X-Ray Absorption Spectroscopy

A database overview of metal-coordination distances in metalloproteins

Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of biological processes. For this reason, their experimental characterization is crucial to obtain improved knowledge of their structure and biological functions. The three-dimensional structure represents highly relevant information since it provides insight into the interaction between the metal ion(s) and the protein fold. Such interactions determine the chemical reactivity of the bound metal. The available PDB structures can contain errors due to experimental factors such as poor resolution and radiation damage. A lack of use of distance restraints during the refinement and validation process also impacts the structure quality. Here, the aim was to obtain a thorough overview of the distribution of the distances between metal ions and their donor atoms through the statistical analysis of a data set based on more than 115 000 metal-binding sites in proteins. This analysis not only produced reference data that can be used by experimentalists to support the structure-determination process, for example as refinement restraints, but also resulted in an improved insight into how protein coordination occurs for different metals and the nature of their binding interactions. In particular, the features of carboxylate coordination were inspected, which is the only type of interaction that is commonly present for nearly all metals.

Palladium K-edge X-ray Absorption Spectroscopy Studies on Controlled Ligand Systems

X-ray absorption spectroscopy (XAS) is widely used across the life and physical sciences to identify the electronic properties and structure surrounding a specific element. XAS is less often used for the characterization of organometallic compounds, especially for sensitive and highly reactive species. In this study, we used solid- and solution-phase XAS to compare a series of 25 palladium complexes in controlled ligand environments. The compounds include palladium centers in the formal I, II, III, and IV oxidation states, supported by tridentate and tetradentate macrocyclic ligands, with different halide and methyl ligand combinations. The Pd K-edge energies increased not only upon oxidizing the metal center but also upon increasing the denticity of the ligand framework, substituting sigma-donating methyl groups with chlorides, and increasing the charge of the overall metal complex by replacing charged ligands with neutral ligands. These trends were then applied to characterize compounds whose oxidation states were otherwise unconfirmed.

Color-controlled nonstoichiometric spinel-type cobalt gallate nanopigments prepared by supercritical hydrothermal synthesis

Spinel-type inorganic pigments with intensive color and chemical/thermal stability are showing extensive applications that could be further broadened by color manipulation and improvement of the material properties through nanosizing. In this study, we report the supercritical hydrothermal synthesis of nonstoichiometric spinel-type cobalt gallate nanoparticles (Co-Ga NPs) with controlled color. Without the conventional calcination procedure, NPs with greenish-blue, blue, and yellowish-green colors were synthesized from precursor solutions at pH 7, 9, and 11, respectively, with a low Co/Ga molar ratio of 0.25. X-ray diffraction, scanning/transmission electron microscopy, and inductively coupled plasma-atomic emission spectroscopy methods suggest that the products were spinel-type cobalt gallate NPs with high crystallinity and a nonstoichiometric composition. Based on an X-ray absorption fine structure investigation, the prepared nonstoichiometric Co-Ga NPs were found to have different cationic configurations from stoichiometric CoGa2O4 produced by a solid-state reaction during calcination. Meanwhile, the degrees of distortions at tetrahedral and octahedral sites in the NPs were evaluated by Raman spectroscopy. In particular, nonstoichiometric Co-Ga NPs with a blue color were prepared without calcination for the first time and were found to have lower tetrahedral cobalt occupancy but comparable octahedral cobalt occupancy and larger polyhedral distortions at tetrahedral sites when compared to calcined CoGa2O4. We also discuss strategies that could realize Co-Ga NPs with a more brilliant blue color using the present technique based on an investigation of the growth process.

Demonstration of Near Edge X-ray Absorption Fine Structure Spectroscopy of Transition Metals Using Xe/He Double Stream Gas Puff Target Soft X-ray Source

A near 1-keV photons from the Xe/He plasma produced by the interaction of laser beam with a double stream gas puff target were employed for studies of L absorption edges of period 4 transitional metals with atomic number Z from 26 to 30. The dual-channel, compact NEXAFS system was employed for the acquisition of the absorption spectra. L_1-3 absorption edges of the samples were identified in transmission mode using broadband emission from the Xe/He plasma to show the applicability of such source and measurement system to the NEXAFS studies of the transition metals, including magnetic materials.

Application of X-ray absorption and X-ray fluorescence techniques to the study of metallodrug action

X-ray absorption spectroscopy and X-ray fluorescence microscopy are two synchrotron-based techniques frequently deployed either individually or in tandem to investigate the fates of metallodrugs and their biotransformation products in physiologically relevant sample material. These X-ray methods confer advantages over other analytical techniques in that they are nondestructive and require minimal chemical or physical manipulation of the sample before analysis, conserving both chemical and spatial information of the element(s) under investigation. In this review, we present selected examples of the use of X-ray absorption spectroscopy and X-ray fluorescence microscopy in studies of metallodrug speciation and localisation in vivo, in cell spheroids and in intact tissues and organs, and offer recent highlights in the advances of these techniques as they pertain to research on metallodrug action.

