredoxin rubredoxin reductase of Pseudomonas aeruginosa

Crude oil spills represent a major ecological threat because of the chemical inertness of the constituent n-alkanes. The Gram-negative bacterium Pseudomonas aeruginosa is one of the few bacterial species able to metabolize such compounds. Three chromosomal genes, rubB, rubA1, and rubA2 coding for an NAD(P)H:rubredoxin reductase (RdxR) and two rubredoxins (Rdxs) are indispensable for this ability. They constitute an electron transport (ET) pathway that shuttles reducing equivalents from carbon metabolism to the membrane-bound alkane hydroxylases AlkB1 and AlkB2. The RdxR-Rdx system also is crucial as part of the oxidative stress response in archaea or anaerobic bacteria. The redox couple has been analyzed in detail as a model system for ET processes. We have solved the structure of RdxR of P. aeruginosa both alone and in complex with Rdx, without the need for cross-linking, and both structures were refined at 2.40- and 2.45-A resolution, respectively. RdxR consists of two cofactor-binding domains and a C-terminal domain essential for the specific recognition of Rdx. Only a small number of direct interactions govern mutual recognition of RdxR and Rdx, corroborating the transient nature of the complex. The shortest distance between the redox centers is observed to be 6.2 A.

Characterization of the signaling domain of the NO-responsive regulator NorR from Ralstonia eutropha H16 by site-directed mutagenesis

In Ralstonia eutropha H16, the nitric oxide (NO)-responsive transcriptional activator NorR controls the expression of a dicistronic operon that encodes a membrane-bound NO reductase, NorB, and a protein of unknown function, NorA. The N-terminal domain (NTD) of NorR is responsible for perception of the signal molecule, nitric oxide. Thirteen out of 29 conserved residues of the NTD were exchanged by site-directed mutagenesis. Replacement of R63, R72, D93, D96, C112, D130, or F137 strongly decreased NorR-dependent promoter activation, while the exchange of Y95 or H110 led to an increase in promoter activity compared to that of the wild type. A purified truncated NorR comprising only the NTD (NorR-NTD) contained one iron atom per molecule and was able to bind NO in the as-isolated state. Based on the iron content of NorR-NTD proteins with single amino acid replacements, residues R72, D93, D96, C112, and D130 are likely candidates for iron ligands. Residues R63, Y95, and H110 appear not to be involved in NO binding but may take part in subsequent steps of the signal transduction mechanism of NorR.

Assessment of protein alignment using 1H-1H residual dipolar coupling measurements

A quick and accurate method is described for assessing protein alignment from residual dipolar coupling (RDC) measurements. In contrast to observing D(2)O resonance splitting, which reflects the orientational order of the alignment medium, the degree of alignment of a protein of interest can be estimated directly from (1)H-(1)H RDCs. In this study, RDCs between aromatic protons in unlabeled Cp-rubredoxin were measured from proton homonuclear J-resolved experiments with high sensitivity, and the alignment was assessed without the need of extensive resonance assignment. Since labeled proteins are not needed, this method provides an efficient way for screening alignment media. In situations where the protein structure is known, as in the case of Cp-rubredoxin, a full set of order tensor parameters can be determined, allowing further studies, such as those of ligand alignment relative to a target protein.

Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules

The structure of a partially deuterated rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus, an organism that grows optimally at 100 degrees C, was determined by using the neutron single-crystal diffractometer dedicated for biological macromolecules (BIX-3) at the JRR-3M reactor of the Japan Atomic Energy Research Institute. Data were collected at room temperature up to a resolution of 1.5 A, and the completeness factor of the data set was 81.9%. The model contains 306 H and 50 D atoms. A total of 37 hydration water molecules were identified, with 15 having all three atoms fully located and the remaining D2O molecules partially defined. The model has been refined to final agreement factors of R = 18.6% and Rfree = 21.7%. Several orientations of the O-D bonds of side chains, whose assignments from x-ray data were previously ambiguous, were clearly visible in the neutron structure. Although most backbone N-H bonds had undergone some degree of H/D exchange throughout the rubredoxin molecule, 5 H atom positions still had distinctly negative (H) peaks. The neutron Fourier maps clearly showed the details of an extensive set of H bonds involving the ND3+ terminus that may contribute to the unusual thermostability of this molecule.

