Joachim Schnabl

Controlling ribozyme activity by metal ions

The observed rates of ribozyme cleavage reactions are strongly dependent on the nature of the metal ion present. Metal ions can thereby exhibit a stronger inhibiting or accelerating effect compared to Mg(2+), which is usually considered the natural cofactor. Alkaline, alkaline earth, transition, d(10), and other metal ions are applied either to gain a spectroscopic handle on the metal center, and/or to elucidate the catalytic mechanism. Here we shortly review some of the most recent publications on the influence of different metal ions on catalysis of the hammerhead, hepatitis delta virus, and group II intron ribozymes. Comparison of the observed cleavage rates of hammerhead ribozymes with the metal ion affinities of different ligands reveals that these rates correlate perfectly with the intrinsic phosphate affinities of the metal ions involved.

Binding of a Designed Anti‐Cancer Drug to the Central Cavity of an RNA Three‐Way Junction

Getting to the heart of it: Co-crystallization of an RNA three-way junction with a cylindrical di-iron(II)-based anti-cancer drug (green) results in π-stacking interactions between the cylinder and the central base pairs of the RNA structure. The shape, size, and cationic nature of the cylinder were found to be responsible for this perfect fit. Native gel electrophoresis studies confirmed stabilization of the RNA three-way junction by the iron(II) cylinder.

Probing the Metal-Ion-Binding Strength of the Hydroxyl Group

Introduction How Is the Extent of a Weak Interaction Best Quantified? Metal-Ion Complexes with Phosph(on)ate Groups as Primary Binding Sites Extent of the Hydroxyl−M2+ Interaction in Complexes of Hydroxymethylphosphonate Metal-Ion−Glycerol 1-Phosphate Systems: A Decreasing Solvent Polarity Favors Hydroxyl−M2+ Interactions Some Generalizations Regarding Phosph(on)ate Ligands with a Weakly Coordinating Second Site Metal-Ion Complexes with Carboxylate Groups as Primary Binding Sites Extent of Chelate Formation in Complexes of Hydroxyacetate and Related Ligands at I = 0.1 M Construction of the Reference Lines for Several M2+−Carboxylate Systems. Extent of Chelate Formation in Metal-Ion Complexes Formed with Hydroxy Carboxylates and Related Ligands Extent of Chelate Formation in Complexes of Hydroxyacetate-Type Ligands at I = 2 M Effect of Chelate-Ring Enlargement on the Hydroxyl−Metal-Ion Interaction Decreasing Solvent Polarity Favors the Hydroxyl−Metal-Ion Interaction in Complexes of Hydroxyacetate and Related O Ligands But Inhibits Thioether Interactions Metal-Ion Complexes with Amino Groups as Primary Binding Sites Estimation of Straight-Line Parameters for Complexes Formed with RCH2−NH2 Ligands Extent of Hydroxyl Group−Metal-Ion Binding in Complexes of 2-Aminoethanol and Related Ligands Comparison of the Metal-Ion-Binding Properties of 2-Aminoethanol and Triethanolamine Imidazole Residue as a Primary Binding Site in Ligands Containing also a Hydroxyl Group Pyridyl Nitrogen Is an Ideal Primary Metal-Ion-Binding Site for a Hydroxyl−Metal-Ion Interaction Isomeric Quantification of Metal-Ion Binding with Ligands Offering Two Hydroxyl Groups Effect of the Primary Binding Site on the Extent of the Hydroxyl−Metal-Ion Interaction Extent of Hydroxyl−Metal-Ion Interactions in Complexes Having a Bidentate Primary Binding Site Metal-Ion Complexes of Ligands with Two or More Hydroxyl Groups and at Least Four Binding Sites Complexes of the Alkaline EarthIons with Bistris and Some Related Buffers: Reduced Solvent Polarity Favors Metal-Ion−Hydroxyl Group Interactions Complexes of Several 3d and Related Metal Ions with Bistris and Derivatives Quest for Selectivity in Metal-Ion Coordination Involving Hydroxyl Groups General Conclusions

MINAS—a database of Metal Ions in Nucleic AcidS

Correctly folded into the respective native 3D structure, RNA and DNA are responsible for uncountable key functions in any viable organism. In order to exert their function, metal ion cofactors are closely involved in folding, structure formation and, e.g. in ribozymes, also the catalytic mechanism. The database MINAS, Metal Ions in Nucleic AcidS (http://www.minas.uzh.ch), compiles the detailed information on innersphere, outersphere and larger coordination environment of >70 000 metal ions of 36 elements found in >2000 structures of nucleic acids contained today in the PDB and NDB. MINAS is updated monthly with new structures and offers a multitude of search functions, e.g. the kind of metal ion, metal-ligand distance, innersphere and outersphere ligands defined by element or functional group, residue, experimental method, as well as PDB entry-related information. The results of each search can be saved individually for later use with so-called miniPDB files containing the respective metal ion together with the coordination environment within a 15 Å radius. MINAS thus offers a unique way to explore the coordination geometries and ligands of metal ions together with the respective binding pockets in nucleic acids.

The X-ray Structures of Six Octameric RNA Duplexes in the Presence of Different Di- and Trivalent Cations.

Due to the polyanionic nature of RNA, the principles of charge neutralization and electrostatic condensation require that cations help to overcome the repulsive forces in order for RNA to adopt a three-dimensional structure. A precise structural knowledge of RNA-metal ion interactions is crucial to understand the mechanism of metal ions in the catalytic or regulatory activity of RNA. We solved the crystal structure of an octameric RNA duplex in the presence of the di- and trivalent metal ions Ca2+, Mn2+, Co2+, Cu2+, Sr2+, and Tb3+. The detailed investigation reveals a unique innersphere interaction to uracil and extends the knowledge of the influence of metal ions for conformational changes in RNA structure. Furthermore, we could demonstrate that an accurate localization of the metal ions in the X-ray structures require the consideration of several crystallographic and geometrical parameters as well as the anomalous difference map.

Sodium and Potassium Ions in Proteins and Enzyme Catalysis

The group I alkali metal ions Na(+) and K(+) are ubiquitous components of biological fluids that surround biological macromolecules. They play important roles other than being nonspecific ionic buffering agents or mediators of solute exchange and transport. Molecular evolution and regulated high intracellular and extracellular M(+) concentrations led to incorporation of selective Na(+) and K(+) binding sites into enzymes to stabilize catalytic intermediates or to provide optimal positioning of substrates. The mechanism of M(+) activation, as derived from kinetic studies along with structural analysis, has led to the classification of cofactor-like (type I) or allosteric effector (type II) activated enzymes. In the type I mechanism substrate anchoring to the enzyme active site is mediated by M(+), often acting in tandem with a divalent cation like Mg(2+), Mn(2+) or Zn(2+). In the allosteric type II mechanism, M(+) binding enhances enzyme activity through conformational transitions triggered upon binding to a distant site. In this chapter, following the discussion of the coordination chemistry of Na(+) and K(+) ions and the structural features responsible for the metal binding site selectivity in M(+)-activated enzymes, well-defined examples of M(+)-activated enzymes are used to illustrate the structural basis for type I and type II activation by Na(+) and K(+).