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At least 19 recordsLinked to original sources
PubMed2006

Femtomolar Zn(II) affinity in a peptide-based ligand designed to model thiolate-rich metalloprotein active sites.

Metal-ligand interactions are critical components of metalloprotein assembly, folding, stability, electrochemistry, and catalytic function. Research over the past 3 decades on the interaction of metals with peptide and protein ligands has progressed from the characterization of amino acid-metal and polypeptide-metal complexes to the design of folded protein scaffolds containing multiple metal cofactors. De novo metalloprotein design has emerged as a valuable tool both for the modular synthesis of these complex metalloproteins and for revealing the fundamental tenets of metalloprotein structure-function relationships. Our research has focused on using the coordination chemistry of de novo designed metalloproteins to probe the interactions of metal cofactors with protein ligands relevant to biological phenomena. Herein, we present a detailed thermodynamic analysis of Fe(II), Co(II), Zn(II), and[4Fe-4S]2(+/+) binding to IGA, a 16 amino acid peptide ligand containing four cysteine residues, H2N-KLCEGG-CIGCGAC-GGW-CONH2. These studies were conducted to delineate the inherent metal-ion preferences of this unfolded tetrathiolate peptide ligand as well as to evaluate the role of the solution pH on metal-peptide complex speciation. The [4Fe-4S]2(+/+)-IGA complex is both an excellent peptide-based synthetic analogue for natural ferredoxins and is flexible enough to accommodate mononuclear metal-ion binding. Incorporation of a single ferrous ion provides the FeII-IGA complex, a spectroscopic model of a reduced rubredoxin active site that possesses limited stability in aqueous buffers. As expected based on the Irving-Williams series and hard-soft acid-base theory, the Co(II) and Zn(II) complexes of IGA are significantly more stable than the Fe(II) complex. Direct proton competition experiments, coupled with determinations of the conditional dissociation constants over a range of pH values, fully define the thermodynamic stabilities and speciation of each MII-IGA complex. The data demonstrate that FeII-IGA and CoII-IGA have formation constant values of 5.0 x 10(8) and 4.2 x 10(11) M-1, which are highly attenuated at physiological pH values. The data also evince that the formation constant for ZnII-IGA is 8.0 x 10(15) M-1, a value that exceeds the tightest natural protein Zn(II)-binding affinities. The formation constant demonstrates that the metal-ligand binding energy of a ZnII(S-Cys)4 site can stabilize a metalloprotein by -21.6 kcal/mol. Rigorous thermodynamic analyses such as those demonstrated here are critical to current research efforts in metalloprotein design, metal-induced protein folding, and metal-ion trafficking.

Binding Sites↗
PubMed2003

Synchrotron techniques for metalloproteins and human disease in post genome era.

Metalloproteins make up some 30% of proteins in known genomes. Metalloproteins are a special class of proteins that utilise the unique properties of metal atoms in conjunction with the macromolecular assembly to perform life-sustaining processes. A number of metalloproteins are known to be involved in many disease states including ageing processes. The incorporation of the metal ion is a very tightly regulated process that, in vivo, very often requires specific chaperones to deliver and help incorporate the metal atom in the macromolecule. The lack of or inappropriate incorporation of metals along with genetic factors can lead to the mis-function of these proteins leading to disease. The mis-functions due to genetic alterations that lead to diseases like ALS (amyotrophic lateral sclerosis or motor neuron disease) and Creutzfeld Jacob disease (CJD) are now well recognised. Synchrotron radiation sources provide a unique set of structural tools, which in combination can prove extremely powerful in providing a comprehensive picture of these complex biological systems. In particular for metalloproteins, the combined use of X-ray crystallography, X-ray solution scattering and X-ray spectroscopy (XAFS) is extremely useful. We are currently engaged in a structural study where our aim is to characterize structurally and functionally metalloproteins and then transfer this knowledge to afford the problem of the mis-function of metalloproteins that lead to these terminal illnesses, either due to a gain of function/property or a loss of function/property. In this context, the benefits of adopting the 'philosophy' being developed for the structural genomics effort are highlighted.

Amyotrophic Lateral Sclerosis↗
PubMed2007

The design of inhibitors for medicinally relevant metalloproteins.