Solution structure of the two-iron rubredoxin of Pseudomonas oleovorans determined by NMR spectroscopy and solution X-ray scattering and interactions with rubredoxin reductase

Here we provide insights into the molecular structure of the two-iron 19-kDa rubredoxin (AlkG) of Pseudomonas oleovorans using solution-state nuclear magnetic resonance (NMR) and small-angle X-ray scattering studies. Sequence alignment and biochemical studies have suggested that AlkG comprises two rubredoxin folds connected by a linker region of approximately 70 amino acid residues. The C-terminal domain (C-Rb) of this unusual rubredoxin, together with approximately 35 amino acid residues of the predicted linker region, was expressed in Escherichia coli, purified in the one-iron form and the structure of the cadmium-substituted form determined at high-resolution by NMR spectroscopy. The structure shows that the C-Rb domain is similar in fold to the conventional one-iron rubredoxins from other organisms, whereas the linker region does not have any discernible structure. This tandem "flexible-folded" structure of the polypeptide chain derived for the C-Rb protein was confirmed using solution X-ray scattering methods. X-ray scattering studies of AlkG indicated that the 70-amino acid residue linker forms a structured, yet mobile, polypeptide segment connecting the globular N- and C-terminal domains. The X-ray scattering studies also showed that the N-terminal domain (N-Rb) has a molecular conformation similar to that of C-Rb. The restored molecular shape indicates that the folded N-Rb and C-Rb domains of AlkG are noticeably separated, suggesting some domain movement on complex formation with rubredoxin reductase to allow interdomain electron transfer between the metal centers in AlkG. This study demonstrates the advantage of combining X-ray scattering and NMR methods in structural studies of dynamic, multidomain proteins that are not suited to crystallographic analysis. The study forms a structural foundation for functional studies of the interaction and electron-transfer reactions of AlkG with rubredoxin reductase, also reported herein.

Use of residual dipolar couplings as restraints inab initio protein structure prediction

NMR residual dipolar couplings (RDCs), in the form of the projection angles between the respective internuclear bond vectors, are used as structural restraints in the ab initio structure prediction of a test set of six proteins. The restraints are applied using a recently developed SICHO (SIde-CHain-Only) lattice protein model that employs a replica exchange Monte Carlo (MC) algorithm to search conformational space. Using a small number of RDC restraints, the quality of the predicted structures is improved as reflected by lower RMSD/dRMSD (root mean square deviation/distance root mean square deviation) values from the corresponding native structures and by the higher correlation of the most cooperative mode of motion of each predicted structure with that of the native structure. The latter, in particular, has possible implications for the structure-based functional analysis of predicted structures.

Hydrogen bonds in rubredoxins from mesophilic and hyperthermophilic organisms

The extent and strength of the hydrogen bond networks in rubredoxins from the hyperthermophile Pyrococcus furiosus (PfRd), and its mesophilic analogue Clostridium pasteurianum (CpRd), are examined and compared using NMR spectroscopy. NMR parameters examined in this study include through-hydrogen bond (h3)J(NC)(') scalar couplings and (1)H, (13)C, and (15)N chemical shifts, as well as covalent (1)J(NH) and (1)J(NC)(') scalar couplings. These parameters have allowed the characterization in solution of 12 hydrogen bonds in each protein. Despite a 83% sequence homology and a low RMSD for the backbone heavy atoms (0.648 A) in the crystalline state, subtle, but definite, changes have been identified in the detailed hydrogen-bonding patterns. CpRd shows an increased number of hydrogen bonds in the triple-stranded beta-sheet and an additional hydrogen bond in the multiple-turn segment including residues 14-32. On the other hand, PfRd exhibits an overall strengthening of N-H...O=C hydrogen bonds in the loops involved at the metal binding site as well as evidence for an additional NH...S(Cys) hydrogen bond involving the alanine residue 44. These data, as well as temperature dependence of the NMR parameters, suggest that the particular NMR hydrogen bond pattern found in the hyperthermophile rubredoxin leads to an increased stabilization at the metal binding pocket. It seems to result from a subtle redistribution of hydrogen-bonding interactions between the triple-stranded beta-sheet and the actual metal binding site.

Docking and electron transfer studies between rubredoxin and rubredoxin:oxygen oxidoreductase

The interaction and electron transfer (ET) between rubredoxin (Rd) and rubredoxin:oxygen oxidoreductase (ROO) from Desulfovibrio gigas is studied by molecular modelling techniques. Experimental kinetic assays using recombinant proteins show that the Rd reoxidation by ROO displays a bell-shaped dependence on ionic strength, suggesting a non-trivial electrostatic dependence of the interaction between these two proteins. Rigid docking studies reveal a prevalence for Rd to interact, in a very specific way, with the surface of the ROO dimer near its FMN cofactors. The optimization of the lowest energy complexes, using molecular dynamics simulation, shows a very tight interaction between the surface of the two proteins, with a high probability for Rd residues (but not the iron centre directly) to be in direct contact with the FMN cofactors of ROO. Both electrostatics and van der Waals interactions contribute to the final energy of the complex. In these complexes, the major contributions for complex formation are polar interactions between acidic residues of Rd and basic residues of ROO, plus substantial non-polar interactions between different groups. Important residues for this process are identified. ET estimates (using the Pathways model), in the optimized lowest energy complexes, suggest that these configurations are efficient for transferring electrons. The experimental bell-shaped dependence of kinetics on ionic strength is analysed in view of the molecular modelling results, and hypotheses for the molecular basis of this phenomenon are discussed.

