Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography

With the recent advances in serial crystallography methods at both synchrotron and X-ray free electron laser sources, more details of intermediate or transient states of the catalytic reactions are being revealed structurally. These structural studies of reaction dynamics drive the need for on-line in crystallo spectroscopy methods to complement the crystallography experiment. The recent applications of combined spectroscopy and crystallography methods enable on-line determination of in crystallo reaction kinetics and structures of catalytic intermediates, sample integrity, and radiation-induced sample modifications, if any, as well as heterogeneity of crystals from different preparations or sample batches. This review describes different modes of spectroscopy that are combined with the crystallography experiment at both synchrotron and X-ray free-electron laser facilities, and the complementary information that each method can provide to facilitate the structural study of enzyme catalysis and protein dynamics.     

High-resolution structure of the photosynthetic Mn4Ca catalyst from X-ray spectroscopy

The application of high-resolution X-ray spectroscopy methods to study the photosynthetic water oxidizing complex, which contains a unique hetero-nuclear catalytic Mn4Ca cluster, is described. Issues of X-ray damage, especially at the metal sites in the Mn4Ca cluster, are discussed. The structure of the Mn4Ca catalyst at high resolution, which has so far eluded attempts of determination by X-ray diffraction, X-ray absorption fine structure (EXAFS) and other spectroscopic techniques, has been addressed using polarized EXAFS techniques applied to oriented photosystem II (PSII) membrane preparations and PSII single crystals. A review of how the resolution of traditional EXAFS techniques can be improved, using methods such as range-extended EXAFS, is presented, and the changes that occur in the structure of the cluster as it advances through the catalytic cycle are described. X-ray absorption and emission techniques (XANES and Kbeta emission) have been used earlier to determine the oxidation states of the Mn4Ca cluster, and in this report we review the use of X-ray resonant Raman spectroscopy to understand the electronic structure of the Mn4Ca cluster as it cycles through the intermediate S-states.     

Correlating EPR and X-ray structural analysis of arsenite-inhibited forms of aldehyde oxidoreductase

Two arsenite-inhibited forms of each of the aldehyde oxidoreductases from Desulfovibrio gigas and Desulfovibrio desulfuricans have been studied by X-ray crystallography and electron paramagnetic resonance (EPR) spectroscopy. The molybdenum site of these enzymes shows a distorted square-pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. Arsenite addition to active as-prepared enzyme or to a reduced desulfo form yields two different species called A and B, respectively, which show different Mo(V) EPR signals. Both EPR signals show strong hyperfine and quadrupolar couplings with an arsenic nucleus, which suggests that arsenic interacts with molybdenum through an equatorial ligand. X-ray data of single crystals prepared from EPR-active samples show in both inhibited forms that the arsenic atom interacts with the molybdenum ion through an oxygen atom at the catalytic labile site and that the sulfido ligand is no longer present. EPR and X-ray data indicate that the main difference between both species is an equatorial ligand to molybdenum which was determined to be an oxo ligand in species A and a hydroxyl/water ligand in species B. The conclusion that the sulfido ligand is not essential to determine the EPR properties in both Mo–As complexes is achieved through EPR measurements on a substantial number of randomly oriented chemically reduced crystals immediately followed by X-ray studies on one of those crystals. EPR saturation studies show that the electron transfer pathway, which is essential for catalysis, is not modified upon inhibition. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

X-ray spectroscopy and imaging of selenium in living systems

Background

Selenium is an essential element with a rich and varied chemistry in living organisms. It plays a variety of important roles ranging from being essential in enzymes that are critical for redox homeostasis to acting as a deterrent for herbivory in hyperaccumulating plants. Despite its importance there are many open questions, especially related to its chemistry in situ within living organisms.

Rapid X-ray Photoreduction of Dimetal-Oxygen Cofactors in Ribonucleotide Reductase

