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Developing electrode-driven biocatalytic systems utilizing the P450 cytochromes for selective oxidations depends not only on achieving electron transfer (ET) but also doing so at rates that favor native-like turnover. Herein we report studies that correlate rates of heme reduction with ET pathways and resulting product distributions. We utilized single-surface cysteine mutants of the heme domain of P450 from Bacillus megaterium and modified the thiols with N-(1-pyrene)-iodoacetamide, affording proteins that could bond to basal-plane graphite. Of the proteins examined, Cys mutants at position 62, 383, and 387 were able to form electroactive monolayers with similar E_(1/2) values (− 335 to − 340 mV vs AgCl/Ag). Respective ET rates (k_so) and heme-cysteine distances for 62, 383, and 387 are 50 s^(-1) and 16 Ǻ, 0.8 s^(–1) and 25 Ǻ, and 650 s^(–1) and 19 Ǻ. Experiments utilizing rotated-disk electrodes were conducted to determine the products of P450-catalyzed dioxygen reduction. We found good agreement between ET rates and product distributions for the various mutants, with larger k_so values correlating with more electrons transferred per dioxygen during catalysis.

The structure and unfolding of metal-free (apo) human wild-type SOD1 and three pathogenic variants of SOD1 (A4V, G93R, and H48Q) that cause familial amyotrophic lateral sclerosis have been studied with amide hydrogen/deuterium exchange and mass spectrometry. The results indicate that a significant proportion of each of these proteins exists in solution in a conformation in which some strands of the beta-barrel (i.e. beta2) are well protected from exchange at physiological temperature (37 degrees C), whereas other strands (i.e. beta3 and beta4) appear to be unprotected from hydrogen/deuterium exchange. Moreover, the thermal unfolding of these proteins does not result in the uniform incorporation of deuterium throughout the polypeptide but involves the local unfolding of different residues at different temperatures. Some regions of the proteins (i.e. the "Greek key" loop, residues 104-116) unfold at a significantly higher temperature than other regions (i.e. beta3 and beta4, residues 21-53). Together, these results show that human wild-type apo-SOD1 and variants have a partially unfolded beta-barrel at physiological temperature and unfold non-cooperatively.

The thermodynamics of zinc binding to metal-free (apo) human and bovine copper-zinc superoxide dismutases (SOD1) were measured using isothermal titration calorimetry. The apparent thermodynamics of zinc binding to the apoproteins were favorable (Ka > 108 M-1), with an observed stoichiometry of one zinc per homodimer. The change in heat capacity for the one-zinc binding event was large and negative (approximately -650 cal mol-1 K-1), suggestive of significant structural changes to the protein upon zinc binding. We further characterized the one-zinc derivative by circular dichroism and determined that this derivative had nearly the same secondary structure as the two-zinc derivative and that both are structurally distinct from the metal-free protein. In addition, we monitored the effect of zinc binding on hydrogen-deuterium exchange and accessibility of histidyl residues to modification by diethyl pyrocarbonate and observed that more than 50% protection was afforded by the binding of one zinc in both assays. Differential scanning calorimetry on the human SOD1 zinc derivatives also showed increased thermostability of the protein due to zinc binding. Further, the melting transitions observed for the one-zinc derivative closely resembled those of the two-zinc derivative. Finally, we observed that the quaternary structure of the protein is stabilized upon binding of one and two zinc ions in analytical ultracentrifugation experiments. Combined, these results suggest communication between the two monomers of SOD1 such that the binding of one zinc ion per homodimer has a more profound effect on the homodimeric protein structure than the binding of subsequent metal ions. The relevance of these findings to amyotrophic lateral sclerosis is discussed.

Hydrogen exchange monitored by mass spectrometry has been used to study the structural behavior of the pathogenic A4V variant of superoxide dismutase 1 (SOD1) in the metal-free (apo) form. Mass spectrometric data revealed that in the disulfide-intact (S-S) form, the A4V variant is destabilized at residues 50-53, in the disulfide subloop of the dimer interface, but many other regions of the A4V protein exhibited hydrogen exchange properties identical to that of the wild type protein. Additionally, mass spectrometry revealed that A4V apoSOD1(S-S) undergoes slow localized unfolding in a large segment of the beta-barrel that included beta3, beta4, and loops II and III. In the disulfide-reduced form, A4V apoSOD1 exchanged like a "random coil" polypeptide at 20 degrees C and began to populate folded states at 4 degrees C. These local and global unfolding events could facilitate intermolecular protein-protein interactions that cause the aggregation or neurotoxicity of A4V SOD1.