Zinc-substituted Desulfovibrio gigas desulforedoxins: resolving subunit degeneracy with nonsymmetric pseudocontact shifts

Desulfovibrio gigas desulforedoxin (Dx) consists of two identical peptides, each containing one [Fe-4S] center per monomer. Variants with different iron and zinc metal compositions arise when desulforedoxin is produced recombinantly from Escherichia coli. The three forms of the protein, the two homodimers [Fe(III)/Fe(III)]Dx and [Zn(II)/Zn(II)]Dx, and the heterodimer [Fe(III)/Zn(II)]Dx, can be separated by ion exchange chromatography on the basis of their charge differences. Once separated, the desulforedoxins containing iron can be reduced with added dithionite. For NMR studies, different protein samples were prepared labeled with (15)N or (15)N + (13)C. Spectral assignments were determined for [Fe(II)/Fe(II)]Dx and [Fe(II)/Zn(II)]Dx from 3D (15)N TOCSY-HSQC and NOESY-HSQC data, and compared with those reported previously for [Zn(II)/Zn(II)]Dx. Assignments for the (13)C(alpha) shifts were obtained from an HNCA experiment. Comparison of (1)H-(15)N HSQC spectra of [Zn(II)/Zn(II)]Dx, [Fe(II)/Fe(II)]Dx and [Fe(II)/Zn(II)]Dx revealed that the pseudocontact shifts in [Fe(II)/Zn(II)]Dx can be decomposed into inter- and intramonomer components, which, when summed, accurately predict the observed pseudocontact shifts observed for [Fe(II)/Fe(II)]Dx. The degree of linearity observed in the pseudocontact shifts for residues >/=8.5 A from the metal center indicates that the replacement of Fe(II) by Zn(II) produces little or no change in the structure of Dx. The results suggest a general strategy for the analysis of NMR spectra of homo-oligomeric proteins in which a paramagnetic center introduced into a single subunit is used to break the magnetic symmetry and make it possible to obtain distance constraints (both pseudocontact and NOE) between subunits.

Leucine 41 is a gate for water entry in the reduction of Clostridium pasteurianum rubredoxin

Biological electron transfer is an efficient process even though the distances between the redox moieties are often quite large. It is therefore of great interest to gain an understanding of the physical basis of the rates and driving forces of these reactions. The structural relaxation of the protein that occurs upon change in redox state gives rise to the reorganizational energy, which is important in the rates and the driving forces of the proteins involved. To determine the structural relaxation in a redox protein, we have developed methods to hold a redox protein in its final oxidation state during crystallization while maintaining the same pH and salt conditions of the crystallization of the protein in its initial oxidation state. Based on 1.5 A resolution crystal structures and molecular dynamics simulations of oxidized and reduced rubredoxins (Rd) from Clostridium pasteurianum (Cp), the structural rearrangements upon reduction suggest specific mechanisms by which electron transfer reactions of rubredoxin should be facilitated. First, expansion of the [Fe-S] cluster and concomitant contraction of the NH...S hydrogen bonds lead to greater electrostatic stabilization of the extra negative charge. Second, a gating mechanism caused by the conformational change of Leucine 41, a nonpolar side chain, allows transient penetration of water molecules, which greatly increases the polarity of the redox site environment and also provides a source of protons. Our method of producing crystals of Cp Rd from a reducing solution leads to a distribution of water molecules not observed in the crystal structure of the reduced Rd from Pyrococcus furiosus. How general this correlation is among redox proteins must be determined in future work. The combination of our high-resolution crystal structures and molecular dynamics simulations provides a molecular picture of the structural rearrangement that occurs upon reduction in Cp rubredoxin.