Prototypic dinuclear metal cofactors with varying metallation constitute a class of O₂-activating catalysts in numerous enzymes such as ribonucleotide reductase. Reliable structures are required to unravel the reaction mechanisms. However, protein crystallography data may be compromised by x-ray photoreduction (XRP). We studied XPR of Fe(III)Fe(III) and Mn(III)Fe(III) sites in the R2 subunit of Chlamydia trachomatis ribonucleotide reductase using x-ray absorption spectroscopy. Rapid and biphasic x-ray photoreduction kinetics at 20 and 80 K for both cofactor types suggested sequential formation of (III,II) and (II,II) species and similar redox potentials of iron and manganese sites. Comparing with typical x-ray doses in crystallography implies that (II,II) states are reached in <1 s in such studies. First-sphere metal coordination and metal-metal distances differed after chemical reduction at room temperature and after XPR at cryogenic temperatures, as corroborated by model structures from density functional theory calculations. The inter-metal distances in the XPR-induced (II,II) states, however, are similar to R2 crystal structures. Therefore, crystal data of initially oxidized R2-type proteins mostly contain photoreduced (II,II) cofactors, which deviate from the native structures functional in O₂ activation, explaining observed variable metal ligation motifs. This situation may be remedied by novel femtosecond free electron-laser protein crystallography techniques.     

Oxidation state changes of the Mn<Subscript>4</Subscript>Ca cluster in Photosystem II

A detailed electronic structure of the Mn₄Ca cluster is required before two key questions for understanding the mechanism of photosynthetic water oxidation can be addressed. They are whether all four oxidizing equivalents necessary to oxidize water to O₂ accumulate on the four Mn ions of the oxygen-evolving complex, or do some ligand-centered oxidations take place before the formation and release of O₂ during the S₃ → [S₄] → S₀ transition, and what are the oxidation state assignments for the Mn during S-state advancement. X-ray absorption and emission spectroscopy of Mn, including the newly introduced resonant inelastic X-ray scattering spectroscopy have been used to address these questions. The present state of understanding of the electronic structure and oxidation state changes of the Mn₄Ca cluster in all the S-states, particularly in the S₂ to S₃ transition, derived from these techniques is described in this review.     

X-ray crystallography of chemical compounds

AimsAccurate knowledge of molecular structure is a prerequisite for rational drug design. This review examines the role of X-ray crystallography in providing the required structural information and advances in the field of X-ray crystallography that enhance or expand its role.Main methodsX-ray crystallography of new drugs candidates and intermediates can provide valuable information of new syntheses and parameters for quantitative structure activity relationships (QSAR).Key findingsCrystallographic studies play a vital role in many disciplines including materials science, chemistry, pharmacology, and molecular biology. X-ray crystallography is the most comprehensive technique available to determine molecular structure. A requirement for the high accuracy of crystallographic structures is that a ‘good crystal’ must be found, and this is often the rate-limiting step. In the past three decades developments in detectors, increases in computer power, and powerful graphics capabilities have contributed to a dramatic increase in the number of materials characterized by X-ray crystallography. More recently the advent of high-throughput crystallization techniques has enhanced our ability to produce that one good crystal required for crystallographic analysis.SignificanceContinuing advances in all phases of a crystallographic study have expanded the ranges of samples which can be analyzes by X-ray crystallography to include larger molecules, smaller or weakly diffracting crystals, and twinned crystals.     

Methods development for diffraction and spectroscopy studies of metalloenzymes at X-ray free-electron lasers

X-ray free-electron lasers (XFELs) open up new possibilities for X-ray crystallographic and spectroscopic studies of radiation-sensitive biological samples under close to physiological conditions. To facilitate these new X-ray sources, tailored experimental methods and data-processing protocols have to be developed. The highly radiation-sensitive photosystem II (PSII) protein complex is a prime target for XFEL experiments aiming to study the mechanism of light-induced water oxidation taking place at a Mn cluster in this complex. We developed a set of tools for the study of PSII at XFELs, including a new liquid jet based on electrofocusing, an energy dispersive von Hamos X-ray emission spectrometer for the hard X-ray range and a high-throughput soft X-ray spectrometer based on a reflection zone plate. While our immediate focus is on PSII, the methods we describe here are applicable to a wide range of metalloenzymes. These experimental developments were complemented by a new software suite, cctbx.xfel. This software suite allows for near-real-time monitoring of the experimental parameters and detector signals and the detailed analysis of the diffraction and spectroscopy data collected by us at the Linac Coherent Light Source, taking into account the specific characteristics of data measured at an XFEL.     