The blue copper sites in Cucumis sativus stellacyanin and Rhus vernicifera stellacyanin have been investigated by X-ray absorption spectroscopy (XAS) in order to probe the effects of axial amide coordination. EXAFS results show a slight lengthening of the Cu−S(Cys) bond in both stellacyanins compared to the classic blue copper site in azurin. The 1s → 3d transition in the Cu K-edge of stellacyanin is ∼0.5 eV lower in energy than those of the classic blue copper sites, consistent with a stronger ligand donor set. A configuration interaction (CI) model applied to the 1s → 4p and 1s → 4p + shakedown transitions in the edge predicts less covalent bonding for stellacyanin than for plastocyanin, which is attributed to a weaker thiolate bond. These studies demonstrate that the strength of the axial ligand interaction inversely affects the strength of the thiolate−copper bond.

The copper chaperone for superoxide dismutase (CCS) gene encodes a protein that is believed to deliver copper ions specifically to copper-zinc superoxide dismutase (CuZnSOD). CCS proteins from different organisms share high sequence homology and consist of three distinct domains; a CuZnSOD-like central domain 2 flanked by domains 1 and 3, which contain putative metal-binding motifs. We report deduced protein sequences from tomato and Arabidopsis, the first functional homologues of CCS identified in plants. We have purified recombinant human (hCCS) and tomato (tCCS) copper chaperone proteins, as well as a truncated version of tCCS containing only domains 2 and 3. Their cobalt(2+) binding properties in the presence and absence of mercury(2+) were characterized by UV-vis and circular dichroism spectroscopies and it was shown that hCCS has the ability to bind two spectroscopically distinct cobalt ions whereas tCCS binds only one. The cobalt binding site that is common to both hCCS and tCCS displayed spectroscopic characteristics of cobalt(2+) bound to four or three cysteine ligands. There are only four cysteine residues in tCCS, two in domain 1 and two in domain 3; all four are conserved in other CCS sequences including hCCS. Thus, an interaction between domain 1 and domain 3 is concluded, and it may be important in the copper chaperone mechanism of these proteins.

The oxidized blue copper proteins azurin and stellacyanin have been investigated through 1H NMR at 800 MHz and the results compared with those for plastocyanin (Bertini, I.; Ciurli, S.; Dikiy, A.; Gasanov, R.; Luchinat, C.; Martini, G.; Safarov, N. J. Am. Chem. Soc. 1999, 121, 2037). By exploiting saturation transfer between the oxidized and the reduced forms, all the hyperfine shifted signals can be assigned, including the β-CH2 protons of the coordinated cysteines, which are so broad not to be detected under direct observation. Both hyperfine shifts and line widths of the latter signals differ dramatically from one protein to another: average hyperfine shifts of about 850, 600, and 400 ppm and average line widths of 1.2, 0.45, and 0.25 MHz are observed for azurin, plastocyanin, and stellacyanin, in that order. The observation of a nuclear line width of 1.2 MHz is unprecedented in high-resolution NMR in solution. These data are interpreted as a measure of the out-of-plane displacement of the copper ion,...

The presence of the copper ion at the active site of human wild type copper-zinc superoxide dismutase (CuZnSOD) is essential to its ability to catalyze the disproportionation of superoxide into dioxygen and hydrogen peroxide. Wild type CuZnSOD and several of the mutants associated with familial amyotrophic lateral sclerosis (FALS) (Ala4 → Val, Gly93 → Ala, and Leu38 → Val) were expressed inSaccharomyces cerevisiae. Purified metal-free (apoproteins) and various remetallated derivatives were analyzed by metal titrations monitored by UV-visible spectroscopy, histidine modification studies using diethylpyrocarbonate, and enzymatic activity measurements using pulse radiolysis. From these studies it was concluded that the FALS mutant CuZnSOD apoproteins, in direct contrast to the human wild type apoprotein, have lost their ability to partition and bind copper and zinc ions in their proper locations in vitro. Similar studies of the wild type and FALS mutant CuZnSOD holoenzymes in the “as isolated” metallation state showed abnormally low copper-to-zinc ratios, although all of the copper acquired was located at the native copper binding sites. Thus, the copper ions are properly directed to their native binding sites in vivo, presumably as a result of the action of the yeast copper chaperone Lys7p (yeast CCS). The loss of metal ion binding specificity of FALS mutant CuZnSODsin vitro may be related to their role in ALS.