Two-iron rubredoxin of Pseudomonas oleovorans: production, stability and characterization of the individual iron-binding domains by optical, CD and NMR spectroscopies

A minigene encoding the C-terminal domain of the 2Fe rubredoxin of Pseudomonas oleovorans was created from the parental alk G gene contained in the expression plasmid pKK223-3. The vector directed the high-level production of the C-terminal domain of this rubredoxin; a simple procedure was used to purify the recombinant domain in the 1Fe form. The 1Fe form of the C-terminal domain was readily converted into the apoprotein and cadmium forms after precipitation with trichloroacetic acid and resolubilization in the presence or absence of cadmium chloride respectively. In steady-state assays, the recombinant 1Fe C-terminal domain is redox-active and able to transfer electrons from reduced rubredoxin reductase to cytochrome c. The absorption spectrum and dichroic features of the CD spectrum for the iron- and cadmium-substituted C-terminal domain are similar to those reported for the iron- and cadmium-substituted Desulfovibrio gigas rubredoxin [Henehen, Pountney, Zerbe and Vasak (1993) Protein Sci. 2, 1756-1764]. Difference absorption spectroscopy of the cadmium-substituted C-terminal domain revealed the presence of four Gaussian-resolved maxima at 202, 225, 240 and 276 nm; from Jørgensen's electronegativity theory, the 240 nm band is attributable to a CysS-Cd(II) charge-transfer excitation. Attempts to express the N-terminal domain of the 2Fe rubredoxin directly from a minigene were unsuccessful. However, the N-terminal domain was isolated through cleavage of an engineered 2Fe rubredoxin in which a factor Xa proteolysis site had been introduced into the putative interdomain linker. The N-terminal domain is characterized by absorption spectra typical of the 1Fe rubredoxins. The domain is folded as determined by CD and NMR spectroscopies and is redox-active. However, the N-terminal domain is less stable than the isolated C-terminal domain, a finding consistent with the known properties of the full-length 2Fe and cadmium-substituted Ps. oleovorans rubredoxin.

Solution structure of a zinc substituted eukaryotic rubredoxin from the cryptomonad alga Guillardia theta

The rubredoxin from the cryptomonad Guillardia theta is one of the first examples of a rubredoxin encoded in a eukaryotic organism. The structure of a soluble zinc-substituted 70-residue G. theta rubredoxin lacking the membrane anchor and the thylakoid targeting sequence was determined by multidimensional heteronuclear NMR, representing the first three-dimensional (3D) structure of a eukaryotic rubredoxin. For the structure calculation a strategy was applied in which information about hydrogen bonds was directly inferred from a long-range HNCO experiment, and the dynamics of the protein was deduced from heteronuclear nuclear Overhauser effect data and exchange rates of the amide protons. The structure is well defined, exhibiting average root-mean-square deviations of 0.21 A for the backbone heavy atoms and 0.67 A for all heavy atoms of residues 7-56, and an increased flexibility toward the termini. The structure of this core fold is almost identical to that of prokaryotic rubredoxins. There are, however, significant differences with respect to the charge distribution at the protein surface, suggesting that G. theta rubredoxin exerts a different physiological function compared to the structurally characterized prokaryotic rubredoxins. The amino-terminal residues containing the putative signal peptidase recognition/cleavage site show an increased flexibility compared to the core fold, but still adopt a defined 3D orientation, which is mainly stabilized by nonlocal interactions to residues of the carboxy-terminal region. This orientation might reflect the structural elements and charge pattern necessary for correct signal peptidase recognition of the G. theta rubredoxin precursor.

Optical and TDPAC spectroscopy of Hg(II)-rubredoxin: model for a mononuclear tetrahedral [Hg(CysS)4]2- center. ISOLDE Collaboration

Rubredoxins possess a well-defined mononuclear tetrahedral tetrathiolate metal binding site, a feature exploited by several investigations to study the spectroscopic characteristics and the coordination chemistry of different metal ions at this binding site. In the present work, Hg(II)-substituted rubredoxin (Rd) from Desulfovibrio gigas has been studied by electronic absorption, circular dichroism (CD), magnetic circular dichroism (MCD), and time differential perturbed angular correlation of gamma-rays (TDPAC) spectroscopies. The TDPAC spectrum of 199mHg-Rd at pH 8 exhibits a prevailing nuclear quadrupole interaction (NQI) with a precession frequency of omega1=0.09 Grad/s and an asymmetry parameter eta=0, features characteristic of a slightly distorted tetrahedral tetrathiolate metal coordination, i.e, a HgCysS4 center. In addition, three minor populated NQIs have also been detected. They may represent a trigonal HgS3 (omega1=1.13 Grad/s, eta=0.21), a digonal HgS2 (omega1= 1.34 Grad/s, eta =0.20), and a digonal Hg(II) coordination (omega = 1.58 Grad/s, eta =0.18) with unidentified ligands. Since similar studies at pH 2.5 revealed a time-dependent increase of the HgCysS4 population, the low populated sites may represent intermediate Hg(II) complexes formed prior to the generation of the thermodynamically stable structure. The metal-induced absorption envelope of Hg-Rd reveals three distinct transitions with Gaussian-resolved maxima located at 230, 257, and 284 nm, which are paralleled by dichroic features in the corresponding difference CD spectrum of Hg(II)-Rd versus apo-Rd. Based on the optical electronegativity theory of J*rgensen, the lowest energy transition has been attributed to a CysS-Hg(II) charge-transfer excitation. The Td type of metal coordination in Hg-Rd is supported by the presence of an unresolved A-term with a negative lobe at 295 nm in the difference MCD spectrum. These results point to the usefulness of optical and TDPAC spectroscopies for studying Hg(II) sites in other proteins.

