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At least 19 recordsLinked to original sources

PubMed2004

COMe: the ontology of bioinorganic proteins.

BACKGROUND: Many characterised proteins contain metal ions, small organic molecules or modified residues. In contrast, the huge amount of data generated by genome projects consists exclusively of sequences with almost no annotation. One of the goals of the structural genomics initiative is to provide representative three-dimensional (3-D) structures for as many protein/domain folds as possible to allow successful homology modelling. However, important functional features such as metal co-ordination or a type of prosthetic group are not always conserved in homologous proteins. So far, the problem of correct annotation of bioinorganic proteins has been largely ignored by the bioinformatics community and information on bioinorganic centres obtained by methods other than crystallography or NMR is only available in literature databases. RESULTS: COMe (Co-Ordination of Metals) represents the ontology for bioinorganic and other small molecule centres in complex proteins. COMe consists of three types of entities: 'bioinorganic motif' (BIM), 'molecule' (MOL), and 'complex proteins' (PRX), with each entity being assigned a unique identifier. A BIM consists of at least one centre (metal atom, inorganic cluster, organic molecule) and two or more endogenous and/or exogenous ligands. BIMs are represented as one-dimensional (1-D) strings and 2-D diagrams. A MOL entity represents a 'small molecule' which, when in complex with one or more polypeptides, forms a functional protein. The PRX entities refer to the functional proteins as well as to separate protein domains and subunits. The complex proteins in COMe are subdivided into three categories: (i) metalloproteins, (ii) organic prosthetic group proteins and (iii) modified amino acid proteins. The data are currently stored in both XML format and a relational database and are available at http://www.ebi.ac.uk/come/. CONCLUSION: COMe provides the classification of proteins according to their 'bioinorganic' features and thus is orthogonal to other classification schemes, such as those based on sequence similarity, 3-D fold, enzyme activity, or biological process. The hierarchical organisation of the controlled vocabulary allows both for annotation and querying at different levels of granularity.

Binding Sites↗

PubMed2003

Bioinorganic chemistry in the postgenomic era.

Genome sequencing has revolutionized all fields of life sciences. Bioinorganic chemistry is certainly not immune to this influence, which is presenting unprecedented challenges. A new goal for bioinorganic chemistry is the investigation of the linkages between inorganic elements and genomic information. This requires new advancements andor the development of new expertise in fields such as bioinformatics and genetics but also provides a driving force to push forward the exploitation of traditional analytical techniques and spectroscopic tools. The "case study" of metal homeostasis in cells is discussed to provide a flavor of the current evolution of the field.

Base Sequence↗

PubMed2000

Bioinorganic motifs: towards functional classification of metalloproteins.

UNLABELLED: The habitat of bioinorganic motifs (BIMs) is at the interface of biological inorganic chemistry and bioinformatics. BIM is defined as a common structural feature shared by functionally related, but not necessarily homologous, proteins, and consisting of the metal atom(s) and first coordination shell ligands. BIMs appear to be suitable for classification of metal centres at any level, from groups of unrelated proteins with similar function to different functional states of the same protein, and for description of possible evolutionary relationships of metalloproteins. However, they have not attracted wide attention from the bioinformatics community. Although their presence is appreciated, they are difficult to predict-therefore the current 'high-throughput' initiatives are likely to miss or ignore them altogether. The protein sequence databases do not distinguish between proteins containing different prosthetic groups (unless they have different sequences) or between apo- and holoprotein. On the other hand, the protein structure databases include data on 'hetero compounds' of various origin but these data are often inconsistent. A number of specialized databases dealing with BIMs and attempts to classify them are reviewed. SUPPLEMENTARY INFORMATION: The additional bibliography and list of Internet resources on bioinorganic chemistry are available at http://www.ebi.ac.uk/ approximately kirill/biometal/

Amino Acid Motifs↗

PubMed1987

Bioinorganic chemistry. Inorganic chemistry in a perspective of biology, medicine and the environment.

A brief overview of recent developments in the area of bioinorganic chemistry is presented. After a description of the field and the relationships with other disciplines, a short presentation of the historical developments in the field are discussed. The main part of the paper deals with a discussion of the current highlights and the applications of bioinorganic principles in other fields. At the end an expectation is presented of future developments.

Animals↗

PubMed2004

Dehalogenation of chlorinated aromatic compounds using a hybrid bioinorganic catalyst on cells of Desulfovibrio desulfuricans.