A reaction cycle is proposed for the mechanism of copper-zinc superoxide dismutase (CuZnSOD) that involves inner sphere electron transfer from superoxide to Cu(II) in one portion of the cycle and outer sphere electron transfer from Cu(I) to superoxide in the other portion of the cycle. This mechanism is based on three yeast CuZnSOD structures determined by X-ray crystallography together with many other observations. The new structures reported here are (1) wild type under 15 atm of oxygen pressure, (2) wild type in the presence of azide, and (3) the His48Cys mutant. Final R-values for the three structures are respectively 20.0%, 17.3%, and 20.9%. Comparison of these three new structures to the wild-type yeast Cu(I)ZnSOD model, which has a broken imidazolate bridge, reveals the following: (i) The protein backbones (the "SOD rack") remain essentially unchanged. (ii) A pressure of 15 atm of oxygen causes a displacement of the copper ion 0.37 A from its Cu(I) position in the trigonal plane formed by His46, His48, and His120. The displacement is perpendicular to this plane and toward the NE2 atom of His63 and is accompanied by elongated copper electron density in the direction of the displacement suggestive of two copper positions in the crystal. The copper geometry remains three coordinate, but the His48-Cu bond distance increases by 0.18 A. (iii) Azide binding also causes a displacement of the copper toward His63 such that it moves 1.28 A from the wild-type Cu(I) position, but unlike the effect of 15 atm of oxygen, there is no two-state character. The geometry becomes five- coordinate square pyramidal, and the His63 imidazolate bridge re-forms. The His48-Cu distance increases by 0.70 A, suggesting that His48 becomes an axial ligand. (iv) The His63 imidazole ring tilts upon 15 atm of oxygen treatment and azide binding. Its NE2 atom moves toward the trigonal plane by 0.28 and 0.66 A, respectively, in these structures. (v) The replacement of His48 by Cys, which does not bind copper, results in a five-coordinate square pyramidal, bridge-intact copper geometry with a novel chloride ligand. Combining results from these and other CuZnSOD crystal structures, we offer the outlines of a structure-based cyclic mechanism.

Using a corrected molar extinction coefficient for yeast apo copper-zinc superoxide dismutase (CuZnSOD), we have confirmed that the metal binding properties of this protein in vitro differ greatly from those of the bovine and human CuZnSOD enzymes. Thus yeast apo CuZnSOD was found to bind only one Co2+ per protein dimer under the conditions in which the bovine and human CuZnSOD apoenzymes readily bind two per dimer. The spectroscopic properties characteristic of the two Cu2+ plus two Co2+ per dimer or four Cu2+ per dimer metal-substituted bovine apo CuZnSOD derivatives were obtained for the yeast apoprotein but by the addition of only half of the appropriate metals, i.e., one Cu2+ plus one Co2+ per dimer or two Cu2+ per dimer. This half-metallated yeast CuZnSOD has been characterized by UV-visible and EPR spectroscopy as well as by native polyacrylamide gel electrophoresis. We conclude that yeast apo CuZnSOD, unlike the bovine and human apoproteins, cannot be reconstituted fully with metal ions under the same conditions. Instead, only one subunit of the homodimer, the "normal" subunit, can be remetalled in a fashion reminiscent of the well-characterized bovine protein. The other "phantom" subunit is not competent to bind metals in this fashion. Furthermore, we have shown that CuZnSOD protein isolated from Saccharomyces cerevisiae that lacks the gene coding for the copper chaperone, Lys7p, contains only one metal ion, Zn2+, per protein dimer. The possibility that yeast CuZnSOD can exist in multiple conformational states may represent an increased propensity of the yeast protein to undergo changes that can occur in all CuZnSODs, and may have implications for amyotrophic lateral sclerosis.

The cDNAs encoding plantacyanin from spinach were isolated and characterized. In addition, four new cDNA sequences from Arabidopsis ESTs were identified that encode polypeptides resembling phytocyanins, plant-specific proteins constituting a distinct family of mononuclear blue copper proteins. One of them encodes plantacyanin from Arabidopsis, while three others, designated as uclacyanin 1, 2, and 3, encode protein precursors that are closely related to precursors of stellacyanins and a blue copper protein from pea pods. Comparative analyses with known phytocyanins allow further classification of these proteins into three distinct subfamilies designated as uclacyanins, stellacyanins, and plantacyanins. This specification is based on (1) their spectroscopic properties, (2) their glycosylation state, (3) the domain organization of their precursors, and (4) their copper-binding amino acids. The recombinant copper binding domain of Arabidopsis uclacyanin 1 was expressed, purified, and shown to bind a copper atom in a fashion known as "blue" or type 1. The mutant of cucumber stellacyanin in which the glutamine axial ligand was substituted by a methionine (Q99M) was purified and shown to possess spectroscopic properties similar to uclacyanin 1 rather than to plantacyanins. Its redox potential was determined by cyclic voltammetry to be +420 mV, a value that is significantly higher than that determined for the wild-type protein (+260 mV). The available structural data suggest that stellacyanins (and possibly other phytocyanins) might not be diffusible electron-transfer proteins participating in long-range electron-transfer processes. Conceivably, they are involved in redox reactions occurring during primary defense responses in plants and/or in lignin formation.