Thermostabilization of proteins by diglycerol phosphate, a new compatible solute from the hyperthermophile Archaeoglobus fulgidus

Diglycerol phosphate accumulates under salt stress in the archaeon Archaeoglobus fulgidus (L. O. Martins, R. Huber, H. Huber, K. O. Stetter, M. S. da Costa, and H. Santos, Appl. Environ. Microbiol. 63:896-902, 1997). This solute was purified after extraction from the cell biomass. In addition, the optically active and the optically inactive (racemic) forms of the compound were synthesized, and the ability of the solute to act as a protecting agent against heating was tested on several proteins derived from mesophilic or hyperthermophilic sources. Diglycerol phosphate exerted a considerable stabilizing effect against heat inactivation of rabbit muscle lactate dehydrogenase, baker's yeast alcohol dehydrogenase, and Thermococcus litoralis glutamate dehydrogenase. Highly homologous and structurally well-characterized rubredoxins from Desulfovibrio gigas, Desulfovibrio desulfuricans (ATCC 27774), and Clostridium pasteurianum were also examined for their thermal stabilities in the presence or absence of diglycerol phosphate, glycerol, and inorganic phosphate. These proteins showed different intrinsic thermostabilities, with half-lives in the range of 30 to 100 min. Diglycerol phosphate exerted a strong protecting effect, with approximately a fourfold increase in the half-lives for the loss of the visible spectra of D. gigas and C. pasteurianum rubredoxins. In contrast, the stability of D. desulfuricans rubredoxin was not affected. These different behaviors are discussed in the light of the known structural features of rubredoxins. The data show that diglycerol phosphate is a potentially useful protein stabilizer in biotechnological applications.

Modulation of the redox potential of the [Fe(SCys)(4)] site in rubredoxin by the orientation of a peptide dipole

Rubredoxins (Rds) may be separated into two classes based upon the correlation of their reduction potentials with the identity of residue 44; those with Ala44 have reduction potentials that are approximately 50 mV higher than those with Val44. The smaller side chain volume occupied by Ala44 relative to that occupied by Val44 has been proposed to explain the increase in the reduction potential, based upon changes in the Gly43-Ala44 peptide bond orientation and the distance to the [Fe(SCys)(4)] center in the Pyrococcus furiosus (Pf) Rd crystal structure compared to those of Gly43-Val44 in the Clostridium pasteurianum (Cp) Rd crystal structure. As an experimental test of this hypothesis, single-site Val44 <--> Ala44 exchange mutants, [V44A]Cp and [A44V]Pf Rds, have been cloned and expressed. Reduction potentials of these residue 44 variants and pertinent features of the X-ray crystal structure of [V44A]Cp Rd are reported. Relative to those of wild-type Cp and Pf Rds, the V44A mutation in Cp Rd results in an 86 mV increase in midpoint reduction potential and the [A44V] mutation in Pf Rd results in a 95 mV decrease in midpoint reduction potential, respectively. In the crystal structure of [V44A]Cp Rd, the peptide bond between residues 43 and 44 is approximately 0.3 A closer to the Fe center and the hydrogen bond distance between the residue 44 peptide nitrogen and the Cys42 gamma-sulfur decreases by 0.32 A compared to the analogous distances in the wild-type Cp Rd crystal structure. The results described herein support the prediction that the identity of residue 44 alone determines whether a Rd reduction potential of about -50 or 0 mV is observed.

