Alkane-oxidizing metalloenzymes in the carbon cycle

This review examines the metalloenzymes that catalyze the oxidation of alkanes in the environment. The focus of the review is on what is known about the relative abundances of these metalloenzymes, their metal ion requirements, and their reaction mechanisms. The relative significance of these reactions in the global transformation of alkanes is discussed.     

The role of metals in neurodegenerative diseases.

There is increasing evidence in a number of neurodegenerative diseases that transition metal-mediated abnormalities play a crucial role in disease pathogenesis. In this treatise, we review the role of metal homeostasis as it pertains to alterations in brain function in neurodegenerative diseases. In fact, while there is documented evidence for alterations in transition metal homeostasis, redox-activity and localization, it is also important to realize that alterations in specific copper- and iron-containing metalloenzymes also appear to play a crucial role in the neurodegenerative process.     

Zinc hydrolases: the mechanisms of zinc-dependent deacetylases

A class of metalloenzymes, known as zinc hydrolases, catalyze a variety of hydrolytic reactions on many different substrates in important metabolic pathways. Deacetylation is an example of one of the types of reactions catalyzed by zinc hydrolases. The biological importance of the reactions catalyzed by many zinc hydrolases, including zinc-dependent deacetylases, has made these enzymes pharmaceutical targets for the development of inhibitors and, therefore, a clear understanding of the mechanisms of these enzymes is warranted. This review focuses on the current understanding of the mechanisms catalyzed by various zinc-dependent deacetylases and, in particular, the reaction mechanism catalyzed by the enzyme UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase, also known as LpxC. In general, the zinc-water functions as the nucleophile with zinc stabilization of the tetrahedral intermediate and general-acid-base catalysis (GABC) provided by enzyme residue(s). Two types of GABC mechanisms have been identified, one that uses a single bifunctional GABC and another that uses a GABC pair.     

Imprinted polymers with transition metal catalysts

The microenvironment of immobilized transition metal catalysts can be manipulated using catalyst-substrate conjugates in combination with the technology of molecular imprinting. Recent results have shown that catalysts with a significantly enhanced activity combined with an improved substrate-, regio- and enantioselectivity can be prepared in this way. These artificial systems resemble metalloenzymes because the catalytic transformation is effectively controlled by a well-defined second coordination sphere.     

Colorimetric and fluorimetric assays to quantitate micromolar concentrations of transition metals

Transition metal ions, although maintained at low concentrations, play diverse important roles in many biological processes. Two assays useful for the rapid quantification of a range of first-row transition metal ions have been developed. The colorimetric assay extends the 4-(2-pyridylazo)resorcinol assay of Hunt et al. (J. Biol. Chem. 255, 14793 (1984)) to measure nanomole quantities of Co(2+), Ni(2+), and Cu(2+) as well as Zn(2+). The fluorimetric assay takes advantage of the coordination of a number of metal ions (Mn(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+)) by Fura-2 and can also be used to measure nanomole quantities of these ions. The assays developed here have the advantage of not requiring the extensive sample preparation necessary for other methodologies, such as atomic absorption spectroscopy and inductively coupled plasma emission spectroscopy (ICPES), while being comparable in accuracy to the detection limits of ICPES for the first-row transition metal ions. To demonstrate the effectiveness of these assays, we determined the affinity of carbonic anhydrase II (CA II), a prototypical zinc enzyme, for Ni(2+) and Cd(2+). These data indicate that CA II binds transition metals with high affinity and is much more selective for Zn(2+) over Ni(2+) or Cd(2+) than most small-molecule chelators or other metalloenzymes.     

The role of metal ions in the mechanism of action of hydrolytic metalloenzymes: Carbonic anhydrase

Metalloenzymes are among the most efficient enzymes. One of the mechanisms available to hydrolytic metalloenzymes consists of using the metal ion, which is embedded in the protein, as a carrier for hydroxide ions in neutral solution. Models for this mechanism are surveyed and analyzed from the point of view of the “charge effect”. The active center of carbonic anhydrase is compared to several of these models, and the similarities are pointed out. It is concluded that the “carrier for hydroxide ions” mechanism is the most plausible one for carbonic anhydrase. It is proposed that the metal ion also plays a role in the regeneration of the active center of the enzyme, i.e. the ionization of the metal-bound water molecule, after each turnover. Some general implications for the mechanism of action of other hydrolytic metalloenzymes are considered.     

Bioinorganic chemistry and molecular biology

The review of the contemporary state of bioinorganic chemistry is presented, illustrated by a series of examples. A short presentation of the chemistry of the complexes of transient metals is given, the importance of the distorsion isomerism is emphasized. The roles of the alkaline and alkaline-earth metals in biology is considered as also the role of Zn, Co, Mo, Cu. The function of iron is presented and the influence of magnetic fields on organisms is discussed. The mechanisms of action of carboxypeptidase A and of nitrogenase are considered. The general properties of metalloenzymes are discussed--the entatic state of the active site, the role of the distorsion isomerism and of the trans-effect as also the electronic-conformational interactions. The physical properties of the biometallic compounds are formulated. The importance of these compounds for medicine is illustrated by the Podymov's theory of lupus, by the cancerogenic role of metals and by the use of the platinum complexes in oncological therapy. The importance of biometallic compounds for enzymology and other branches of molecular biology is emphasized.     