A number of metalloproteins are important medicinal targets for conditions ranging from pathogenic infections to cancer. Many but not all of these metalloproteins contain a zinc(II) ion in the protein active site. Small-molecule inhibitors of these metalloproteins are designed to bind directly to the active site metal ions. In this review several metalloproteins of interest are discussed, including matrix metalloproteinases (MMPs), histone deacetylases (HDACs), anthrax lethal factor (LF), and others. Different strategies that have been employed to design effective inhibitors against these proteins are described, with an effort to highlight the strengths and drawbacks of each approach. An emphasis is placed on examining the bioinorganic chemistry of these metal active sites and how a better understanding of the coordination chemistry in these systems may lead to improved inhibitors. It is hoped that this review will help inspire medicinal, biological, and inorganic chemists to tackle this important problem by considering all aspects of metalloprotein inhibitor design.

Animals↗
PubMed2000

Metal ligand aromatic cation-pi interactions in metalloproteins: ligands coordinated to metal interact with aromatic residues.

Cation-pi interactions between aromatic residues and cationic amino groups in side chains and have been recognized as noncovalent bonding interactions relevant for molecular recognition and for stabilization and definition of the native structure of proteins. We propose a novel type of cation-pi interaction in metalloproteins; namely interaction between ligands coordinated to a metal cation--which gain positive charge from the metal--and aromatic groups in amino acid side chains. Investigation of crystal structures of metalloproteins in the Protein Data Bank (PDB) has revealed that there exist quite a number of metalloproteins in which aromatic rings of phenylalanine, tyrosine, and tryptophan are situated close to a metal center interacting with coordinated ligands. Among these ligands are amino acids such as asparagine, aspartate, glutamate, histidine, and threonine, but also water and substrates like ethanol. These interactions play a role in the stability and conformation of metalloproteins, and in some cases may also be directly involved in the mechanism of enzymatic reactions, which occur at the metal center. For the enzyme superoxide dismutase, we used quantum chemical computation to calculate that Trp163 has an interaction energy of 10.09 kcal mol(-1) with the ligands coordinated to iron.

Alcohol Dehydrogenase↗
PubMed2006

Investigation of structure, dynamics and function of metalloproteins with electrospray ionization mass spectrometry.

Electrospray ionization mass spectrometry (ESI MS) has emerged recently as a powerful tool for analyzing many structural and behavioral aspects of metalloproteins in great detail. In this review we discuss recent developments in the field, placing particular emphasis on the unique features of ESI MS that lend themselves to metalloprotein characterization at a variety of levels. Direct mass measurement enables the determination of protein-metal ion binding stoichiometry in solution and metalloprotein higher order structure in the case of multi-subunit proteins. MS techniques have been developed for determining the locations of metal-binding centers, metal oxidation states and reaction intermediates of metal-containing enzymes. Other ESI MS techniques are also discussed, such as protein ion charge state distributions and hydrogen/deuterium exchange studies, which can be used to measure metal binding affinities and to shed light on vital dynamic aspects of the functional properties of metalloproteins endowed by metal binding.

Binding Sites↗
PubMed1986

The use of metalloproteins as standards for X-ray microanalysis of biological material.

Thin films of metalloprotein, deposited directly onto carbon-formvar-coated electron microscope grids, provide a potentially useful, but little developed, type of standard for biological transmission X-ray microanalysis. The possibility of using various metalloproteins was investigated in terms of their suitability as standards, and compared with an evaporated film of gelatin-salt mixture. The metalloproteins that were selected comprised conalbumin (containing detectable S, Fe), hemocyanin (S, K, Ca, Fe and Cu), insulin (S, Zn), phosvitin (P, Ca, Fe, and Zn) and alpha-lactalbumin (S, Ca). In each case, the metalloprotein preparation was homogeneous at the microlevel (unlike evaporated gelatin-salt mixtures), and was stable in the electron beam up to a current of 120 nA, over a lifetime of 200 s.

Electron Probe Microanalysis↗
PubMed2004

Insights into partially folded or unfolded States of metalloproteins from nuclear magnetic resonance.

Nuclear magnetic resonance (NMR) provides detailed insights into the conformational features of unfolded and partially folded proteins. In the case of metalloproteins, special attention should be devoted to the characterization of the properties of the metal binding sites, and specific approaches need to be developed depending on the nature of the metal ion and its coordination environment. At the same time, metal-based NMR parameters may help in getting a better picture of the average structural properties of the metalloprotein. A critical evaluation of the limits of applicability of paramagnetic effects for solution structure determination in partially folded or unfolded proteins is presented. The coupling between NMR characterization of structure and dynamic of the polypeptide chain and of the metal environment provides insights into the stabilizing role of metal ions in metalloproteins. The overall approach is illustrated for some case examples of increasing flexibility obtained far from native conditions for cytochrome c and superoxide dismutase, two metalloproteins that have been extensively studied in our lab and whose misfolded forms may be relevant for important biological processes.