Novel Rubredoxin Model Tetrathiolato Iron(II) and Cobalt(II) Complexes Containing Intramolecular Single and Double NH.S Hydrogen Bonds

Simple rubredoxin model complexes with o-(acylamino)benzenethiolato and 2,6-(diacylamino)benzenethiolato were synthesized and characterized by (1)H NMR, IR, and electrochemical properties. The structures of (NEt(4))(2)[Fe(II)(S-o-t-BuCONHC(6)H(4))(4)].2EtCN (3a), (NEt(4))(2)[Co(II)(S-o-t-BuCONHC(6)H(4))(4)].2EtCN (3b), and (PPh(4))(2)[Co(II){S-2,6-(CF(3)CONH)(2)C(6)H(3)}(4)].Et(2)O (5b') were determined by X-ray analysis. The complexes have intramolecular single or double NH.S hydrogen bonds. The mean Fe-S and Co-S distances are significantly shorter than those of non-hydrogen-bonding complexes, [M(SPh)(4)](2-) (M = Fe(II), Co(II)), by 0.024 Å (3a), 0.032 Å (3b), and 0.029 Å (5b'), respectively. (NMe(4))(2)[Fe(II)(S-o-CH(3)CONHC(6)H(4))(4)] (2a) and (NMe(4))(2)[Fe(II){S-2,6-(CH(3)CONH)(2)C(6)H(3)}(4)] (6a) have remarkably positive shifted Fe(III)/Fe(II) redox couples by the single and double NH.S hydrogen bond, respectively. The shifts are +0.25 for 2a and +0.56 for 6a from the redox potential of [Fe(II)(SPh)(4)](2-), which indicate additivity of the effect of the NH.S hydrogen bond. The formation and the structure of a novel chelating amido(thiolato) complex (PPh(4))(2)[Co(II){S-2,6-(CF(3)CONH)(2)C(6)H(3)}(2)(S-2-CF(3)CONH-6-CF(3)CONC(6)H(3))].Et(2)O (9) are also described.

Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin

Molecular dynamics simulations in solution are performed for a rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus (RdPf) and one from the mesophilic organism Desulfovibrio vulgaris (RdDv). The two proteins are simulated at four temperatures: 300 K, 373 K, 473 K (two sets), and 500 K; the various simulations extended from 200 ps to 1,020 ps. At room temperature, the two proteins are stable, remain close to the crystal structure, and exhibit similar dynamic behavior; the RMS residue fluctuations are slightly smaller in the hyperthermophilic protein. An analysis of the average energy contributions in the two proteins is made; the results suggest that the intraprotein energy stabilizes RdPf relative to RdDv. At 373 K, the mesophilic protein unfolds rapidly (it begins to unfold at 300 ps), whereas the hyperthermophilic does not unfold over the simulation of 600 ps. This is in accord with the expected stability of the two proteins. At 473 K, where both proteins are expected to be unstable, unfolding behavior is observed within 200 ps and the mesophilic protein unfolds faster than the hyperthermophilic one. At 500 K, both proteins unfold; the hyperthermophilic protein does so faster than the mesophilic protein. The unfolding behavior for the two proteins is found to be very similar. Although the exact order of events differs from one trajectory to another, both proteins unfold first by opening of the loop region to expose the hydrophobic core. This is followed by unzipping of the beta-sheet. The results obtained in the simulation are discussed in terms of the factors involved in flexibility and thermostability.

Recombinant two-iron rubredoxin of Pseudomonas oleovorans: overexpression, purification and characterization by optical, CD and 113Cd NMR spectroscopies

The gene (alk G) encoding the two-iron rubredoxin of Pseudomonas oleovorans was amplified from genomic DNA by PCR and subcloned into the expression vector pKK223-3. The vector directed the high-level production of rubredoxin in Escherichia coli. A simple three-step procedure was used to purify recombinant rubredoxin in the 1Fe form. 1Fe-rubredoxin was readily converted to the 2Fe, apoprotein and cadmium forms after precipitation with trichloroacetic acid and resolubilization in the presence or absence of ferrous ammonium sulphate or CdCl2 respectively. Recombinant 1Fe and 2Fe rubredoxins are redox-active and able to transfer electrons from reduced spinach ferredoxin reductase to cytochrome c. The absorption spectrum and dichroic features of the CD spectrum for the cadmium-substituted protein are similar to those reported for cadmium-substituted Desulfovibrio gigas rubredoxin [Henehan, Poutney, Zerbe and Vasak (1993) Protein Sci. 2, 1756-1764]. Difference absorption spectroscopy of cadmium-substituted rubredoxin revealed the presence of four Gaussian-resolved maxima at 207, 228, 241 and 280 nm; the 241 nm band is attributable, from Jorgensen's electronegativity theory, to a CysS-CdII charge-transfer excitation. The 113Cd NMR spectrum of the 113Cd-substituted rubredoxin contains two 113Cd resonances with chemical shifts located at 732.3 and 730 p.p.m. The broader linewidth and high frequency shift of the resonance at 730 p. p.m. indicates that the Cd2+ ion is undergoing chemical exchange and, consistent with the difference absorption spectra, is bound less tightly than the Cd2+ ion, giving rise to the chemical shift at 732.3 p.p.m.