The electronic structures of the perturbed blue copper proteins stellacyanin (STC) and cucumber basic protein (CBP, also called plantacyanin, PNC) are defined relative to that of the well-understood “classic” site found in plastocyanin (PLC) by combining the results of low-temperature optical absorption, circular dichroism, and magnetic circular dichroism spectra with density functional calculations. Additionally, absorption and magnetic circular dichroism spectra of Alcaligenes denitrificans wild-type and M121Q azurin are presented and compared to PLC and STC, respectively. These studies show that the principal electronic structure changes in CBP/PNC, with respect to PLC, are a small shift of the ligand field transitions to higher energy and a rotation of the Cu dx2-y2 half-filled HOMO which increases the pseudo-σ and decreases the π interactions of the cysteine (Cys) sulfur with Cu dx2-y2 and, in addition, mixes some methionine (Met) sulfur character into the HOMO. The geometrical distortion responsible...

The cDNA encoding the 182 amino acid long precursor stellacyanin from Cucumis sativus was isolated and characterized. The protein precursor consists of four sequence domains: I, a 23 amino acid hydrophobic N-terminal signal peptide with features characteristic of secretory proteins; II, a 109 amino acid copper-binding domain; III, a 26 amino acid hydroxyproline- and serine-rich peptide characteristic of motifs found in the extension family, extracellular structural glycoproteins found in plant cell walls; and IV, a 22 amino acid hydrophobic extension. Maturation of the protein involves posttranslational processing of domains I and IV. The copper-binding domain (domain II), which shares high sequence identity with other stellacyanins, has been expressed without its carbohydrate attachment sites, refolded from the Escherichia coli inclusion bodies, purified, and characterized by electronic absorption, EPR, ESEEM, and RR spectroscopy. Its spectroscopic properties are nearly identical to those of stellacyanin from the Japanese lacquer tree Rhus vernicifera, the most extensively studied and best characterized stellacyanin, indicating that this domain folds correctly, even in the absence of its carbohydrate moiety. The presence of a hydroxyproline- and serine-rich domain III suggests that stellacyanin may have a function other than that of a diffusible electron transfer protein, conceivably participating in redox reactions localized at the plant cell wall, which are known to occur in response to wounding or infection of the plant.

We report identification and preliminary characterization of novel proteinaceous anticoagulants from two marine crustacea, Elthusa vulgaris and Phrixocephalus cincinnatus. We also propose naming them Occipodins in honor of the college where this undergraduate research has been initiated. The organisms were collected at 25-125 meters depth off the coast of Los Angeles. Both organisms are hematophagous arthropods that anchor onto their host species and induce the extravasation of host blood into their digestive organs. Female P. cincinnatus display host specificity infecting the eyes of flatfish by anchoring to the choroid membrane and subsequently developing rami, an elaborate dendritic network, that facilitates the ingestion of extravasated blood from retinal blood vessels (Figure 1). The described species E. vulgaris is an isopod that similarly parasitizes a variety of marine fish by anchoring to the blood-rich gill filaments of their hosts (Figure 2). The accumulation of blood and attenuation of coagulation responses visually observed in the copepod trunk prompted us to initiate the identification of the anticoagulant factors in both hematophagous marine species. A crude cellular extract was prepared by homogenizing 10 specimens with a mortar and pestle frozen in liquid nitrogen resulting in a fine powder. The homogenate was resuspended in 15ml of 50mM Hepes buffer, pH7.4, containing 150mM NaCl and 3mM CaCl2 and mixed on a rotary shaker for 20min at room temperature. The resulting tissue suspension was centrifuged at 15,000xg 15 min and the supernatant was filtered through a 0.2 μm syringe filter. 10μl aliquots of extracts were used for all anticoagulant activity tests using FACT plasma for aPTT and PT assays on a Stago STart 4 hemostasis analyzer (Table 1). The extracts from both parasites were found to have exclusive anticoagulation activity on the intrinsic pathway (APTT assay) but no prolongation of coagulation time was observed in PT assays. Several biochemical tests were employed to further characterize the occipodins. First, size exclusion tests were performed using series of Millipore centrifugal filter units ranging from 10 to 100kD molecular weight cutoff. The size of the occipodin from P. cincinnatus was determined to be larger than 100kD while the anticoagulant isolated from Elthusa was estimated to be ~50kD. In order to identify whether these large macromolecules require a folded structure for activity we employed heat denaturation tests at 96°C for 15min. The P. cincinnatus occipodin showed substantial loss of anticoagulant activity following heat denaturation while E. vulgaris retained some residual anticoagulant activity, indicating the presence of non-proteinaceous, heat-resistant components (Table 1). A preliminary purification procedure of the anticoagulant isolated from Elthusa was established using a DEAE anion exchange chromatography. The crude tissue extract was diluted two fold with 50mM Hepes buffer, pH7.4 and applied on a 22ml column packed with DEAE-Sephacel (GE Healthcare) anion exchange matrix equilibrated with 50mM HEPES buffer, pH 7.4, containing 75mM NaCl. To elute occipodins, a step gradient ranging from 150 to 500mM NaCl (in the same HEPES buffer) was applied, after an extensive washing step with 120ml equilibration buffer. The anticoagulant activity was detected in fractions eluted between 125mM and 500mM NaCl with main pick centered at fractions eluted with buffer containing 150mM NaCl (Table 2) Identification of the site of inhibitory action of occipodins on the intrinsic coagulation pathway is currently in progress. In addition, further experiments will be targeted towards purification of occipodins and identification of their partial amino acid sequences. This sequence information will be used for cloning of cDNAs encoding these proteins. Disclosures No relevant conflicts of interest to declare.