Algorithms↗
PubMed2000

Retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.

De novo protein design provides an attractive approach for the construction of models to probe the features required for function of complex metalloproteins. The metal-binding sites of many metalloproteins lie between multiple elements of secondary structure, inviting a retrostructural approach to constructing minimal models of their active sites. The backbone geometries comprising the metal-binding sites of zinc fingers, diiron proteins, and rubredoxins may be described to within approximately 1 A rms deviation by using a simple geometric model with only six adjustable parameters. These geometric models provide excellent starting points for the design of metalloproteins, as illustrated in the construction of Due Ferro 1 (DF1), a minimal model for the Glu-Xxx-Xxx-His class of dinuclear metalloproteins. This protein was synthesized and structurally characterized as the di-Zn(II) complex by x-ray crystallography, by using data that extend to 2.5 A. This four-helix bundle protein is comprised of two noncovalently associated helix-loop-helix motifs. The dinuclear center is formed by two bridging Glu and two chelating Glu side chains, as well as two monodentate His ligands. The primary ligands are mostly buried in the protein interior, and their geometries are stabilized by a network of hydrogen bonds to second-shell ligands. In particular, a Tyr residue forms a hydrogen bond to a chelating Glu ligand, similar to a motif found in the diiron-containing R2 subunit of Escherichia coli ribonucleotide reductase and the ferritins. DF1 also binds cobalt and iron ions and should provide an attractive model for a variety of diiron proteins that use oxygen for processes including iron storage, radical formation, and hydrocarbon oxidation.

Amino Acid Sequence↗
PubMed2004

A hint to search for metalloproteins in gene banks.

MOTIVATION: With the advent of genome sequencing, a huge database of protein primary sequences has been accumulating. In parallel, a number of tools to investigate and expand upon this information, e.g. reconstructing and building relationships between protein families and superfamilies, have been developed. Metalloproteins are proteins capable of binding one or more metal ions, which are required for their biological function or for regulation of their activities or for structural purposes. Sometimes, metal binding can be observed in vitro but not be physiologically relevant. At present, there is a lack of specific tools to address the matter of the identification of metalloproteins in databases of gene sequences. RESULTS: In the present work, an approach exploiting metal-binding patterns (MBPs) of metalloproteins present in the Protein Data Bank to search gene banks for new metalloproteins is presented and applied to copper proteins. Nearly 100 different MBPs have been identified and then used for subsequent applications. The ensemble of sequences of the whole PDB is used to assess the potentiality and limits of the method and to identify levels of confidence for the predictions output by the search. It appears that copper-binding capabilities are identified with a confidence >90% when the percentage of identical amino acids aligned around the MBP by PHI-BLAST is at least 20% with respect to the entire protein domain length. If this percentage is between 10% and 20%, the level of confidence is approximately 50%. Application of the methodology to the entire genome sequences of Pyrococcus furiosus, Escherichia coli, Drosophila melanogaster and Homo sapiens suggests some differentiation between prokaryotes and eukaryotes. SUPPLEMENTARY INFORMATION: A table reporting statistics on the MBP identified; a list of all hits retrieved for the four organisms considered; a figure showing the number of hits for the four organisms as a function of I(d)(Global).

Algorithms↗
PubMed1982

Association of acylglyceride and retinyl palmitate hydrolase activities with zinc and copper metalloproteins in a high molecular weight lipid-protein aggregate fraction from chick liver cytosol.

A lipid-protein aggregate fraction of molecular weight approx. 1.8 . 10(6) was isolated by gel filtration from chick liver cytosol. This aggregate fraction had a hydrated density range of 1.06-1.13, was 45% lipid, contained zinc and copper and was associated with triolein, phosphatidylcholine and retinyl palmitate hydrolase activity. Hydrolytic activities were stimulated by albumin and cholate, but not by dihydroxy bile acids, and inhibited by serine esterase and sulphydryl inhibitors. Incubation of the aggregate with fatty acid-labelled acylglycerides resulted in protein-binding fatty acid fractions with molecular weights of 150,000, 60,000, 13,000 and approx. 2000. Incubation of the aggregate with [3H]retinyl palmitate yielded retinol-containing fractions with molecular weights of 150,000, 60,000 and 15,000. The latter peak appears, on the basis of amino acid composition, to be similar to the cellular retinol-binding protein. In addition, on incubation of the aggregate fraction, zinc and copper peaks are found with molecular weights of 150,000, 60,000 and 12,000-8000. The latter were further purified to yield a copper-rich metalloprotein similar to 'copper-chelatin' and a zinc-rich metalloprotein, possibly zinc-metallothionein. Both these metalloprotein fractions had acyl hydrolase activity which was depressed in zinc-depleted animals. This may provide a possible explanation for the documented nutritional interactions between zinc and retinol.