Protein contributions to redox potentials of homologous rubredoxins: an energy minimization study

The energetic contributions of the protein to the redox potential in an iron-sulfur protein are studied via energy minimization, comparing homologous rubredoxins from Clostridium pasteurianum, Desulfovibrio gigas, Desulfovibrio vulgaris, and Pyrococcus furiosus. The reduction reaction was divided into 1) the change in the redox site charge without allowing the protein to respond and 2) the relaxation of the protein in response to the new charge state, focusing on the latter. The energy minimizations predict structural relaxation near the redox site that agrees well with that in crystal structures of oxidized and reduced P. furiosus rubredoxin, but underpredicts it far from the redox site. However, the relaxation energies from the energy-minimized structures agree well with those from the crystal structures, because the polar groups near the redox site are the main determinants and the charged groups are all located at the surface and thus are screened dielectrically. Relaxation energies are necessary for good agreement with experimentally observed differences in reduction energies between C. pasteurianum and the other three rubredoxins. Overall, the relaxation energy is large (over 500 mV) from both the energy-minimized and the crystal structures. In addition, the range in the relaxation energy for the different rubredoxins is large (300 mV), because even though the structural perturbations of the polar groups are small, they are very near the redox site. Thus the relaxation energy is an important factor to consider in reduction energetics.

Conformation Control of Peptides by Metal Ions. Coordination Conformation Correlation Observed in a Model for Cys-X-Y-Cys/M(2+) in Proteins

The structure of [(Boc-Cys(1)-Pro-Leu-Cys(4)-OMe)(S-tert-C(4)H(9))Hg](-) (Boc: butoxycarbonyl), 1, was studied in N,N-dimethylformamide (DMF) and compared with that of [(Boc-Cys(1)-Pro-Leu-Cys(4)-OMe)Hg], 2, in order to discuss the intrinsic structural feature of the cysteine-containing metal-binding sites of proteins: Cys(i)-X-Y-Cys(i)(+3)/M(2+). 1 was generated by the reaction of 2 with NaS-tert-C(4)H(9). The geometry of the mercury ion (Hg(2+)) in 1 was proposed to be trigonal planar by UV-vis spectroscopy and Hg L(III) edge X-ray absorption fine structure (XAFS) measurements. Extended X-ray absorption fine structure (EXAFS) calculations yielded r(Hg-S) = 2.42 Å. Analyses of the nuclear Overhauser and exchange spectroscopy (NOESY) and the rotating frame nuclear Overhauser effect spectroscopy (ROESY) spectra of 1 in DMF-d(7) gave approximate distances for the 21 (1)H-(1)H pairs of the main chain loop. These results on distance information were processed by distance geometry (DG) and restrained molecular dynamics (RMD) calculations in order to optimize the molecular structure of 1. Molecular dynamics (MD) calculations were also performed. We proposed that the trigonal planar Hg(2+) in 1 regulates the hydrogen-bonding schemes of the peptide in the same manner as the tetrahedral ions involved in the Cys(i)-X-Y-Cys(i)(+3)/M(2+) core sites in natural proteins, forming two hydrogen bonds, Cys(1) S-Leu H(N) and Cys(1) S-Cys(4) H(N). This is in contrast to 2, where the linear coordinate mercury causes another type of hydrogen-bonding scheme, Cys(1) S-Leu H(N) and Pro CO-Cys(4) H(N). Details of the effect of trigonal planar Hg(2+) on the peptide conformation were analyzed with respect to the phi, varphi, and chi torsion angles of the peptide chain. The effect of the change of the angleS-Hg-S bite angle on the conformation of Cys-Pro-Leu-Cys was also discussed on the basis of MD calculations. The distribution area of Leu (phi, varphi) in the Ramachandran plot moves from near the alpha helix region to the turn structure region as the bite angle increases from 90 to 180 degrees, accompanying the change in the hydrogen-bonding scheme. The critical bite angle is around 140 degrees. The analysis revealed that angleS-Hg-S congruent with 110 degrees, which corresponds to the tetrahedral coordination geometry of the central metal ion, allows a high flexibility of the Cys-Pro-Leu-Cys skeleton.