A novel bioinorganic catalyst was obtained via reduction of Pd(II) to Pd0 on to the surface of cells of Desulfovibrio desulfuricans at the expense of H2. Palladised biomass, supplied with formate or H2 as an electron donor, catalysed the dehalogenation of 2-chlorophenol and polychlorinated biphenyls. In the example of 2,3,4,5-tetrachlorobiphenyl, the bioinorganic catalyst promoted a rate of chloride release of 9.33 +/- 0.17 nmol min(-1) mg (-1) and only approximately 5% of this value was obtained using chemically reduced or commercially available Pd0. In the case of 2,2',4,4',6,6'-hexachlorobiphenyl the rate was more than four orders of magnitude faster than the degradation reported using a sulfidogenic culture. Negligible chloride release occurred from any of the chloroaromatic compounds using biomass alone, or from palladised biomass challenged with hexane carrier solvent only. Analysis of the spent solution showed that in addition to catalysis of reductive dehalogenation the new material was able to remove very effectively the organic residua, with neither any PCB nor any breakdown products identifiable by GC/MS.

Biodegradation, Environmental↗

PubMed2001

Bioinorganic composites for enzyme electrodes.

Sparingly soluble redox salts were combined with a model enzyme, glucose oxidase, in a host matrix of a biopolymer chitosan to form bioinorganic composite films on the surface of glassy carbon electrodes. Four redox salts, each containing the Ru(NH3)6(3+) cation and a selected anion, such as Ru(CN)6(4-), Fe(CN)6(4-), Co(CN)6(3-) or IrCl6(3-), were studied. The composition and catalytic properties of such composite materials toward glucose oxidation were investigated by spectroscopic and electrochemical methods. The composite films provided an oxygen-independent electrical communication between the enzyme's redox centers and a glassy carbon surface at a potential as low as -0.10 V vs Ag/AgCl(3 M Cl-). The nature of the electrical communication is discussed in terms of redox mediation by the Ru(NH3)6(3+)-containing ion pairs formed inside the biocomposites. The kinetic significance of the mediator's charge is considered by postulating that neutral ion pairs are more efficient redox mediators of the enzymatic reaction than those negatively charged. The low operating potential of enzyme electrodes based on the bioinorganic composites allows for an interference-free determination of glucose. The design of the biocomposites is generic and can incorporate oxidoreductase enzymes other than glucose oxidase to provide a host of biosensors for biologically and environmentally important analytes.

Biosensing Techniques↗

PubMed2001

Evolution of bioinorganic motifs in P450-containing systems.

The choice of bioinorganic motifs by Nature results in a spectacular variety of active-site structures even within the same protein family. Here, we use the concept of the bioinorganic motif to discuss the function and evolution of P450-containing and other related systems. Apart from P450, these systems include a FAD flavoprotein or domain, a FMN domain, ferredoxins and cytochrome b(5). Analysis of available complete genomes can shed light on what an ancestral P450-containing system could be.

Amino Acid Motifs↗

PubMed2006

Metal-thiolate bonds in bioinorganic chemistry.

Metal-thiolate active sites play major roles in bioinorganic chemistry. The M--S(thiolate) bonds can be very covalent, and involve different orbital interactions. Spectroscopic features of these active sites (intense, low-energy charge transfer transitions) reflect the high covalency of the M--S(thiolate) bonds. The energy of the metal-thiolate bond is fairly insensitive to its ionic/covalent and pi/sigma nature as increasing M--S covalency reduces the charge distribution, hence the ionic term, and these contributions can compensate. Thus, trends observed in stability constants (i.e., the Irving-Williams series) mostly reflect the dominantly ionic contribution to bonding of the innocent ligand being replaced by the thiolate. Due to high effective nuclear charges of the Cu(II) and Fe(III) ions, the cupric- and ferric-thiolate bonds are very covalent, with the former having strong pi and the latter having more sigma character. For the blue copper site, the high pi covalency couples the metal ion into the protein for rapid directional long range electron transfer. For rubredoxins, because the redox active molecular orbital is pi in nature, electron transfer tends to be more localized in the vicinity of the active site. Although the energy of hydrogen bonding of the protein environment to the thiolate ligands tends to be fairly small, H-bonding can significantly affect the covalency of the metal-thiolate bond and contribute to redox tuning by the protein environment.

Chemistry, Bioinorganic↗

PubMed2006

Transition metal spin state energetics and noninnocent systems: challenges for DFT in the bioinorganic arena.

Although density functional theory (DFT) provides a generally good description of transition metal systems, we have identified several cases, involving Fe(III) porphyrins and related systems, where common functionals fail to correctly describe the energetics of the different low-lying spin states. The question of metal- versus ligand-centered oxidation in high-valent transition metal complexes is also a challenging one for DFT calculations, as I have tried to illustrate with examples from among porphyrin, corrole, biliverdine, and NO complexes. In a number of cases, I have compared results obtained with different exchange-correlation functionals; in addition, I have added a discussion on the relative performance of pure versus hybrid functionals. Finally, I have offered some thoughts on the role that traditional wavefunction-based ab initio methods, now essentially absent from the bioinorganic arena, might play in the future.