Subcellular Localization of Copper-Cellular Bioimaging with Focus on Neurological Disorders

As an essential trace element, copper plays a pivotal role in physiological body functions. In fact, dysregulated copper homeostasis has been clearly linked to neurological disorders including Wilson and Alzheimer’s disease. Such neurodegenerative diseases are associated with progressive loss of neurons and thus impaired brain functions. However, the underlying mechanisms are not fully understood. Characterization of the element species and their subcellular localization is of great importance to uncover cellular mechanisms. Recent research activities focus on the question of how copper contributes to the pathological findings. Cellular bioimaging of copper is an essential key to accomplish this objective. Besides information on the spatial distribution and chemical properties of copper, other essential trace elements can be localized in parallel. Highly sensitive and high spatial resolution techniques such as LA-ICP-MS, TEM-EDS, S-XRF and NanoSIMS are required for elemental mapping on subcellular level. This review summarizes state-of-the-art techniques in the field of bioimaging. Their strengths and limitations will be discussed with particular focus on potential applications for the elucidation of copper-related diseases. Based on such investigations, further information on cellular processes and mechanisms can be derived under physiological and pathological conditions. Bioimaging studies might enable the clarification of the role of copper in the context of neurodegenerative diseases and provide an important basis to develop therapeutic strategies for reduction or even prevention of copper-related disorders and their pathological consequences.

Nucleobase carbonyl groups are poor Mg2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey

Precise knowledge of Mg²⁺ inner-sphere binding site properties is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, which represents the main source of Mg²⁺ binding sites, contains a substantial number of assignment issues that blur our understanding of the functions of these ions. Here, following a previous study devoted to Mg²⁺ binding to nucleobase nitrogens, we surveyed nucleic acid X-ray structures from the PDB with resolutions ≤2.9 Å to classify the Mg²⁺ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether, and phosphodiester oxygen atoms. From this classification, we derived a set of "prior-knowledge" nucleobase Mg²⁺ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg²⁺ binding sites are fewer than expected since many of those are associated with misidentified Na⁺ or K⁺ We also emphasize that binding of Na⁺ and K⁺ to nucleic acids is much more frequent than anticipated. Overall, we provide evidence derived from X-ray structures that nucleobases are poor inner-sphere binders for Mg²⁺ but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline Mg²⁺ stereochemistry is observed, alternative placement of Na⁺, K⁺, or Ca²⁺ must be considered. We also critically examine the use of lanthanides (Yb³⁺, Tb³⁺) as Mg²⁺ substitutes in crystallography experiments.

Intratumoral Visualization of Oxaliplatin within a Liposomal Formulation Using X-ray Fluorescence Spectrometry

Microsynchrotron radiation X-ray fluorescence spectrometry (μ-SR-XRF) is an X-ray procedure that utilizes synchrotron radiation as an excitation source. μ-SR-XRF is a rapid, nondestructive technique that allows mapping and quantification of metals and biologically important elements in cell or tissue samples. Generally, the intratumor distribution of nanocarrier-based therapeutics is assessed by tracing the distribution of a labeled nanocarrier within tumor tissue, rather than by tracing the encapsulated drug. Instead of targeting the delivery vehicle, we employed μ-SR-XRF to visualize the intratumoral microdistribution of oxaliplatin (l-OHP) encapsulated within PEGylated liposomes. Tumor-bearing mice were intravenously injected with either l-OHP-containing PEGylated liposomes (l-OHP liposomes) or free l-OHP. The intratumor distribution of l-OHP within tumor sections was determined by detecting the fluorescence of platinum atoms, which are the main elemental components of l-OHP. The l-OHP in the liposomal formulation was localized near the tumor vessels and accumulated in tumors at concentrations greater than those seen with the free form, which is consistent with the results of our previous study that focused on fluorescent labeling of PEGylated liposomes. In addition, repeated administration of l-OHP liposomes substantially enhanced the tumor accumulation and/or intratumor distribution of a subsequent dose of l-OHP liposomes, presumably via improvements in tumor vascular permeability, which is also consistent with our previous results. In conclusion, μ-SR-XRF imaging efficiently and directly traced the intratumor distribution of the active pharmaceutical ingredient l-OHP encapsulated in liposomes within tumor tissue. μ-SR-XRF imaging could be a powerful means for estimating tissue distribution and even predicting the pharmacological effect of nanocarrier-based anticancer metal compounds.

CheckMyMetal: a macromolecular metal-binding validation tool

Metals are essential in many biological processes, and metal ions are modeled in roughly 40% of the macromolecular structures in the Protein Data Bank (PDB). However, a significant fraction of these structures contain poorly modeled metal-binding sites. CheckMyMetal (CMM) is an easy-to-use metal-binding site validation server for macromolecules that is freely available at http://csgid.org/csgid/metal_sites. The CMM server can detect incorrect metal assignments as well as geometrical and other irregularities in the metal-binding sites. Guidelines for metal-site modeling and validation in macromolecules are illustrated by several practical examples grouped by the type of metal. These examples show CMM users (and crystallographers in general) problems they may encounter during the modeling of a specific metal ion.

Electronic State of Sodium trans-[Tetrachloridobis(1H-indazole)ruthenate(III)] (NKP-1339) in Tumor, Liver and Kidney Tissue of a SW480-bearing Mouse

Ruthenium complexes are promising candidates for anticancer agents, especially NKP-1339 (sodium trans-[tetrachloridobis(1H-indazole)ruthenate(III)]), which is on the edge to clinical applications. The anticancer mechanism seems to be tightly linked to the redox chemistry but despite progress in human clinical trials the in vivo Ru oxidation state and the coordination of Ru remains unclear. The Ru-based anticancer drug NKP-1339 was studied applying XANES (Cl K- and Ru L_2,3-edges) in tumor, kidney and liver tissue of a SW480 bearing mouse. Based on coordination charge and 3D XANES plots containing a series of model compounds as well as pre-edge analysis of the ligand Cl K-edge it is suggested that NKP-1339 remains in its +III oxidation state after 24 hours and at least one of the four chlorido ligands remain covalently bound to the Ru ion showing a biotransformation from Ru^IIIN₂Cl₄ to Ru^IIICl_x(N/O)_6−x (X = 1 or 2).