The "prismane" protein resolved: X-ray structure at 1.7 Å and multiple spectroscopy of two novel 4Fe clusters

The three-dimensional structure of the native "putative prismane" protein from Desulfovibrio vulgaris (Hildenborough) has been solved by X-ray crystallography to a resolution of 1.72?Å. The molecule does not contain a [6Fe-6S] prismane cluster, but rather two 4Fe clusters some 12?Å apart and situated close to the interfaces formed by the three domains of the protein. Cluster 1 is a conventional [4Fe-4S] cubane bound, however, near the N-terminus by an unusual, sequential arrangement of four cysteine residues (Cys 3, 6, 15, 21). Cluster 2 is a novel 4Fe structure with two μ₂-sulfido bridges, two μ₂-oxo bridges, and a partially occupied, unidentified μ₂ bridge X. The protein ligands of cluster 2 are widely scattered through the second half of the sequence and include three cysteine residues (Cys 312, 434, 459), one persulfido-cysteine (Cys 406), two glutamates (Glu 268, 494), and one histidine (His 244). With this unusual mixture of bridging and external type of ligands, cluster 2 is named the "hybrid" cluster, and its asymmetric, open structure suggests that it could be the site of a catalytic activity. X-ray absorption spectroscopy at the Fe K-edge is readily interpretable in terms of the crystallographic model when allowance is made for volume contraction at 10?K; no Fe··Fe distances beyond 3.1?Å could be identified. EPR, Mössbauer and MCD spectroscopy have been used to define the oxidation states and the magnetism of the clusters in relation to the crystallographic structure. Reduced cluster 1 is a [4Fe-4S]¹⁺ cubane with S?=?3/2; it is the first biological example of a "spin-admixed" iron-sulfur cluster. The hybrid cluster 2 has four oxidation states from (formally) all Fe^III to three Fe^II plus one Fe^III. The four iron ions are exchange coupled resulting in the system spins S?=?0, 9/2, 0 (and 4), 1/2, respectively, for the four redox states. Resonance Raman spectroscopy suggests that the bridging ligand X which could not be identified unambiguously in the crystal structure is a solvent-exchangeable oxygen.     

Reductive thiocyanolysis of tetraoxorhenate (VII): Synthesis, crystal structure, catalytic oxidation and kinetic studies of (PPh4)2[Re(NCS)6] and (PPh4)2[ReO(NCS)5]

Thiocyanate ions reduce perrhenate in aqueous acidic solution, and on addition of a suitable countercation (PPh₄Cl) afford (PPh₄)₂[Re(NCS)₆] (1) and (PPh₄)₂[ReO(NCS)₅] (2), which have been confirmed by X-ray crystallography. The kinetics of the above reaction has been studied. Both the complexes exhibit efficient and highly selective catalytic epoxidation ability in the presence of NaHCO₃ as a co-catalyst and competent catalytic properties in the selective oxidation of alcohols to the corresponding aldehydes or ketones in the presence of pyrazole as an additive and sulfides to sulfoxides and sulfones. H₂O₂ was used as the terminal oxidant in all the above-mentioned oxidation reactions.     

Unusual lithium coordinated platinum and rhodium hydride dimers

Two unusual lithium coordinated binuclear platinum- and rhodium-hydride complexes [M(dippe)(H)]₂·LiHBEt₃ were synthesized and characterized by NMR spectroscopy and X-ray crystallography. Not only does the lithium ion interact with the metal hydrides, but also with the B-H bond of the borohydride.     

X-ray Absorption Spectroscopy and Magnetism of Synthetic Greigite and Greigite Magnetosomes in Magnetotactic Bacteria

Scanning transmission X-ray microscopy at the Fe 2p (L_2,3), O1s, C1s, and S2p edges was used to study greigite magnetosomes and other cellular content of a magnetotactic bacterium known as a multicellular magnetotactic prokaryote (MMP). X-ray absorption spectrum (XAS) and X-ray magnetic circular dichroism (XMCD) spectra of greigite (Fe₃S₄) nanoparticles, synthesized via a hydrothermal method, were measured. Although XAS of the synthetic greigite nanoparticles and biotic magnetosome crystals in MMPs are slightly different due to partial oxidation of the MMP greigite, the XMCD spectra of the two materials are in good agreement. The Fe 2p XAS and XMCD spectra of Fe₃S₄ are quite different from those of its oxygen analog, magnetite (Fe₃O₄), suggesting Fe₃S₄ has a different electronic and magnetic structure than Fe₃O₄ despite having the same crystal structure. Sulfate and sulfide species were also identified in MMPs, both of which are likely involved in sulfur metabolism.     