Chemistry, Bioinorganic↗

PubMed2002

Effect of pressure on electron transfer reactions in inorganic and bioinorganic chemistry.

Kinetic and thermodynamic studies involving the application of different high-pressure techniques, are very useful in gaining mechanistic information on the basis of volume changes that occur during inorganic and bioinorganic electron transfer reactions. The most fundamental type of electron transfer reaction concerns self-exchange reactions, for which the overall reaction volume is zero, and activation volumes can be measured and discussed. In the case of non-symmetrical electron transfer reactions, intra- and intermolecular processes can be studied and volume profiles can be constructed. Precursor complex formation can in some cases be recognized kinetically in such systems. Typical values of activation and reaction volumes are reviewed for various reversible and irreversible electron transfer reactions. Mechanistic conclusions reached on the basis of these parameters are presented. Volume profiles for electron transfer reactions enable a simplistic presentation of the reaction mechanism on the basis of intrinsic and solvational volume changes along the reaction coordinate.

Chemical Phenomena↗

PubMed2001

Invited award contribution for ACS Award in Inorganic Chemistry. Geometric and electronic structure contributions to function in bioinorganic chemistry: active sites in non-heme iron enzymes.

Spectroscopy has played a major role in the definition of structure/function correlations in bioinorganic chemistry. The importance of spectroscopy combined with electronic structure calculations is clearly demonstrated by the non-heme iron enzymes. Many members of this large class of enzymes activate dioxygen using a ferrous active site that has generally been difficult to study with most spectroscopic methods. A new spectroscopic methodology has been developed utilizing variable temperature, variable field magnetic circular dichroism, which enables one to obtain detailed insight into the geometric and electronic structure of the non-heme ferrous active site and probe its reaction mechanism on a molecular level. This spectroscopic methodology is presented and applied to a number of key mononuclear non-heme iron enzymes leading to a general mechanistic strategy for O2 activation. These studies are then extended to consider the new features present in the binuclear non-heme iron enzymes and applied to understand (1) the mechanism of the two electron/coupled proton transfer to dioxygen binding to a single iron center in hemerythrin and (2) structure/function correlations over the oxygen-activating enzymes stearoyl-ACP Delta9-desaturase, ribonucleotide reductase, and methane monooxygenase. Electronic structure/reactivity correlations for O2 activation by non-heme relative to heme iron enzymes will also be developed.

Animals↗

PubMed2000

Preparation and characterization of a new bioinorganic composite: collagen and hydroxyapatite.

Studies on biomineralization in bone have opened new arenas in the field of fabrication and engineering of bone-graft devices. A new bioinorganic composite was prepared by introducing processed collagenous matrices into the calcifying solutions at pH 7.8-8.0. The calcifying solutions were prepared by using a saturated dicalcium salt solution. Hydroxyapatite grew on the matrix over a period of 3-5 days in a specially designed crystallizing chamber. Changes in biochemical characters and biophysical parameters have given interesting insights into factors affecting and effecting initiation and progression of calcification on organic matrices.

Animals↗

PubMed2003

The bioinorganic chemistry of iron in oxygenases and supramolecular assemblies.

The bioinorganic chemistry of iron is central to life processes. Organisms must recruit iron from their environment, control iron storage and trafficking within cells, assemble the complex, iron-containing redox cofactors of metalloproteins, and manage a myriad of biochemical transformations by those enzymes. The coordination chemistry and the variable oxidation states of iron provide the essential mechanistic machinery of this metabolism. Our current understanding of several aspects of the chemistry of iron in biology are discussed with an emphasis on the oxygen activation and transfer reactions mediated by heme and nonheme iron proteins and the interactions of amphiphilic iron siderophores with lipid membranes.

Chemistry, Bioinorganic↗

PubMed1992

Mössbauer effect studies on some bioinorganic complexes of europium.

The bioinorganic complexes of europium with N-acetyl-DL-alanine, N-acetyl-DL-valine, and DL-alanyl-DL-alanine have been synthesized and the Mössbauer spectra at room temperature have been measured for these solid state complexes. The Mössbauer parameters indicate that the water molecules in these complexes are not directly linked to the central europium ion and are outside the coordination sphere of europium and biological ligands, and that the chemical bond between the europium ion and the ligands may be predominantly ionic in character, with the possibility of partial covalent contribution.

Alanine↗

PubMed2001

Bioinorganic and bioorganic studies of liver alcohol dehydrogenase.