Animals↗
PubMed1987

SQUID measurement of metalloprotein magnetization. New methods applied to the nitrogenase proteins.

New techniques have been developed to exploit the sensitivity of a commercial SQUID susceptometer in the study of the magnetization of metalloproteins. Previous studies have ignored both the slow relaxation (hours) of spin I = 1/2 nuclei and residual ferromagnetic impurities in sample holders. These potential sources of noise were at or below the sensitivity of previous instruments. With these noise sources under control, one can now decrease the protein concentration by a factor of ten. In addition careful characterization of the frozen magnetization sample, including the use of a multi-instrument holder for combined study of the magnetization sample with Mössbauer spectroscopy, is required for reliable interpretation of the data in the face of paramagnetic impurities common to metalloprotein samples. Many previous magnetic studies of metalloproteins have been carried out in the Curie region. Saturation magnetization studies down to 1.8 K and up to 5 T can determine zero-field splitting parameters in addition to the spin and exchange coupling parameters measured in previous studies at lower fields and higher temperatures. Applications of these techniques to the study of the nitrogenase proteins of Azotobacter vinelandii are presented as examples.

Azotobacter↗
PubMed1998

Coordination geometries of selected transition metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+) in metalloproteins.

In order to determine preferred coordination geometries of six divalent cations (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+), two sources of experimental data were exploited: Protein Data Bank and Cambridge Structural Database. Metal-binding sites of approximately 100 metalloproteins and 3000 smaller transition metal complexes were analyzed and classified. The correlation between the geometries of small-molecule crystal structures and the metal-binding sites in metalloproteins was investigated. The abundance of amino acid residues participating in coordination metal-protein bonds of metalloproteins was evaluated. From the performed analysis it follows that the octahedral arrangement is preferred by Co2+ and Ni2+, tetrahedral by Zn2+, square planar by Cu2+, and linear by Hg2+. Cadmium (II) cation tends to bind in both tetrahedral and octahedral arrangements and single coordination geometry cannot be unambiguously ascribed to it.

Animals↗
PubMed1998

Separation of metalloprotein complexes in serum by size-exclusion chromatography. Optimisation of the separation parameters retention behaviour and recovery employing radiotracers.

A suitable procedure was developed for speciation analysis of metalloprotein complexes in serum using directly coupled size-exclusion chromatography and an element-specific detector. Two column matrices used for size-exclusion chromatography (TSK G 3000 SW and Asahipak GS 520) were investigated with respect to the recovery and retention behaviour for metalloprotein complexes. Optimisation of the separation parameters (buffer type, concentration, pH) was achieved by means of metalloprotein complexes marked with radiotracers. For speciation of serum the matrix in the Asahipak GS column is more efficient. Given optimal eluent characteristics (100 mM Tris, pH 7.4) the recovery of the elements investigated (sodium, calcium, iron and zinc) was 100%. Further, the retention behaviour (retention time, ratios of the peak areas) remained unchanged for several successive separations.

Buffers↗
PubMed2001

Metalloprotein and redox protein design.

Metalloprotein and redox protein design are rapidly advancing toward the chemical synthesis of novel proteins that have predictable structures and functions. Current data demonstrate a breadth of successful approaches to metallopeptide and metalloprotein design based on de novo, rational and combinatorial strategies. These sophisticated synthetic analogs of natural proteins constructively test our comprehension of metalloprotein structure/function relationships. Additionally, designed redox proteins provide novel constructs for examining the thermodynamics and kinetics of biological electron transfer.

Algorithms↗
PubMed2001

Engineering and design in the bioelectrochemistry of metalloproteins.

Engineered metalloproteins offer interesting systems for electrochemical studies of protein structure/function and their applications in nanobiotechnology. Scanning probe microscopy and cyclic voltammetry of engineered metalloproteins and electrodes have proved to be a powerful combination of tools contributing to the field of bioelectrochemistry. The ability to engineer tags, such as histidine tags and biotin-acceptor peptides, and to site-specifically introduce cysteine residues enabled the creation of ordered immobilised protein structures that can be characterised both electrochemically and topographically. Gene fusion and de novo combinatorial synthesis of metalloproteins are emerging to provide structures with the desired electrochemical properties.