Structural origins of redox potentials in Fe-S proteins: electrostatic potentials of crystal structures

Redox potentials often differ dramatically for homologous proteins that have identical redox centers. For two types of iron-sulfur proteins, the rubredoxins and the high-potential iron-sulfur proteins (HiPIPs), no structural explanations for these differences have been found. We calculated the classical electrostatic potential at the redox site using static crystal structures of four rubredoxins and four HiPIPs to identify important structural determinants of their redox potentials. The contributions from just the backbone and polar side chains are shown to explain major features of the experimental redox potentials. For instance, in the rubredoxins, the presence of Val 44 versus Ala 44 causes a backbone shift that explains a approximately 50 mV lower redox potential in one of the four rubredoxins. This result is consistent with experimental redox potentials of five additional rubredoxins with known sequence. Also, we attribute the unusually lower redox potentials of two of the HiPIPs studied to a less positive electrostatic environment around their redox sites. Finally, molecular dynamics simulations of solvent around static rubredoxin crystal structures indicate that water alone is a major factor in dampening the contribution of charged side chains, in accord with experiments showing that mutations of surface charges produce relatively little effect on redox potentials.

Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein

The Zn(Scys)4 unit is present in numerous proteins, where it assumes structural, regulatory, or catalytic roles. The same coordination is found naturally around iron in rubredoxins, several structures of which have been refined at resolutions of, or near to, 1 A. The fold of the small protein rubredoxin around its metal ion is an excellent model for many zinc finger proteins. Zn-substituted rubredoxin and its Fe-containing counterpart were both obtained as the products of the expression in Escherichia coli of the rubredoxin-encoding gene from Clostridium pasteurianum. The structures of both proteins have been refined with an anisotropic model at atomic resolution (1.1 A, R = 8.3% for Fe-rubredoxin, and 1.2 A, R = 9.6% for Zn-rubredoxin) and are very similar. The most significant differences are increased lengths of the M-S bonds in Zn-rubredoxin (average length, 2.345 A) as compared with Fe-rubredoxin (average length, 2.262 A). An increase of the CA-CB-SG-M dihedral angles involving Cys-6 and Cys-39, the first cysteines of each of the Cys-Xaa-Xaa-Cys metal binding motifs, has been observed. Another consequence of the replacement of iron by zinc is that the region around residues 36-46 undergoes larger displacements than the remainder of the polypeptide chain. Despite these changes, the main features of the FeS4 site, namely a local 2-fold symmetry and the characteristic network of N-H...S hydrogen bonds, are conserved in the ZnS4 site. The Zn-substituted rubredoxin provides the first precise structure of a Zn(Scys)4 unit in a protein. The nearly identical fold of rubredoxin around iron or zinc suggests that at least in some of the sites where the metal has mainly a structural role-e.g., zinc fingers-the choice of the relevant metal may be directed by its cellular availability and mobilization processes rather than by its chemical nature.

Establishing isostructural metal substitution in metalloproteins using 1H NMR, circular dichroism, and Fourier transform infrared spectroscopy

Far-UV CD, 1H-NMR, and Fourier transform infrared (FTIR) spectroscopy are three of the most commonly used methods for the determination of protein secondary structure composition. These methods are compared and evaluated as a means of establishing isostructural metal substitution in metalloproteins, using the crystallographically defined rubredoxin from Desulfovibrio gigas and its well-characterized cadmium derivative as a model system. It is concluded that analysis of the FTIR spectrum of the protein amide I resonance represents the most facile and generally applicable method of determining whether the overall structure of a metalloprotein has been altered upon metal reconstitution. This technique requires relatively little biological material (ca. 300 micrograms total protein) and, unlike either CD or 1H-NMR spectroscopy, is unaffected by the presence of different metal ions, thus allowing the direct comparison of FTIR spectra before and after metal substitution.

A comparative picosecond-resolved fluorescence study of tryptophan residues in iron-sulfur proteins

The fluorescence intensity and anisotropy decays of the intrinsic tryptophan emission from six Fe/S proteins (ranging from the very simplest ones to enzyme complexes containing one, two or more Trp residues) were measured. All proteins were examined in the reduced and the oxidized state. In either redox state each protein exhibits ultrarapid tryptophan fluorescence decay on the picosecond timescale contributing up to 93% of the total decay. Correlation times in the range of 1 ns or less were found for all six iron-sulfur proteins reflecting internal Trp motion. In addition, some proteins exhibit longer correlation times reflecting segmental motion and overall protein tumbling. The ultrarapid fluorescence decay in iron-sulfur proteins indicates efficient radiationless energy transfer between distant tryptophan residues and iron-sulfur clusters. Such an energy transfer mechanism can be accounted for by referring to the three-dimensional structures of rubredoxin and ferredoxin in calculating the transfer efficiency of the single tryptophan-iron-sulfur couple.