Julien J. H. Cotelesage

Metalloprotein active site structure determination: synergy between X-ray absorption spectroscopy and X-ray crystallography.

Structures of metalloprotein active sites derived from X-ray crystallography frequently contain chemical anomalies such as unexpected atomic geometries or elongated bond-lengths. Such anomalies are expected from the known errors inherent in macromolecular crystallography (ca. 0.1-0.2Å) and from the lack of appropriate restraints for metal sites which are often without precedent in the small molecule structure literature. Here we review the potential of X-ray absorption spectroscopy to provide information and perspective which could aid in improving the accuracy of metalloprotein crystal structure solutions. We also review the potential problem areas in analysis of the extended X-ray absorption fine structure (EXAFS) and discuss the use of density functional theory as another possible source of geometrical restraints for crystal structure analysis of metalloprotein active sites.

Structural basis of enzymatic benzene ring reduction

In chemical synthesis, the widely used Birch reduction of aromatic compounds to cyclic dienes requires alkali metals in ammonia as extremely low-potential electron donors. An analogous reaction is catalyzed by benzoyl-coenzyme A reductases (BCRs) that have a key role in the globally important bacterial degradation of aromatic compounds at anoxic sites. Because of the lack of structural information, the catalytic mechanism of enzymatic benzene ring reduction remained obscure. Here, we present the structural characterization of a dearomatizing BCR containing an unprecedented tungsten cofactor that transfers electrons to the benzene ring in an aprotic cavity. Substrate binding induces proton transfer from the bulk solvent to the active site by expelling a Zn(2+) that is crucial for active site encapsulation. Our results shed light on the structural basis of an electron transfer process at the negative redox potential limit in biology. They open the door for biological or biomimetic alternatives to a basic chemical synthetic tool.

The solution structure of the copper clioquinol complex

Clioquinol (5-chloro-7-iodo-8-hydroxyquinoline) recently has shown promising results in the treatment of Alzheimers disease and in cancer therapy, both of which also are thought to be due to clioquinols ability as a lipophilic copper chelator. Previously, clioquinol was used as an anti-fungal and anti-protozoal drug that was responsible for an epidemic of subacute myelo-optic neuropathy (SMON) in Japan during the 1960s, probably a myeloneuropathy arising from a clioquinol-induced copper deficiency. Previous X-ray absorption spectroscopy of solutions of copper chelates of clioquinol suggested unusual coordination chemistry. Here we use a combination of electron paramagnetic, UV-visible and X-ray absorption spectroscopies to provide clarification of the chelation chemistry between clioquinol and copper. We find that the solution structures for the copper complexes formed with stoichiometric and excess clioquinol are conventional 8-hydroxyquinolate chelates. Thus, the promise of clioquinol in new treatments for Alzheimers disease and in cancer therapy is not likely to be due to any novel chelation chemistry, but rather due to other factors including the high lipophilicity of the free ligand and chelate complexes.

X-ray Absorption Spectroscopy of a Quantitatively Mo(V) Dimethyl Sulfoxide Reductase Species

Molybdenum K-edge X-ray absorption spectroscopy (XAS) has been used to probe the structure of a Mo(V) species that has been suggested to be a catalytic intermediate in the reaction of dimethyl sulfoxide (DMSO) reductase with the alternative substrate trimethylamine N-oxide (Bennet et al. Eur. J. Biochem. 1994, 255, 321-331; Cobb et al. J. Biol. Chem. 2005, 280, 11007-11017; Mtei, et al. J. Am. Chem. Soc. 2011, 133, 9672-9774). The oxidized Mo(VI) state of DMSO reductase has previously been structurally characterized as being six coordinate, with four sulfurs from pyranopterin dithiolene molybdenum cofactors, a terminal oxygen ligand, and an additional oxygen coordination from a serine residue. We find the most plausible structure for the Mo(V) active site is a five-coordinate species with four sulfur donors from the two pyranopterin dithiolene ligands, with an average Mo-S bond-length of 2.35 Å, plus a single oxygen donor at 1.99 Å, very likely from an Mo-OH ligand. Our results thus suggest that the oxygen of the serine residue has dissociated from the metal ion, suggesting hitherto unsuspected flexibility of the active site, and calling into question whether this putative intermediate is catalytically relevant. The relevance to previous Mo(V) electron paramagnetic resonance and other spectroscopic studies on DMSO reductase is discussed. XAS of an extensively studied Mo(V) form of Rhodobacter sphaeroides DMSO reductase (the high-g split species) shows that previously suggested structures for the active site are likely incorrect.