Dynamic and structural properties of glucose oxidase enzyme

The catalytic oxidation of β-D-glucose by the enzyme glucose oxidase involves a redox change of the flavin coenzyme. The structure and the dynamics of the two extreme glucose oxidase forms were studied by using infrared absorption spectroscopy of the amide I′ band, tryptophan fluorescence quenching and hydrogen isotopic exchange. The conversion of FAD to FADH₂ does not change the amount of α-helix present in the protein outer shell, but reorganises a fraction of random coil to β-sheet structure. The dynamics of the protein interior vary with the redox states of the flavin without affecting the motions of the structural elements near the protein surface. From the structure of glucose oxidase given by X-ray crystallography, these results suggest that the dynamics of the interface between the two monomers are involved in the catalytic mechanism. Received: 27 December 1996 / Accepted: 18 July 1997     

Synthesis, X-ray structures and properties of the first tris-dioximate cobalt clathrochelates with nonequivalent chelate ribbed fragments

One-pot macrocyclization and reduction of the kinetically inert nonmacrocyclic cobalt(III) bis-α-benzyldioximate and dimethylglyoximate with BF₃·O(C₂H₅)₂ and metallic silver followed by cycloaddition of the corresponding α-dioxime to the generated insitu macrocyclic cobalt(II) bis-dioximates afforded the cobalt(II) clathrochelates with nonequivalent α-dioximate fragments. The complexes obtained were characterized using elemental analysis, MALDI-TOF mass spectrometry, IR, UV-Vis, ¹H, ¹³C{¹H} and ¹⁹F NMR spectroscopies, magnetochemistry, EPR, and X-ray crystallography. The coordination polyhedra of an encapsulated in a three-dimensional macrobicyclic ligand cavity cobalt(II) ion have a distorted trigonal prismatic geometry. The displacement of a caged metal ion from the centers of these polyhedra is caused mainly by the Jahn-Teller effect. Magnetochemical data for cobalt(II) clathrochelates obtained characterize them as the low-spin complexes in the temperature range of 2-400 K. The cyclic voltammograms of the synthesized clathrochelates contain the one-electron oxidation and reduction waves. The increase of the electron-donating properties of the ribbed substituents causes the negative shift of these waves. A comparative analysis of the reduction and oxidation potentials allowed to assign these processes to the cobalt-centered reduction and oxidation. The “electrochemical gap” values for clathrochelates studied are very small and characteristic of the complexes with the redox processes localized on the molecular orbitals which are close in energy.     

In situ X-ray absorption spectroelectrochemical study of hydroxocobalamin

 An in situ X-ray absorption spectroscopy (XAS) spectroelectrochemical study of aquocobalamin (system B_12a-B_12r-B_12s) has been carried out in aqueous solutions buffered at different pH values. To the best of our knowledge, this is the first structural study of aquocobalamin at room temperature under controlled oxidation conditions. Most of the previous work was in fact performed using frozen samples chemically treated to produce the species. The spectroelectrochemical approach offers several advantages: (1) the reduction products may be studied without poisoning the system with chemical reductive reagents and (2) any possible variation of the oxidation state owing to the electrons produced by the incident beam is avoided as the electrode, under potentiostatic control, acts as a scavenger. The spectroelectrochemical approach, together with more careful data analysis, has led to an improved interpretation of the XAS data. These conditions were not met in previous works where the oxidation state was not controlled and multiple scattering contributions were not taken into account. The general shape of the XAS spectra of the different species is not greatly affected by pH. A signature for the base-off square-planar coordination has been evidenced for the Co(II) compound at basic pH. A new signature for Co(I), indicating square-planar coordination, has been identified on the experimental spectra and simulated in theoretical X-ray absorption near-edge structure (XANES) studies. The flexibility of the electrochemical approach, that permits to unambiguously establish the formal oxidation state, has led to very reliable values for energy shift and peak intensity variations. The experimental XANES and extended X-ray absorption fine structure (EXAFS) spectra with a very good signal-to-noise ratio have been processed using the GNXAS package that takes into account multiple scattering contributions. EXAFS and XANES independent analysis result in the same structural model. The reduction from Co(III) to Co(II) produces the most significant structural changes: the cobalt coordination number decreases from six to five, and the edge position shifts by 2.4±0.3 eV. In addition, the XANES spectra are strongly modified. The reduction from Co(II) to Co(I) produces mainly electronic effects with no apparent change of the coordination number. A discussion of the limits and potentialities of EXAFS in this type of study has also been included. Received: 26 July 1999 / Accepted: 22 October 1999     

Biological X-ray absorption spectroscopy (BioXAS): a valuable tool for the study of trace elements in the life sciences

Using X-ray absorption spectroscopy (XAS) the binding modes (type and number of ligands, distances and geometry) and oxidation states of metals and other trace elements in crystalline as well as non-crystalline samples can be revealed. The method may be applied to biological systems as a 'stand-alone' technique, but it is particularly powerful when used alongside other X-ray and spectroscopic techniques and computational approaches. In this review, we highlight how biological XAS is being used in concert with crystallography, spectroscopy and computational chemistry to study metalloproteins in crystals, and report recent applications on relatively rare trace elements utilised by living organisms and metals involved in neurodegenerative diseases.     