Liver alcohol dehydrogenase (E.C.1.1.1.1) is an NAD(+)/NADH dependent enzyme with a broad substrate specificity being active on an assortment of primary and secondary alcohols. It catalyzes the reversible oxidation of a wide variety of alcohols to the corresponding aldehydes and ketones as well as the oxidation of certain aldehydes to their related carboxylic acids. Although the bioinorganic and bioorganic aspects of the enzymatic mechanism, as well as the structures of various ternary complexes, have been extensively studied, the kinetic significance of certain intermediates has not been fully evaluated. Nevertheless, the availability of computer-assisted programs for kinetic simulation and molecular modeling make it possible to describe the biochemical mechanism more completely. Although the true physiological substrates of this zinc metalloenzyme are unknown, alcohol dehydrogenase effectively catalyzes not only the interconversion of all-trans-retinol and all-trans-retinal but also the oxidation of all-trans-retinal to the corresponding retinoic acid. Retinal and related vitamin A derivatives play fundamental roles in many physiological processes, most notably the vision process. Furthermore, retinoic acid is used in dermatology as well as in the prevention and treatment of different types of cancer. The enzyme-NAD(+)-retinol complex has an apparent pK(a) value of 7.2 and loses a proton rapidly. Proton inventory modeling suggests that the transition state for the hydride transfer step has a partial negative charge on the oxygen of retinoxide. Spectral evidence for an intermediate such as E-NAD(+)-retinoxide was obtained with enzyme that has cobalt(II) substituted for the active site zinc(II). Biophysical considerations of water in these biological processes coupled with the inverse solvent isotope effect lead to the conclusion that the zinc-bound alkoxide makes a strong hydrogen bond with the hydroxyl group of Ser48 and is thus activated for hydride transfer. Moderate pressure accelerates enzyme action indicative of a negative volume of activation. The data with retinol is discussed in terms of enzyme stability, mechanism, adaptation to extreme conditions, as well as water affinities of substrates and inhibitors. Our data concern all-trans, 9-cis, 11-cis, and 13-cis retinols as well as the corresponding retinals. In all cases the enzyme utilizes an approximately ordered mechanism for retinol-retinal interconversion and for retinal-retinoic acid transformation.

Alcohol Dehydrogenase↗

PubMed1998

Bioinorganic chemistry and drug design: here comes zinc again.

The structures and reactions of metal ions in proteins are of tremendous interest in bioinorganic chemistry, as is the potential for metals in creating novel medicines. New results combine these aspects in describing an unexpected mode for metal-mediated drug efficacy that relies on well-established principles of metalloprotein structure.

Animals↗

PubMed2006

Biorecovered precious metals from industrial wastes: single-step conversion of a mixed metal liquid waste to a bioinorganic catalyst with environmental application.

The complete and continuous reduction of 1 mM Cr(VI) to Cr(III) was achieved in a flow-through reactor using a novel bioinorganic catalyst ("MM-bio-Pd(0)"), which was produced by single-step reduction of platinum group metals (PGM) from industrial waste solution onto biomass of Desulfovibrio desulfuricans ATCC 29577. Two flow-through reactor systems were compared using both "MM-bioPd(0)" and chemically reduced Pd(0). Reactors containing the latter removed Cr(VI) for 1 week only at the expense of formate as the electron donor, whereas the former gave complete Cr(VI) removal for 3 months of continuous operation. Mass balance analysis showed 100% reduction of Cr(VI) to soluble Cr(III) in the bioreactor exit solution. With the use of electron paramagnetic resonance (EPR) no intermediate Cr(V) species could be detected. Pd(0) was biodeposited similarly using Escherichia coliMC4100 and "bio-Pd(0)". The latter was used to recover Pd(II) from two acidic industrial waste leachates to generate two types of "MM-bio-Pd(0)": "SI-bio-Pd(0)" and "SII-bio-Pd(0)", respectively. The biomaterial composition was comparable in both cases, and the catalytic activity was related inversely to the amount of chloride in the waste leachate from which it was derived.

Biomass↗

PubMed2003

Characterization of metal centers in bioinorganic complexes using ab initio calculations of 113Cd chemical shifts.

Determination of (113)Cd chemical shift is of significant interest in NMR characterization of metal porphyrins, metal-histidine interactions, and other metal-ligand interactions in many bioinorganic complexes and metalloproteins. In this study, we present a detailed account of a number of quantum chemical investigations aimed at relating isotropic and anisotropic (113)Cd chemical shifts to the structure of several biologically relevant complexes with discrete and polymeric structures. Calculated and experimentally determined chemical shift values are compared to correlate the variation of the chemical shift values with the structural changes around the metal center. Our results infer that the density functional theory using the Sadlej basis set on the cadmium atom is a suitable method for estimating cadmium shielding values to a reasonable accuracy.

Cadmium↗