Copper Proteins with Type 1 Sites is a general review that focuses on single-domain proteins that bind ‘blue’ or ‘type 1’ copper. Larger, multidomain proteins that contain type 1 copper in addition to other types of copper centers are not discussed at any length in this article. Blue copper proteins are so named because in solution they are a brilliant blue/azure color when the copper ion is in its Cu(II) oxidation state. The bright blue color comes from a charge transfer (CT) between Cu(II) and the sulfur (thiolate) of a ligating cysteine residue. Because of this intense color, type 1 copper proteins were among the first to be isolated because they could be tracked easily during purification processes. This, together with their unique spectroscopic properties that have no parallel in small-molecule copper complexes, has made them the subject of intense study over the last 35 years. This article focuses on three main aspects of type 1 copper proteins: (1) their occurrence, distribution, and classification based on analyses of genomic and expressed sequence tag data; (2) their three-dimensional structures as determined by the well-established tools of single-crystal X-ray diffraction and nuclear magnetic resonance (NMR); and (3) their electronic, spectroscopic, and electron-transfer properties. Keywords: type 1 copper; blue copper; X-ray crystallography; entatic state; electron paramagnetic resonance; resonance Raman; EXAFS/XAS; electron transfer; cupredoxins; phytocyanins

Determining the composition of aggregated superoxide dismutase 1 (SOD1) species associated with amyotrophic lateral sclerosis (ALS), especially with respect to co-aggregated proteins and post-translational modifications, could identify cellular or biochemical factors involved in the formation of these aggregates and explain their apparent neurotoxicity. The results of mass spectrometric and shotgun-proteomic analyses of SOD1-containing aggregates isolated from spinal cords of symptomatic transgenic ALS mice using two different isolation strategies are presented, including 1) resistance to detergent extraction and 2) size exclusion-coupled anti-SOD1 immunoaffinity chromatography. Forty-eight spinal cords from three different ALS-SOD1 mutant mice were analyzed, namely G93A, G37R, and the unnatural double mutant H46R/H48Q. The analysis consistently revealed that the most abundant proteins recovered from aggregate species were full-length unmodified SOD1 polypeptides. Although aggregates from some spinal cord samples contained trace levels of highly abundant proteins, such as vimentin and neurofilament-3, no proteins were consistently found to co-purify with mutant SOD1 in stoichiometric quantities. The results demonstrate that the principal protein in the high molecular mass aggregates whose appearance correlates with symptoms of the disease is the unmodified, full-length SOD1 polypeptide.

The thermodynamics of zinc binding to metal-free (apo) human and bovine copper-zinc superoxide dismutases (SOD1) were measured using isothermal titration calorimetry. The apparent thermodynamics of zinc binding to the apoproteins were favorable (Ka108 M-1), with an observed stoichiometry of one zinc per homodimer. The change in heat capacity for the one-zinc binding event was large and negative (approximately -650 cal mol-1 K-1), suggestive of significant structural changes to the protein upon zinc binding. We further characterized the one-zinc derivative by circular dichroism and determined that this derivative had nearly the same secondary structure as the two-zinc derivative and that both are structurally distinct from the metal-free protein. In addition, we monitored the effect of zinc binding on hydrogen-deuterium exchange and accessibility of histidyl residues to modification by diethyl pyrocarbonate and observed that more than 50% protection was afforded by the binding of one zinc in both assays. Differential scanning calorimetry on the human SOD1 zinc derivatives also showed increased thermostability of the protein due to zinc binding. Further, the melting transitions observed for the one-zinc derivative closely resembled those of the two-zinc derivative. Finally, we observed that the quaternary structure of the protein is stabilized upon binding of one and two zinc ions in analytical ultracentrifugation experiments. Combined, these results suggest communication between the two monomers of SOD1 such that the binding of one zinc ion per homodimer has a more profound effect on the homodimeric protein structure than the binding of subsequent metal ions. The relevance of these findings to amyotrophic lateral sclerosis is discussed.