Binding Sites↗
PubMed2005

Potential for using isotopically altered metalloproteins in species-specific isotope dilution analysis of proteins by HPLC coupled to inductively coupled plasma mass spectrometry.

The production and evaluation of an isotopically enriched metalloprotein standard for use as a calibrant in species-specific isotope dilution analysis by HPLC coupled to inductively coupled plasma mass spectrometry is described. Using a model system involving the copper-containing protein rusticyanin (Rc) from the bacterium Acido-thiobacillus ferrooxidans, it was possible to demonstrate the analytical conditions that could be used for the measurement of metalloproteins by on-line IDMS analysis. Rc was chosen because it is a well-characterized protein with an established amino acid sequence and can be produced in suitable quantities using a bacterial recombinant system. Three different forms of the protein were studied by organic and inorganic mass spectrometry: the native form of the protein containing a natural isotopic profile for copper, an isotopically enriched species containing virtually all of its copper as the 65Cu isotope, and the nonmetalated apo form. Incorporation of the copper isotopes into the apo form of the protein was determined using a UV-vis spectrophotometric assay and shown to be complete for each of the copper-containing species. The experimental conditions required to maintain the conformational form of the protein with a nonexchangeable copper center were established using +ve electrospray mass spectrometry. A pH 7.0 buffer was found to afford the most appropriate conditions, and this was then used with HPLC-ICP-MS to verify the stability of the copper center by analysis of mixtures of different isotopic solutions. No exchange of the enriched copper isotope from Rc with an added naturally abundant inorganic copper cation was observed under a neutral pH environment, indicating that species-specific ID-MS analysis of metalloproteins is possible.

Acidithiobacillus thiooxidans↗
PubMed2005

A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands.

To alleviate the problems in the receptor-based design of metalloprotein ligands due to inadequacies in the force-field description of coordination bonds, a four-tier approach was devised. Representative ligand-metalloprotein interaction energies are obtained by subsequent application of (1) docking with metal-binding-guided selection of modes, (2) optimization of the ligand-metalloprotein complex geometry by combined quantum mechanics and molecular mechanics (QM/MM) methods, (3) conformational sampling of the complex with constrained metal bonds by force-field-based molecular dynamics (MD), and (4) a single point QM/MM energy calculation for the time-averaged structures. The QM/MM interaction energies are, in a linear combination with the desolvation-characterizing changes in the solvent-accessible surface areas, correlated with experimental data. The approach was applied to structural correlation of published binding free energies of a diverse set of 28 hydroxamate inhibitors to zinc-dependent matrix metalloproteinase 9 (MMP-9). Inclusion of steps 3 and 4 significantly improved both correlation and prediction. The two descriptors explained 90% of variance in inhibition constants of all 28 inhibitors, ranging from 0.08 to 349 nM, with the average unassigned error of 0.318 log units. The structural and energetic information obtained from the time-averaged MD simulation results helped understand the differences in binding modes of related compounds.

Binding Sites↗
PubMedDate not supplied

Essential viral and cellular zinc and iron containing metalloproteins as targets for novel antiviral and anticancer agents: implications for prevention and therapy of viral diseases and cancer.

In this review the authors summarize the experimental data on the role of a selected group of metalloproteins, particularly viral (v) and cellular (c) zinc finger proteins (ZFP) and iron containing proteins which are involved in cell proliferation, neovascularization, apoptosis, and viral infection. Furthermore, this review summarizes the data embracing the hypothesis that disruption of certain metalloproteins by novel pharmacological agents is a key factor in controlling viral and proliferative diseases. The primary goal of this review is to show the potential therapeutic applications of ZFP disrupting agents, zinc chelators and iron chelators in the control of viral diseases and cancer. It is known that zinc or iron deficiency, resulting from exposure of culture cells to membrane-permeable Zn2+ or Fe(2+)-chelators, can induced apoptosis in virally transformed cells while normal cells remain unaffected under these conditions. Apoptosis is possibly due to simultaneous inactivation of vZFP, cZFP, and/or iron containing proteins, which are essential for maintenance of cellular and viral structure and which are activated in virally transformed cells. New insights concerning apoptosis, viral metalloproteins, and novel antiviral agents will also be reviewed. From the evidence reviewed, one can infer that development of a variety of drugs that control or neutralize vZFP may lead to a new therapeutic approach directed at controlling and preventing a wide spectrum of viral diseases and cancer. Furthermore, the results suggest that these agents may be useful to prevent transmission of viral diseases. Finally, this review not only points out the limits of our understanding of this system, but also directs scientists to opportunities for future research.

Amino Acid Sequence↗