Models for dioxygen activation by the CuB site of dopamine β-monooxygenase and peptidylglycine α-hydroxylating monooxygenase

On the basis of spectroscopic and crystallographic data for dopamine beta-monooxygenase and peptidylglycine alpha-hydroxylating monooxygenase (PHM), a variety of ligand sets have been used to model the oxygen-binding Cu site in these enzymes. Calculations which employed a combination of density functional and multireference second-order perturbation theory methods provided insights into the optimal ligand set for supporting eta (1) superoxo coordination as seen in a crystal structure of a precatalytic Cu/O(2) complex for PHM (Prigge et al. in Science 304:864-867, 2004). Anionic ligand sets stabilized eta (2) dioxygen coordination and were found to lead to more peroxo-like Cu-O(2) complexes with relatively exergonic binding free energies, suggesting that these adducts may be unreactive towards substrates. Neutral ligand sets (including a set of two imidazoles and a thioether), on the other hand, energetically favored eta (1) dioxygen coordination and exhibited limited dioxygen reduction. Binding free energies for the 1:1 adducts with Cu supported by the neutral ligand sets were also higher than with their anionic counterparts. Deviations between the geometry and energetics of the most analogous models and the PHM crystal structures suggest that the protein environment influences the coordination geometry at the Cu(B) site and increases the lability of water bound to the preoxygenated reduced form. Another implication is that a neutral ligand set will be critical in biomimetic models in order to stabilize eta (1) dioxygen coordination.     

The example of gastrointestinal damage induced by ionising radiation: are there accessible markers?

Ionising radiation exposure occurs during radiotherapy, diagnostic tests or by accident. In all cases the gastrointestinal tract, which is highly sensitive to radiation, may be at risk. Each region may respond differently to radiation exposure which to some extent is reflected by clinical symptoms. The evaluation of injury, whether acute or chronic, depends on the utilization of a variety of techniques. It appears that no definitive tests exist and that a multiparametric analysis should be undertaken. This review addresses the question of accessible markers associated with radiation-induced intestinal pathologies. Several approaches are discussed which include clinical observations, measurement of faecal parameters, changes in inflammatory mediators and possible applications of imaging techniques.     

Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition?

Structural studies of protein-DNA complexes have shown that there are many distinct families of DNA-binding proteins, and have shown that there is no simple "code" describing side-chain/base interactions. However, systematic analysis and comparison of protein-DNA complexes has been complicated by the diversity of observed contacts, the sheer number of complexes currently available and the absence of any consistent method of comparison that retains detailed structural information about the protein-DNA interface. To address these problems, we have developed geometric methods for characterizing the local structural environment in which particular side-chain/base interactions are observed. In particular, we develop methods for analyzing and comparing spatial relationships at the protein-DNA interface. Our method involves attaching local coordinate systems to the DNA bases and to the C(alpha) atoms of the peptide backbone (these are relatively rigid structural units). We use these tools to consider how the position and orientation of the polypeptide backbone (with respect to the DNA) helps to determine what contacts are possible at any given position in a protein-DNA complex. Here, we focus on base contacts that are made in the major groove, and we use spatial relationships in analyzing: (i) the observed patterns of side-chain/base interactions; (ii) observed helix docking orientations; (iii) family/subfamily relationships among DNA-binding proteins; and (iv) broader questions about evolution, altered specificity mutants and the limits for the design of new DNA-binding proteins. Our analysis, which highlights differences in spatial relationships in different complexes and at different positions in a complex, helps explain why there is no simple, general code for protein-DNA recognition.     

Devising a pathway for hyaluronan catabolism: are we there yet?

Hyaluronan is a negatively charged, high molecular weight glycosaminoglycan found predominantly in the extracellular matrix. Intracellular locations for hyaluronan have also been documented in cytoplasm, nucleus, and nucleolus. The polymer has an extraordinarily high rate of turnover in vertebrate tissues. The focus here is to formulate a metabolic pathway for hyaluronan degradation using all available data, including the recently acquired information on the hyaluronidase gene family. Such a catabolic scheme has defied explication up to now. In somatic tissues, stepwise processing occurs, from the extracellular high molecular weight space filling, antiangiogenic approximately 107-kDa polymer, to intermediate sized highly angiogenic, inflammatory, and immune-stimulating fragments, and ultimately to tetrasaccharides that are antiapoptotic and potent inducers of heat-shock proteins. It is proposed that the high molecular weight extracellular polymer is tethered to the cell surface by the combined efforts of hyaluronan receptors and hyaluronidase-2 (Hyal-2). The hyaluronan is cleaved to a 20-kDa intermediate-sized fragment, the limit product of Hyal-2 digestion. These fragments are delivered to endosomal- and ultimately lysosomal-like structures. Further catabolism occurs there by Hyal-1, coordinated with the activity of two lysosomal beta-exoglycosidases, beta-glucuronidase and beta-N-acetyl-glucosaminidase. A membrane-associated mini-organelle is postulated, the hyaluronasome, in which coordinated synthetic and catabolic enzyme reactions occur. The hyaluronasome can respond to the physiological states of the cell by a series of membrane-bound and soluble hyaluronan-associated receptors, binding proteins, and cofactors that trigger enzymatic events and signal transduction pathways. These in turn can be modulated by the amounts and sizes of the hyaluronan polysaccharides generated in the catabolic cascade. Most of these highly dynamic interactions remain to be determined. It is also proposed that malignant cells can commandeer some of these interactions for facilitating tumor growth and spread.     

Pharmacogenetic studies of epilepsy drugs: are we there yet?

