Metal Sites In Metalloproteins Research Articles

Parameterization of a Dioxygen Binding Metal Site Using the MCPB.py Program.

The MCPB.py program greatly facilitates force field parameterization for metal sites in metalloproteins and organometallic compounds. Herein we present an example of MCPB.py to the parameterization of the dioxygen binding metal site of peptidylglycine-alphahydroxylating monooxygenase (PHM), which contains a copper ion. In this example, we also extend the functionality of MCPB.py to support molecular dynamics (MD) simulations in GROMACS through a python script. Illustrative MD simulations were performed using GROMACS and the results were analyzed. Notes about the program were also provided in this chapter, to assist MCPB.py users for metal site parameterizations.

X‐Ray absorption spectroscopic studies on iron in soybean lipoxygenase: A model for mammalian lipoxygenases

AbstractX‐ray absorption spectroscopy studies are contributing both to the refinement of the geometry of metal sites already known from crystallographic studies and the elucidation of the coordination sphere in metal sites in metalloproteins where only limited information was available. Specific problems in the analysis of coordinating imidazoles can be overcome by applying multiple‐scattering simulations. The model for the lipoxygenase iron site derived from the EXAFS study, a coordination sphere predominated by imidazoles, may require some adjustment in view of the possibility of coordination by water, and has received independent confirmation from studies of amino acid sequence homologies and the interaction with catechols.The spectroscopy of lipoxygenase is not consistent with the presence of the organic cofactor, PQQ, nor with its coordination to iron, but would be consistent with the presence, but not the coordination to iron, of the carboxy‐hydroxy‐indoloquinone‐glutamic acid cofactor, CHIQG. From the observed amino acid sequence homologies it is concluded that plant lipoxygenases can be good models for the studies of mammalian lipoxygenases.

Strategies in the development of synthetic model compounds for dinuclear and polynuclear metal sites in metalloproteins

Many of the known metalloproteins and metalloenzymes contain more than one metal ion at the active site. The metal ions can be relatively close together (with a bridging ligand in between them), or separated over more than 5-6 Å. This paper will only deal with the first category. The ligand-bridged dinuclear or polynuclear centers can either be homopolyatomic (such as the copper dimers in hemocyanin [1] and the iron tetramers [2] in ferredoxin), or heteropolyatomic (such as the CuZn site in bovine syperoxide dismutase [3], the Fe and Mo-containing cofactor in nitrogenase [4], and the CuFe site in cytochrome c oxides [5]). In some cases, such as in the ironsulfur proteins, the polynuclear coordination entity can be extracted from the proteins, without decomposition [6]. In developing strategies for the synthesis of low-molecular weight analogs for these dinuclear and polynuclear metal sites, two approaches can be followed, i.e.: 1. Use of small ligands that are well known to form bridges between two (or more) metal ions. Examples are OH − (for Cu dimers) [7], S 2− (for ironsulfur clusters) [8] and deprotonated imidazole (for copper dimers) [9]. Under these circumstances dinuclear or polynuclear metal units can only be formed in certain cases, and generalisations are difficult to make. 2. Use of binucleating (or polynucleating) chelating ligands to hold two (or more) metal ions bound to the same ligand [10]. In addition small bridging ligands, such as OH −, may be present. These systems may or may not contain a ligand atom bridging two or more metal ions. Asymmetric binucleating chelating ligands can be designed to synthesize asymmetric dimers, which may even hold two different metal ions [11]. Steric constraints and/or intramolecular interactions ( e.g. hydrogen bonding) can be used to generate a certain coordination geometry, or to regulate metal–ligand distances [12]. The most successful results have been obtained so far, when method (b) was used. However, many clusters have also been prepared according to method (a). The present paper will mainly deal with nitrogen (amine, imidazole) and oxygen (phenolate, alcoholate) as ligand donor atoms in binucleating and polynucleating chelating ligands. Special attention will be given to ligand system accessible via relatively simple synthetic methods. The formation of the dinuclear and polynuclear coordination compounds, their molecular structures, and their chemical and spectroscopic properties will be discussed in detail for a few selected systems.

How much do we know about metal-metal interactions?

Abstract Clusters of metal ions are present in many metalloproteins and metalloenzymes, such as in several copper proteins, in hemocyanin, in hemerithrin, in ironsulphur proteins, in cytochrome c oxidase, etc. In all these cases the metal ions are interacting in such a way that the electronic structure of the cluster differs appreciably from the sum of the electronic structures of the individual metal ions. When it occurs we may say that the metal-metal interactions are operative. We will be interested in this round table to interactions between paramagnetic ions which are easily monitored through measurements which are sensitive to the magnetic properties of the cluster and to mixed valence interactions which occur when the same metal is present in two different oxidation states. The topics which will be covered will be the fundamental theory underlying the mechanism of exchange interactions which determine magnetic coupling in metal clusters, the strategy for the development of synthetic model compounds for binuclear and polynuclear metal sites in metalloproteins, a survey of experimental data on the interactions between metal ions separated by single atom and polyatomic bridges, including mixed valence interactions, exchange interactions on tetranuclear copper(II) complexes, and magnetic resonance spectra of exchange coupled systems. For the last topic the attention will be focussed on oligonuclear clusters, i.e. on systems involving 2, 3 and 4 similar or dissimilar metal ions. The EPR parameters of the cluster will be related to those of the individual metal ions in the assumption of substantial isotropic coupling and the theoretical expectations will be compared with experimental data. The role of anistropic and antisymmetric exchange on the EPR spectra of metal clusters will also be discussed. In a series of dinuclear complexes it will be shown how these terms, which are usually smaller than the isotropic term, may influence the g and D values and divertions, and how it is possible to correlate the exchange interactions involving one ion in the ground state and the other in the excited state with structural and electronic parameters. Finally a brief mention will be made of the NMR spectra of dinuclear metal complexes, showing how the proton isotropic shifts and longitudinal relaxation time are influenced by the presence of two metal ions.

Evidence for two types of binding sites in cadmium metallothionein determined by perturbed angular correlation of .gamma.-rays

Recent /sup 113/Cd NMR as well as ESR and magnetic susceptibility measurements on Co(II)-metallothionein strongly suggest the existence of a unique metal-thiolate cluster structure in this protein. However, additional knowledge on the details of molecular architecture of the seven metal-binding sites in metallothionein (approx.6-7 g-atoms/mol, usually Zn/sup 2 +/ and Cd/sup 2 +/) is required in order to establish a realistic model of the molecule and to understand its function. Since metallothionein is the only known protein in which cadmium is found naturally, perturbed angular correlation of gamma rays (PAC) employing /sup 111/Cd nuclei offers itself particularly for such a study. Analysis of PAC spectra using /sup 111/Cd has proven to be useful in the structural elucidation of specific metal sites in metalloproteins under both crystalline and noncrystalline conditions. We report here PAC measurements performed on fully and partially saturated /sup 111/Cd metallothionein.