Binding of Copper and Cisplatin to Atox1 Is Mediated by Glutathione through the Formation of Metal–Sulfur Clusters

Copper is an essential nutrient required for many biological processes involved in primary metabolism, but free copper is toxic due to its ability to catalyze formation of free radicals. To prevent toxic effects, in the cell copper is bound to proteins and low molecular weight compounds, such as glutathione, at all times. The widely used chemotherapy agent cisplatin is known to bind to copper-transporting proteins, including copper chaperone Atox1. Cisplatin interactions with Atox1 and other copper transporters are linked to cancer resistance to platinum-based chemotherapy. Here we analyze the binding of copper and cisplatin to Atox1 in the presence of glutathione under redox conditions that mimic intracellular environment. We show that copper(I) and glutathione form large polymers with a molecular mass of approximately 8 kDa, which can transfer copper to Atox1. Cisplatin also can form polymers with glutathione, albeit at a slower rate. Analysis of simultaneous binding of copper and cisplatin to Atox1 under physiological conditions shows that both metals are bound to the protein through copper-sulfur-platinum bridges.

Insights into the Nature of the Chemical Bonding in Thiophene-2-thiol from X-ray Absorption Spectroscopy.

Thiophenes are the simplest aromatic sulfur-containing compounds; they are widespread in fossil fuels and a variety of natural products, and they have vital roles in determining characteristic aromas that are important in food chemistry. We used a combination of sulfur K-edge X-ray absorption spectroscopy and density functional theory to investigate the chemical bonding in the novel sulfur-containing heterocycle thiophene-2-thiol. We show that solutions of thiophene-2-thiol contain significant quantities of the thione tautomer, which may be the energetically preferred 5H-thiophene-2-thione or the more accessible 3H-thiophene-2-thione.

Photochemically Generated Thiyl Free Radicals Observed by X-ray Absorption Spectroscopy

Sulfur-based thiyl radicals are known to be involved in a wide range of chemical and biological processes, but they are often highly reactive, which makes them difficult to observe directly. We report herein X-ray absorption spectra and analysis that support the direct observation of two different thiyl species generated photochemically by X-ray irradiation. The thiyl radical sulfur K-edge X-ray absorption spectra of both species are characterized by a uniquely low energy transition at about 2465 eV, which occurs at a lower energy than any previously observed feature at the sulfur K-edge and corresponds to a 1s→3p transition to the singly occupied molecular orbital of the free radical. Our results constitute the first observation of substantial levels of thiyl radicals generated by X-ray irradiation and detected by sulfur K-edge X-ray absorption spectroscopy.

Chemical Sensitivity of the Sulfur K-Edge X-ray Absorption Spectra of Organic Disulfides

Sulfur K-edge X-ray absorption spectroscopy increasingly is used as a tool to provide speciation information about the sulfur chemical form in complex samples, with applications ranging from fossil fuels to soil science to health research. As part of an ongoing program of systematic investigations of the factors that affect the variability of sulfur K near-edge spectra, we have examined the X-ray absorption spectra of a series of organic symmetric disulfide compounds. We have used polarized sulfur K-edge spectra of single crystals of dibenzyl disulfide to confirm the assignments of the major transitions in the spectrum as 1s → (S-S)σ* and 1s → (S-C)σ*. We also have examined the solution spectra of an extended series of disulfides and show that the spectra change in a systematic and predictable manner with the nature of the external group.

The active site structure and catalytic mechanism of arsenite oxidase

Arsenite oxidase is thought to be an ancient enzyme, originating before the divergence of the Archaea and the Bacteria. We have investigated the nature of the molybdenum active site of the arsenite oxidase from the Alphaproteobacterium Rhizobium sp. str. NT-26 using a combination of X-ray absorption spectroscopy and computational chemistry. Our analysis indicates an oxidized Mo(VI) active site with a structure that is far from equilibrium. We propose that this is an entatic state imposed by the protein on the active site through relative orientation of the two molybdopterin cofactors, in a variant of the Rây-Dutt twist of classical coordination chemistry, which we call the pterin twist hypothesis. We discuss the implications of this hypothesis for other putatively ancient molybdopterin-based enzymes.

Biological iron-sulfur storage in a thioferrate-protein nanoparticle.

Iron–sulfur clusters are ubiquitous in biology and function in electron transfer and catalysis. They are assembled from iron and cysteine sulfur on protein scaffolds. Iron is typically stored as iron oxyhydroxide, ferrihydrite, encapsulated in 12 nm shells of ferritin, which buffers cellular iron availability. Here we have characterized IssA, a protein that stores iron and sulfur as thioferrate, an inorganic anionic polymer previously unknown in biology. IssA forms nanoparticles reaching 300 nm in diameter and is the largest natural metalloprotein complex known. It is a member of a widely distributed protein family that includes nitrogenase maturation factors, NifB and NifX. IssA nanoparticles are visible by electron microscopy as electron-dense bodies in the cytoplasm. Purified nanoparticles appear to be generated from 20 nm units containing ∼6,400 Fe atoms and ∼170 IssA monomers. In support of roles in both iron–sulfur storage and cluster biosynthesis, IssA reconstitutes the [4Fe-4S] cluster in ferredoxin in vitro.