Vesicle reconstitution from lipid-detergent mixed micelles

The process of formation of lipid vesicles using the technique of detergent removal from mixed-micelles is examined. Recent studies on the solubilization and reconstitution of liposomes participated to our knowledge of the structure and properties of mixed lipid-detergent systems. The mechanisms involved in both the lipid self assembly and the micelle-vesicle transition are first reviewed. The simplistic three step minimum scheme is described and criticized in relation with isothermal as well as a function of the [det]/[lip] ratio, phase diagram explorations. The techniques of detergent elimination are reviewed and criticized for advantages and disadvantages. New methods inducing micelle-vesicle transition using enzymatic reaction and T-jump are also described and compared to more classical ones. Future developments of these techniques and improvements resulting of their combinations are also considered. Proper reconstitution of membrane constituents such as proteins and drugs into liposomes are examined in the light of our actual understanding of the micelle-vesicle transition.     

Diverse aberrancies target yeast mRNAs to cytoplasmic mRNA surveillance pathways

Eukaryotic gene expression is a complex, multistep process that needs to be executed with high fidelity and two general methods help achieve the overall accuracy of this process. Maximizing accuracy in each step in gene expression increases the fraction of correct mRNAs made. Fidelity is further improved by mRNA surveillance mechanisms that degrade incorrect or aberrant mRNAs that are made when a step is not perfectly executed. Here, we review how cytoplasmic mRNA surveillance mechanisms selectively recognize and degrade a surprisingly wide variety of aberrant mRNAs that are exported from the nucleus into the cytoplasm.     

Emerging strategies for expanding the toolbox of enzymes in biocatalysis

Expanding the repertoire of reactions available to enzymes is an enduring challenge in biocatalysis. Owing to the synthetic versatility of transition metals, metalloenzymes have been favored targets for achieving new catalytic functions. Although less well explored, enzymes lacking metal centers can also be effective catalysts for non-natural reactions, providing access to reaction modalities that compliment those available to metals. By understanding how these activation modes can reveal new functions, strategies can be developed to access novel biocatalytic reactions. This review will cover discoveries in the last two years which access catalytic reactions that go beyond the native repertoire of metal-free biocatalysts.     

Effect of sugar-phosphate mixtures on the stability of DPPC membranes in dehydrated systems

The stabilizing role of sugars on dehydrated membranes is well established. The formation of a glassy matrix and the direct interaction between the sugars and the lipids are some of the mechanisms proposed to be involved in this stabilizing effect. Phospholipidic systems have been studied extensively as models for biological membranes and also due to the practical applications of liposomes as vehicles for drug delivery. In this work, we evaluate the effect of sugar-phosphate mixtures on the transition temperature of dehydrated 1,2-dipalmitoylphosphatidylcholine, and also examine some physical characteristics of these mixtures, such as the glass transition temperature and water sorption properties. The addition of phosphate salts to sugar systems has several interesting features that merit its consideration in formulations to protect dehydrated labile biomaterials. In particular, sucrose-phosphate mixtures provide an interesting alternative to pure saccharide formulations due to their high glass transition temperatures and their increased ability to maintain a low melting transition temperature in the presence of small amounts of water.     

A simple assay for detection of small-molecule redox activity

In addition to selecting molecules of pharmacological interest, high-throughput screening campaigns often generate hits of undesirable mechanism, which cannot be exploited for drug discovery as they lead to obvious problems of specificity and developability. Examples of undesirable mechanisms are target alkylation/acylation and compound aggregation. Both types of "promiscuous" mechanisms have been described in the literature, as have methods for their detection. In addition to these mechanisms, compounds can also inhibit by oxidizing susceptible enzyme targets, such as metalloenzymes and cysteine-using enzymes. However, this redox phenomenon has been documented infrequently, and an easy method for detecting this behavior is missing. In this article, the authors describe direct proof of small-molecule oxidation of a cysteine protease by liquid chromatography/tandem mass spectrometry, develop a simple assay to predict this oxidizing behavior by compounds, and show the utility of this assay by demonstrating its ability to distinguish nuisance redox compounds from well-behaved inhibitors in 3 historical GlaxoSmithKline drug discovery efforts.     

Spectroscopic methods and their applicability for high‐throughput characterization of mammalian cell cultures in automated cell culture systems

The number and use of automated cell culture systems for mammalian cell culture are steadily increasing. Automated cell culture systems require miniaturized analytics with a high throughput to obtain as much information as possible from single experiments. Standard analytics commonly used for conventional bioreactor samples cannot handle the high throughput and the low sample volumes. Spectroscopic methods provide a means of meeting this analytical requirement and afford fast and direct access to process information. In the first part of this review, UV/VIS, fluorescence, Raman, near‐infrared, and mid‐infrared spectroscopy are presented. In the second part of the review, these spectroscopic methods are evaluated in terms of their applicability in the new field of mammalian cell culture processes in automated cell culture systems. Unlike standard bioreactors, these automated systems have special requirements that apply to the use of spectroscopic methods. Therefore, they are compared with regard to cell culture automation, throughput, and required sample volume.     