Metal complexes of cyclic hydroxamates. Synthesis and crystal structures of 3-hydroxy-2-methyl-3H-quinazolin-4-one (ChaH) and of its Fe(III), Co(II), Ni(II), Cu(II) and Zn(II) complexes

The attempted acetylation of anthranilic hydroxamic acid (2-aminobenzohydroxamic acid) as a possible dual inhibitor of the catalytic sites in prostaglandin-H-synthase (PGHS) gave the cyclic hydroxamic acid 3-hydroxy-2-methyl-3H-quinazolin-4-one (ChaH) which was characterised by spectroscopy and X-ray crystallography. The length of the hydroxamic acid C-N bond, 1.3998(17) Å, in ChaH is longer than normal (∼1.33 Å) indicative of reduced delocalisation of the nitrogen lone pair of electrons into the hydroxamic acid π system. This is confirmed by the appearance of the ν(CO) band at a considerably higher wavenumber in the IR spectrum than normal. The complexes Fe(Cha)₂(Cl)(H₂O)·⁷/₂H₂O, Co(Cha)₂(EtOH)₂, Ni(Cha)₂(EtOH)₂, Cu(Cha)(H₂O)(Cl) and Zn(Cha)₂(H₂O), have been synthesised and their structures determined by X-ray crystallography. The X-ray data confirmed coordination by Cha^- through the carbonyl and deprotonated hydroxamate oxygen in all cases. The M-O (hydroxamate) bonds are shorter than the M-O (carbonyl) bonds by between 0.0930 Å for the Co(II) complex and 0.0448 Å for the Ni(II) complex. The geometries of all complexes conform to the coordination requirements of the particular metal ion involved. Speciation studies for ChaH and its complexes with Ni(II) and Zn(II) were carried out using pH-metric methods. The results show that ChaH is much more acidic than related acyclic hydroxamic acids and that its metal complexes are correspondingly less stable.     

Structure of the Mn<Subscript>4</Subscript>–Ca cluster as derived from X-ray diffraction

The catalytic centre for light-induced water oxidation in photosystem II (PSII) is a multinuclear metal cluster containing four manganese and one calcium cations. Knowing the structure of this biological catalyst is of utmost importance for unravelling the mechanism of water oxidation in photosynthesis. In this review we describe the current state of the X-ray structure determination at 3.0 A resolution of the water oxidation complex (WOC) of PSII. The arrangement of metal cations in the cluster, their coordination and protein surroundings are discussed with regard to spectroscopic and mutagenesis studies. Limitations of the presently available structural data are pointed out and possible perspectives for the future are outlined, including the combination of X-ray diffraction and X-ray spectroscopy on single crystals.     

Structural isomers of the S2 state in photosystem II: do they exist at room temperature and are they important for function?

In nature, an oxo‐bridged Mn₄CaO₅ cluster embedded in photosystem II (PSII), a membrane‐bound multi‐subunit pigment protein complex, catalyzes the water oxidation reaction that is driven by light‐induced charge separations in the reaction center of PSII. The Mn₄CaO₅ cluster accumulates four oxidizing equivalents to enable the four‐electron four‐proton catalysis of two water molecules to one dioxygen molecule and cycles through five intermediate S‐states, S₀ – S₄ in the Kok cycle. One important question related to the catalytic mechanism of the oxygen‐evolving complex (OEC) that remains is, whether structural isomers are present in some of the intermediate S‐states and if such equilibria are essential for the mechanism of the O‐O bond formation. Here we compare results from electron paramagnetic resonance (EPR) and X‐ray absorption spectroscopy (XAS) obtained at cryogenic temperatures for the S₂ state of PSII with structural data collected of the S₁, S₂ and S₃ states by serial crystallography at neutral pH (～6.5) using an X‐ray free electron laser at room temperature. While the cryogenic data show the presence of at least two structural forms of the S₂ state, the room temperature crystallography data can be well‐described by just one S₂ structure. We discuss the deviating results and outline experimental strategies for clarifying this mechanistically important question.