Detailed electronic and geometric structural descriptions of the blue copper sites in wild-type (WT) stellacyanin and its Q99M and Q99L axial mutants have been obtained using a combination of XAS, resonance Raman, MCD, EPR, and DFT calculations. The results show that the origin of the short Cu-S(Cys) bond in blue copper proteins is the weakened axial interaction, which leads to a shorter (based on EXAFS results) and more covalent (based on S K-edge XAS) Cu-S bond. XAS pre-edge energies show that the effective nuclear charge on the copper increases going from O(Gln) to S(Met) to no axial (Leu) ligand, indicating that the weakened axial ligand is not fully compensated for by the increased donation from the thiolate. This is further supported by EPR results. MCD data show that the decreased axial interaction leads to an increase in the equatorial ligand field, indicating that the site acquires a more trigonally distorted tetrahedral structure. These geometric and electronic structural changes, which result from weakening the bonding interaction of the axial ligand, allow the site to maintain efficient electron transfer (high H(DA) and low reorganization energy), while modulating the redox potential of the site to the biologically relevant range. These spectroscopic studies are complemented by DFT calculations to obtain insight into the factors that allow stellacyanin to maintain a trigonally distorted tetrahedral structure with a relatively strong axial Cu(II)-oxygen bond.

The relative stabilities and structural properties of a representative set of 20 ALS-mutant Cu,Zn-superoxide dismutase apoproteins were examined by using differential scanning calorimetry and hydrogen-deuterium (H/D) exchange followed by MS. Contrary to recent reports from other laboratories, we found that ALS-mutant apoproteins are not universally destabilized by the disease-causing mutations. For example, several of the apoproteins with substitutions at or near the metal binding region (MBR) (MBR mutants) exhibited melting temperatures ( T m ) in the range 51.6°C to 56.2°C, i.e., similar to or higher than that of the WT apoprotein ( T m = 52.5°C). The apoproteins with substitutions remote from the MBR (WT-like mutants) showed a wide range of T m s, 40.0°C to 52.4°C. The H/D exchange properties of the mutants were also wide-ranging: the MBR mutant apoproteins exhibited H/D exchange kinetics similar to the WT apoprotein, as did some of the more stable WT-like mutant apoproteins, whereas the less stable apoproteins exhibited significantly less protection from H/D exchange than the WT apoprotein. Most striking were the three mutant apoproteins, D101N, E100K, and N139K, which have apparently normal metallation properties, and differ little from the WT apoprotein in either thermal stability or H/D exchange kinetics. Thus, the ALS mutant Cu,Zn-superoxide dismutase apoproteins do not all share reduced global stability, and additional properties must be identified and understood to explain the toxicity of all of the mutant proteins.

Publisher Summary This chapter introduces the blue copper-binding (BCB) domain-containing proteins based on the analysis of the genomic and expressed sequence tag (EST) sequence data, and presents the classification system. This classification is based on their ability to bind copper and the specific features of their domain organization. Members of the first three classes harbor single or multiple type 1, blue copper-binding sites, while members of the fourth class do not appear to bind copper. Some analysis of codon usage for conserved amino acids involved in copper binding will be used to trace the evolutionary history of the blue copper-binding (BCB) domains within a single genorne. The chapter also discusses the structural and physical characteristics of each kind of blue copper-binding (BCB) domain protein. The large number of blue copper-binding (BCB) domain proteins in plants may be explained by the phenomenon of genome duplication, believed to occur widely in the plant kingdom, as well as by different lateral gene transfers The blue copper-binding (BCB) domain-containing proteins evolved by gene duplication and fusion with other structural modules, resulting in diverse subcellular localization and the ability to carry out complex reactions that often differ from that of the ancestral protein. They are also modified by extensive amino acid substitutions and insertions.

Mutations in copper-zinc superoxide dismutase (CuZnSOD) cause 25% of familial amyotrophic lateral sclerosis (FALS) cases. This paper examines one such mutant, H46R, which has no superoxide dismutase activity yet presumably retains the gain-of-function activity that leads to disease. We demonstrate that Cu(2+) does not bind to the copper-specific catalytic site of H46R CuZnSOD and that Cu(2+) competes with other metals for the zinc binding site. Most importantly, Cu(2+) was found to bind strongly to a surface residue near the dimer interface of H46R CuZnSOD. Cysteine was identified as the new binding site on the basis of multiple criteria including UV-vis spectroscopy, RR spectroscopy, and chemical derivatization. Cysteine 111 was pinpointed as the position of the reactive ligand by tryptic digestion of the modified protein and by mutational analysis. This solvent-exposed residue may play a role in the toxicity of this and other FALS CuZnSOD mutations. Furthermore, we propose that the two cysteine 111 residues, found on opposing subunits of the same dimeric enzyme, may provide a docking location for initial metal insertion during biosynthesis of wild-type CuZnSOD in vivo.