One of the mantras of scientists working in the field of pharmacogenetics is 'the right dose for the right patient'. A recent article has gone someway towards demonstrating that this goal can be achieved using genetic approaches. It is one of the first reports to show that a specific polymorphism can predict the maximum tolerated dose of two anti-epileptic drugs. However, further studies are necessary to validate these observations.     

Therefore,what are recombination proteins there for?

The order of discovery can have a profound effect upon the way in which we think about the function of a gene. In E. coli, recA is nearly essential for cell survival in the presence of DNA damage. However, recA was originally identified, as a gene required to obtain recombinant DNA molecules in conjugating bacteria. As a result, it has been frequently assumed that recA promotes the survival of bacteria containing DNA damage by recombination in which DNA strand exchanges occur. We now know that several of the processes that interact with or are controlled by recA, such as excision repair and translesion synthesis, operate to ensure that DNA replication occurs processively without strand exchanges. Yet the view persists in the literature that recA functions primarily to promote recombination during DNA repair. With the benefit of hindsight and more than three decades of additional research, we reexamine some of the classical experiments that established the concept of DNA repair by recombination, and we consider the possibilities that recombination is not an efficient mechanism for rescuing damaged cells, and that recA may be important for maintaining processive replication in a manner that does not generally promote recombination.     

How many species of Cladocera are there?

An estimation of the number of taxa within families, genera and local faunas of Cladocera reveals that only c. 129 species (17% of all known species) may be considered as sufficiently well described (valid species), and c. 146 as rather well described (fair species) but needing further study using modern methods of investigation. The status of all other species is vague. The families Chydoridae, Daphniidae and Sididae and genera Diaphanosoma, Daphnia, (including Daphniopsis), Megafenestra, Scapholeberis, Eurycercus, Chydorus, Ephemeroporus and Pleuroxus have been comparatively studied best. The largest number of valid species is known from Europe, North America, Australia and South America, and the smallest number from Africa. Presence of large number of vague species of Cladocera negatively affects faunistic, zoogeographic, and ecological studies of continental waters.Dedicated to the memory of Professor D. J. Frey     

Phylogenetic distribution of catalase-peroxidases: are there patches of order in chaos?

Hydrogen peroxide features in many biological oxidative processes and must be continuously degraded enzymatically either via a catalatic or a peroxidatic mechanism. For this purpose ancestral bacteria evolved a battery of different heme and non-heme enzymes, among which heme-containing catalase-peroxidases (CP) are one of the most widespread representatives. They are unique since they can follow both H(2)O(2)-degrading mechanisms, the catalase activity being clearly dominant. With the fast increasing amount of genomic data available, we were able to perform an extensive search for CP and found almost 300 sequences covering a large range of microorganisms. Most of them were encoded by bacterial genomes, but we could also find some in eukaryotic organisms other than fungi, which has never been shown until now. Our screen also reveals that approximately 60% of the bacteria do not possess CP genes. Chaotic distribution among species and incongruous phylogenetic reconstruction indicated existence of numerous lateral gene transfers in addition to duplication events and regular speciation. The results obtained show an impressively complex gene transmission pattern, and give some new insights about the role of CP and the origin of life on earth. Finally, we propose for the first time bacterial candidates that may have participated in the transfer of CP from bacteria to eukaryotes.     

Treatment and prevention of cryptosporidiosis: what options are there for a country like Zambia?

Cryptosporidiosis is a major infection of humans, leading to diarrhoea and growth failure in children, diarrhoea and malnutrition in immunocompromised adults, and is associated with increased mortality in all age groups. Using the country of Zambia as an example, I review the possible approaches to treatment and prevention in a tropical setting. The current optimal therapy for cryptosporidiosis is nitazoxanide which works well in HIV uninfected children, but treatment in patients with HIV infection remains remarkably difficult. No single drug has demonstrated efficacy in a randomised trial. No vaccine is available, so the best option for prevention for the moment is filtration and clean storage of drinking water. This would be expected to reduce cryptosporidiosis dramatically, but this needs to be demonstrated directly. Water filtration would have the added benefit of protection against many other pathogens, but the paucity of alternative approaches highlights the need for a better understanding of this important human pathogen.     

Functionally and structurally relevant residues of enzymes: are they segregated or overlapping?

There is a delicate balance between stability and flexibility needed for enzyme function. To avoid undesirable alteration of the functional properties during the evolutionary optimization of the structural stability under certain circumstances, and vice versa, to avoid unwanted changes of stability during the optimization of the functional properties of proteins, common sense would suggest that parts of the protein structure responsible for stability and parts responsible for function developed and evolved separately. This study shows that nature did not follow this anthropomorphic logic: the set of residues involved in function and those involved in structural stabilization of enzymes are rather overlapping than segregated.     

Prostaglandins as reducing agents: a model of adenylate cyclase activation?

It has been suggested that adenylate cyclase activation involves reduction of a disulfide linkage. Prostaglandin E1 (PGE1), prostaglandin E2 (PGE2), prostaglandin I2 (PGI2) and prostaglandin F2 alpha (PGF2 alpha) were tested for their ability to act as reducing agents with either cytochrome c, or the disulfide 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB), the latter with a catalytic amount of ferric chloride. PGE1, PGE2, and PGI2 significantly reduced cytochrome c while PGF2 alpha did not. PGE1, PGE2 and PGI2 reduced DTNB while PGF2 alpha did not. The results are consistent with the postulate that prostaglandins which are effective in activating adenylate cyclase can act as reducing agents and might be involved in reductive activation of adenylate cyclase.