Lipid peroxidation in erythrocytes

Erythrocytes might be expected to be highly susceptible to peroxidation. Their membranes are rich in polyunsaturated fatty acids; they are continuously exposed to high concentrations of oxygen; and they contain a powerful transition metal catalyst. In fact, autoxidation is held in check in vivo by extremely efficient protective antioxidant mechanisms. These involve cellular enzymes such as superoxide dismutase and glutathione peroxidase, as well as vitamin E; but they mainly reflect effective structural compartmentalisation. This review surveys mechanisms which lead to red cell lipid autoxidation and the role of haemoglobin in these processes. The influence of haemoglobinopathies, of lipid composition and of abnormalities in antioxidant mechanisms induced by exogenous oxidant stress is also considered.     

"Quorum sensing" or social behavior of bacteria

The review deals with the data of literature on the role of the "quorum sensing" (QS) system ensuring the social behavior of bacteria in the regulation of virulence genes. The mechanisms of the action of these systems in Gram-negative and Gram-positive bacteria, as well as the influence of acyl-homoserine lactones, one of the components of the QS system, on the immune response of the infected host are discussed. In addition, in this review the data of literature on the existence of bacteria in the form of biofilms are presented. The methods of the identification of biofilms, the methods of their experimental preparation and the role of the QS system in the process of their formation are considered.     

Chemistry and biochemistry of 4-hydroxynonenal, malonaldehyde and related aldehydes

Lipid peroxidation often occurs in response to oxidative stress, and a great diversity of aldehydes are formed when lipid hydroperoxides break down in biological systems. Some of these aldehydes are highly reactive and may be considered as second toxic messengers which disseminate and augment initial free radical events. The aldehydes most intensively studied so far are 4-hydroxynonenal, 4-hydroxyhexenal, and malonaldehyde. The purpose of this review is to provide a comprehensive summary on the chemical properties of these aldehydes, the mechanisms of their formation and their occurrence in biological systems and methods for their determination. We will also review the reactions of 4-hydroxyalkenals and malonaldehyde with biomolecules (amino acids, proteins, nucleic acid bases), their metabolism in isolated cells and excretion in whole animals, as well as the many types of biological activities described so far, including cytotoxicity, genotoxicity, chemotactic activity, and effects on cell proliferation and gene expression. Structurally related compounds, such as acrolein, crotonaldehyde, and other 2-alkenals are also briefly discussed, since they have some properties in common with 4-hydroxyalkenals.     

Quantum chemical calculations of spectroscopic properties of metalloproteins and model compounds: EPR and Mössbauer properties

Recently developed theoretical methods to predict EPR and M?ssbauer parameters open the way for close interactions between theorists and experimentalists to elucidate the geometric and electronic structures of metalloenzymes and model complexes and to obtain insight into their reactive properties. Spectral calculations (g-values, hyperfine couplings, zero-field splittings, isomer shifts and quadrupole splittings) are also a means to validate theoretical approaches and therefore complement the prediction of geometries, reaction energies and transition states.     

Mathematical modeling of bioassays

The high affinity and specificity of biological receptors determine the demand for and the intensive development of analytical systems based on use of these receptors. Therefore, theoretical concepts of the mechanisms of these systems, quantitative parameters of their reactions, and relationships between their characteristics and ligand–receptor interactions have become extremely important. Many mathematical models describing different bioassay formats have been proposed. However, there is almost no information on the comparative characteristics of these models, their assumptions, and predic- tive insights. In this review we suggested a set of criteria to classify various bioassays and reviewed classical and contempo- rary publications on these bioassays with special emphasis on immunochemical analysis systems as the most common and in-demand techniques. The possibilities of analytical and numerical modeling are discussed, as well as estimations of the minimum concentrations that may be detected in bioassays and recommendations for the choice of assay conditions.     

Recent advances in maximum entropy biasing techniques for molecular dynamics

ABSTRACT

This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in molecular simulation by minimally modifying the thermodynamic ensemble. This is especially important where force fields are approximate, such as when employing coarse-grain models, or where high accuracy is required, such as when attempting to mimic a multiscale self-assembly process. The authors review here the experiment directed simulation (EDS) and experiment directed metadynamics (EDM) methods that allow matching averages and distributions in simulations, respectively. Important system-specific considerations are discussed such as using enhanced sampling simultaneously, the role of pressure, treating uncertainty, and implementations of these methods. Recent examples of EDS and EDM are reviewed including applications to ab initio molecular dynamics of water, incorporating environmental fluctuations inside of a macromolecular protein complex, improving RNA force fields, and the combination of enhanced sampling with minimal biasing to model peptides