Characterization of “spectroscopically quiet” metals in biology

Penner‐Hahn, James E.

doi:10.1016/j.ccr.2004.03.011

Cited by 153 publications

(169 citation statements)

References 116 publications

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“…X-ray absorption near edge structure (XANES) and extended x-ray absorption fine structure (EXAFS) are metal-specific techniques that provide information about the average ligand environment of metals. These techniques are especially useful for investigating the structures of Zn 2þ and other d 10 metals that are silent in other spectroscopic methods (24). Large RNAs bind multiple metal ions, a situation that usually renders XANES and EXAFS uninformative, as XAS data report on an average metal environment.…”

Section: Xas Revealsmentioning

confidence: 99%

NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P

Koutmou

Casiano-Negroni

Getz

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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Functionally critical metals interact with RNA through complex coordination schemes that are currently difficult to visualize at the atomic level under solution conditions. Here, we report a new approach that combines NMR and XAS to resolve and characterize metal binding in the most highly conserved P4 helix of ribonuclease P (RNase P), the ribonucleoprotein that catalyzes the divalent metal ion-dependent maturation of the 5′ end of precursor tRNA. Extended X-ray absorption fine structure (EXAFS) spectroscopy reveals that the Zn 2þ bound to a P4 helix mimic is sixcoordinate, with an average Zn-O/N bond distance of 2.08 Å. The EXAFS data also show intense outer-shell scattering indicating that the zinc ion has inner-shell interactions with one or more RNA ligands. NMR Mn 2þ paramagnetic line broadening experiments reveal strong metal localization at residues corresponding to G378 and G379 in B. subtilis RNase P. A new "metal cocktail" chemical shift perturbation strategy involving titrations with CoðNH 3 Þ 3þ 6 , Zn 2þ , and CoðNH 3 Þ 3þ 6 ∕Zn 2þ confirm an inner-sphere metal interaction with residues G378 and G379. These studies present a unique picture of how metals coordinate to the putative RNase P active site in solution, and shed light on the environment of an essential metal ion in RNase P. Our experimental approach presents a general method for identifying and characterizing inner-sphere metal ion binding sites in RNA in solution.manganese | ribozyme | RNase P | X-ray absorption spectroscopy | zinc R NA molecules are large polyanions that associate with numerous divalent metal ions that stabilize their structure and promote catalysis. Identification of the RNA moieties involved in metal-binding and discerning the nature of these interactions is an important outstanding question in the field (1, 2). Whereas RNA-bound metals can be characterized at the atomic level in the solid-state by X-crystallography there are not yet techniques for characterizing the binding sites and coordination schemes for RNA-bound metals in solution. Techniques based on NMR, EPR, and Raman spectroscopy as well as nucleotide analog interference mapping (NAIM) and phosphorothioate substitution exist for identifying RNA residues involved in metal-binding; however the geometry of the bound metal and the nature of the coordination scheme cannot be resolved based on these experiments alone.RNase P is a metal-dependent ribozyme that catalyzes precursor tRNA (pre-tRNA) maturation by cleaving a specific phosphodiester bond (3). In RNase P, metal ions stabilize the folded RNase P RNA (PRNA) structure, enhance ligand affinity, and stabilize the transition state for cleavage (4); in vivo the metal requirement is fulfilled by Mg 2þ ions (5, 6). A majority of the ∼150 divalent metal ions associated with PRNA bind nonspecifically via electrostatic interactions whereas only a handful of ions form specific contacts with RNase P (5, 7). Discerning the position and structure of the few divalent ions that site-specifically interact with RNA is a majo...

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Section: Xas Revealsmentioning

confidence: 99%

NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P

Koutmou

Casiano-Negroni

Getz

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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“…It is specifically useful for studying metals that are otherwise spectroscopically silent; i.e., those that possess filled or empty d-shells and have no spectroscopic signature. [58] XAS is beneficial for the study of bioinorganic systems such as metal-and metalloid-containing drugs and enzymes since it is an extremely versatile and highly sensitive technique capable of providing information regarding metals in many physical states and chemical environments. [58][59][60] The technique can be applied to bulk or microprobe analyses of samples which include: solids, biological solutions, electrophoresis gels, and healthy or diseased mammalian cells and tissue.…”

Section: X-ray Absorption Spectroscopymentioning

confidence: 99%

“…[58] XAS is beneficial for the study of bioinorganic systems such as metal-and metalloid-containing drugs and enzymes since it is an extremely versatile and highly sensitive technique capable of providing information regarding metals in many physical states and chemical environments. [58][59][60] The technique can be applied to bulk or microprobe analyses of samples which include: solids, biological solutions, electrophoresis gels, and healthy or diseased mammalian cells and tissue. [58][59][60] XAS, in contrast to XRF spectroscopy, cannot feasibly be performed using a laboratory X-ray source.…”