We have investigated factors that influence the properties of the zinc binding site in yeast copper-zinc superoxide dismutase (CuZnSOD). The properties of yeast CuZnSOD are essentially invariant from pH 5 to pH 9. However, below this pH range there is a change in the nature of the zinc binding site which can be interpreted as either (1) a change in metal binding affinity from strong to weak, (2) the expulsion of the metal bound at this site, or (3) a transition from a normal distorted tetrahedral ligand orientation to a more symmetric arrangement of ligands. This change is strongly reminiscent of a similar pH-induced transition seen for the bovine protein and, based on the data presented herein, is proposed to be a property that is conserved among CuZnSODs. The transition demonstrated for the yeast protein is not only sensitive to the pH of the buffering solution but also to the occupancy and redox status of the adjacent copper binding site. Furthermore, we have investigated the effect of single site mutations on the pH- and redox-sensitivity of Co2+ binding at the zinc site. Each of the mutants H46R, H48Q, H63A, H63E, H80C, G85R, and D83H is capable of binding Co2+ to a zinc site with a distorted tetrahedral geometry similar to that of wild-type. However, they do so only if Cu+ is bound at the copper site or if the pH in raised to near physiological levels, indicating that the change at the zinc binding site seen in the wild-type is conserved in the mutants, albeit with an altered pK a. The mutants H71C and D83A did not bind Co2+ in a wild-type-like fashion under any of the conditions tested. This study reveals that the zinc binding site is exquisitely sensitive to changes in the protein environment. Since three of the mutant yeast proteins investigated here contain mutations analogous to those that cause ALS (amyotrophic lateral sclerosis) in humans, this finding implicates improper metal binding as a mechanism by which CuZnSOD mutants exert their toxic gain of function.

Copper-zinc superoxide dismutase (CuZnSOD) acquires its catalytic copper ion through interaction with another polypeptide termed the copper chaperone for SOD. Here, we combine X-ray crystallographic and analytical ultracentrifugation methods to characterize rigorously both truncated and full-length forms of apo-LYS7, the yeast copper chaperone for SOD. The 1.55 A crystal structure of LYS7 domain 2 alone (L7D2) was determined by multiple-isomorphous replacement (MIR) methods. The monomeric structure reveals an eight-stranded Greek key beta-barrel similar to that found in yeast CuZnSOD, but it is substantially elongated at one end where the loop regions of the beta-barrel come together to bind a calcium ion. In agreement with the crystal structure, sedimentation velocity experiments indicate that L7D2 is monomeric in solution under all conditions and concentrations that were tested. In contrast, sedimentation velocity and sedimentation equilibrium experiments show that full-length apo-LYS7 exists in a monomer-dimer equilibrium under nonreducing conditions. This equilibrium is shifted toward the dimer by approximately 1 order of magnitude in the presence of phosphate anion. Although the basis for the specificity of the LYS7-SOD interaction as well as the exact mechanism of copper insertion into SOD is unknown, it has been suggested that a monomer of LYS7 and a monomer of SOD may associate to form a heterodimer via L7D2. The data presented here, however, taken together with previously published crystallographic and analytical gel filtration data on full-length LYS7, suggest an alternative model wherein a dimer of LYS7 interacts with a dimer of yeast CuZnSOD. The advantages of the dimer-dimer model over the heterodimer model are enumerated.

The X-ray crystal structure of a human copper/zinc superoxide dismutase mutant (G37R CuZnSOD) found in some patients with the inherited form of Lou Gehrig's disease (FALS) has been determined to 1.9 angstroms resolution. The two SOD subunits have distinct environments in the crystal and are different in structure at their copper binding sites. One subunit (subunit[intact]) shows a four-coordinate ligand geometry of the copper ion, whereas the other subunit (subunit[broken]) shows a three-coordinate geometry of the copper ion. Also, subunit(intact) displays higher atomic displacement parameters for backbone atoms ((B) = 30 +/- 10 angstroms2) than subunit(broken) ((B) = 24 +/- 11 angstroms2). This structure is the first CuZnSOD to show large differences between the two subunits. Factors that may contribute to these differences are discussed and a possible link of a looser structure to FALS is suggested.

Stellacyanins are blue (type I) copper glycoproteins that differ from other members of the cupredoxin family in their spectroscopic and electron transfer properties. Until now, stellacyanins have eluded structure determination. Here we report the three-dimensional crystal structure of the 109 amino acid, non-glycosylated copper binding domain of recombinant cucumber stellacyanin refined to 1.6 A resolution. The crystallographic R-value for all 18,488 reflections (sigma > 0) between 50-1.6 A is 0.195. The overall fold is organized in two beta-sheets, both with four beta-stands. Two alpha-helices are found in loop regions between beta-strands. The beta-sheets form a beta-sandwich similar to those found in other cupredoxins, but some features differ from proteins such as plastocyanin and azurin in that the beta-barrel is more flattened, there is an extra N-terminal alpha-helix, and the copper binding site is much more solvent accessible. The presence of a disulfide bond at the copper binding end of the protein confirms that cucumber stellacyanin has a phytocyanin-like fold. The ligands to copper are two histidines, one cysteine, and one glutamine, the latter replacing the methionine typically found in mononuclear blue copper proteins. The Cu-Gln bond is one of the shortest axial ligand bond distances observed to date in structurally characterized type I copper proteins. The characteristic spectroscopic properties and electron transfer reactivity of stellacyanin, which differ significantly from those of other well-characterized cupredoxins, can be explained by its more exposed copper site, its distinctive amino acid ligand composition, and its nearly tetrahedral ligand geometry. Surface features on the cucumber stellacyanin molecule that could be involved in interactions with putative redox partners are discussed.