Section: X-ray Absorption Spectroscopymentioning

confidence: 99%

“…[58][59][60] The technique can be applied to bulk or microprobe analyses of samples which include: solids, biological solutions, electrophoresis gels, and healthy or diseased mammalian cells and tissue. [58][59][60] XAS, in contrast to XRF spectroscopy, cannot feasibly be performed using a laboratory X-ray source. Instead the highly intense and tunable X-rays generated at a synchrotron are essential for XAS.…”

Section: X-ray Absorption Spectroscopymentioning

confidence: 99%

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Synchrotron Radiation Spectroscopic Techniques as Tools for the Medicinal Chemist: Microprobe X-Ray Fluorescence Imaging, X-Ray Absorption Spectroscopy, and Infrared Microspectroscopy

Dillon

2012

Aust. J. Chem.

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. (2012). Synchrotron radiation spectroscopic techniques as tools for the medicinal chemist: microprobe X-Ray fluorescence imaging, X-Ray absorption spectroscopy, and infrared microspectroscopy. Australian Journal of Chemistry: an international journal for chemical science, 65 (3), 204-217. Synchrotron radiation spectroscopic techniques as tools for the medicinal chemist: microprobe X-Ray fluorescence imaging, X-Ray absorption spectroscopy, and infrared microspectroscopy AbstractThis review updates the recent advances and applications of three prominent synchrotron radiation techniques, microprobe X-ray fluorescence spectroscopy/imaging, X-ray absorption spectroscopy, and infrared microspectroscopy, and highlights how these tools are useful to the medicinal chemist. A brief description of the principles of the techniques is given with emphasis on the advantages of using synchrotron radiation-based instrumentation rather than instruments using typical laboratory radiation sources. This review focuses on several recent applications of these techniques to solve inorganic medicinal chemistry problems, focusing on studies of cellular uptake, distribution, and biotransformation of established and potential therapeutic agents. The importance of using these synchrotron-based techniques to assist the development of, or validate the chemistry behind, drug design is discussed. AbstractThis review updates the recent advances and applications of three prominent synchrotron radiation techniques, microprobe X-ray fluorescent spectroscopy/imaging, X-ray absorption spectroscopy and infrared microspectroscopy, and highlights how these tools are useful to the medicinal chemist. A brief description of the principles of the techniques is given with emphasis on the advantages of using synchrotron radiation-based instrumentation rather than instruments using typical laboratory radiation sources. This review focuses on a number of recent applications of these techniques to solve inorganic medicinal chemistry problems, focusing on studies of cellular uptake, distribution and biotransformation of established and potential therapeutic agents. The importance of using these synchrotron-based techniques to assist the development, or validate the chemistry behind, drug design is discussed.3

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“…Detection is possible in dilute solution and metal ions that are classified as spectroscopically silent (like Na + , K + , Mg 2+ , or Ca 2+ , Cu + , and Zn 2+ ) are accessible [170].…”

Section: X-ray Absorption Spectroscopymentioning

confidence: 99%

Characterization of Metal Ion-Nucleic Acid Interactions in Solution

Pechlaner

Sigel

2011

Metal Ions in Life Sciences

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Metal ions are inextricably involved with nucleic acids due to their polyanionic nature. In order to understand the structure and function of RNAs and DNAs, one needs to have detailed pictures on the structural, thermodynamic, and kinetic properties of metal ion interactions with these biomacromolecules. In this review we first compile the physicochemical properties of metal ions found and used in combination with nucleic acids in solution. The main part then describes the various methods developed over the past decades to investigate metal ion binding by nucleic acids in solution. This includes for example hydrolytic and radical cleavage experiments, mutational approaches, as well as kinetic isotope effects. In addition, spectroscopic techniques like EPR, lanthanide(III) luminescence, IR and Raman as well as various NMR methods are summarized. Aside from gaining knowledge about the thermodynamic properties on the metal ion-nucleic acid interactions, especially NMR can be used to extract information on the kinetics of ligand exchange rates of the metal ions applied. The final section deals with the influence of anions, buffers, and the solvent permittivity on the binding equilibria between metal ions and nucleic acids. Little is known on some of these aspects, but it is clear that these three factors have a large influence on the interaction between metal ions and nucleic acids.

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Characterization of “spectroscopically quiet” metals in biology

Cited by 153 publications

References 116 publications

NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P

NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P

Synchrotron Radiation Spectroscopic Techniques as Tools for the Medicinal Chemist: Microprobe X-Ray Fluorescence Imaging, X-Ray Absorption Spectroscopy, and Infrared Microspectroscopy

Characterization of Metal Ion-Nucleic Acid Interactions in Solution

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