A series of mutant human and yeast copper-zinc superoxide dismutases has been prepared, with mutations corresponding to those found in familial amyotrophic lateral sclerosis (ALS; also known as Lou Gehrig's disease). These proteins have been characterized with respect to their metal-binding characteristics and their redox reactivities. Replacement of Zn2+ ion in the zinc sites of several of these proteins with either Cu2+ or Co2+ gave metal-substituted derivatives with spectroscopic properties different from those of the analogous derivative of the wild-type proteins, indicating that the geometries of binding of these metal ions to the zinc site were affected by the mutations. Several of the ALS-associated mutant copper-zinc superoxide dismutases were also found to be reduced by ascorbate at significantly greater rate than the wild-type proteins. We conclude that similar alterations in the properties of the zinc binding site can be caused by mutations scattered throughout the protein structure. This finding may help to explain what is perhaps the most perplexing question in copper-zinc superoxide dismutase-associated familial ALS-i.e., how such a diverse set of mutations can result in the same gain of function that causes the disease.

Cu-thionein isolated from cucumber roots was used for reconstitution of plantacyanin from cucumber. The rate of the copper transfer from Cu-thionein to apoplantacyanin was found to depend on pH, ionic strength and concentrations of the proteins. The rate of reconstitution with Cu-thionein was 10-times higher than with copper ions. No intermediate was observed during reconstitution with Cu-thionein. The incubation of oxidized holoplantacyanin with Cu-thionein or apothionein brings about the reduction of plantacyanin copper. This process, however, was found to be slow as compared to the rate of copper transfer from Cu-thionein to apoplantacyanin. Cytochrome oxidase from heart mitochondria was detected to possess some plantacyanin oxidase activity with the turnover number 5 min-1. The activity of the enzyme towards plantacyanin as well as with cytochrome c as a substrate was established to be lipid and ionic strength-dependent, and it was inhibited by CN- and N3-. Lineweaver-Burk plots show that the inhibitory effect of ionic strength on plantacyanin oxidase activity is connected with changes of Michaelis constant rather than of the maximal rate. Plantacyanin which is known to be very resistant towards many cationic, anionic and nonionic detergents, becomes, as well as cytochrome c, autooxidable in the presence of cardiolipin.

PS2 particles prepared from chloroplasts of three plant species were shown to contain the basic blue copper protein, plantacyanin, which may be extracted from the particles by concentrated saline solutions containing Triton X-100. Antibodies to plantacyanin were found to inhibit the photosynthetic oxygen evolution performed by the particles. Thus, evidences were obtained for participation of this protein in the oxygen-evolving activity of PS2 particles.

Absorbance, CD and MCD spectra of plantacyanins from spinach leaves and cucumber peelings were compared, and the effects of high pH and the reduction and the removal of copper in these spectra were considered. Using the approach of Hennessey and Johnson (Hennessey, J.P., Jr. and Johnson, W.C., Jr. (1981) Biochemistry 20, 1085–1094) the secondary structure parameters of the proteins were determined. The secondary structure consists mainly of α- and 310-helix, antiparallel β-sheet and random structure, although different types of β-turn also contribute to some extent. Secondary structure parameters were found to be sensitive to the redox state and the presence of copper as well as pH. Differences in the secondary structure of two plantacyanins were also noted. It was established that the copper of plantacyanins, besides having its characteristics bands in the visible spectrum also contributes to a certain extent to the UV spectrum at 250 nm and to the CD spectrum of the ‘aromatic’ region. These UV bands seem to belong to the copper-sulphur bond. MCD spectra reveal that the tryptophan cntent in cucumber plantacyanin was twice as high as in spinach plantacyanin. Antibodies to spinach and cucumber plantacyanins were obtained, and it was shown that no cross-reactivity between spinach antibodies and cucumber protein, or spinach protein and cucumber antibodies occurs. The reduction or the removal of copper does not change the antigenic properties of plantacyanins.

High-resolution 1H-NMR studies of spinach plantacyanin in its oxidized, reduced and apo-forms revealed that two histidines, one tryptophan and at least one methionine are very close to copper. These amino acids seem to be considered as possible ligands of copper in the protein. Spinach plantacyanin, as well as the cucumber protein, has the hydrophobic core around its copper.

The 300-MHz proton NMR spectra of oxidized, reduced and apo-forms of plantacyanin were studied. The data obtained show that one of two histidines is far from copper whereas the other is a ligand of the metal. Ligands of copper are also two methionines and, possibly, tryptophan. Although the surrounding of copper in plastocyanin consists of two sulfur and two nitrogen atoms, only histidine and methionine are invariant ligand amino acids of the metal in these two copper proteins from plants.