A Historical Perspective for the Catalytic Reaction Mechanism of Glycosidase; So As to Bring about Breakthrough in Confusing Situation

Various catalytic reaction models have been proposed as the reaction mechanisms of glycosidases, but a reasonable and unitary model capable of interpreting both “inverting” and “retaining” glycosidase reactions remains to be established. As for the models proposed to date, the nucleophilic displacement mechanism and the oxocarbenium ion intermediate mechanism are widely known, but recently the former is widely accepted, and so the general tendency of world opinion appears to favor it. This reaction model, however, is considered to comprise some inconsistencies that cannot be neglected from the viewpoint of reactivity in organic chemistry. While the nucleophilic displacement mechanism is often applied to reactions of glycosidases, it appears unlikely that such reactions actually occur. This review argues that the oxocarbenium ion intermediate reaction mechanism is more rational than the nucleophilic displacement reaction mechanism, as the action mode of glycosidases and related enzymes.     

The influence of different lipid environments on the structure and function of the hepatitis C virus p7 ion channel protein

Abstract

The hepatitis C virus (HCV) encodes the p7 protein that oligomerizes to form an ion channel. The 63 amino acid long p7 monomer is an integral membrane protein predominantly found in the endoplasmic reticulum (ER). Although it is currently unknown whether p7 is incorporated into secreted virions, its presence is crucial for the release of infectious virus. The molecular and biophysical mechanism employed by the p7 ion channel is largely unknown, but in vivo it is likely to be embedded in membranes undergoing changes in lipid composition. In this study we analyze the influence of the lipid environment on p7 ion channel structure and function using electrophysiology and synchrotron radiation circular dichroism (SRCD) spectroscopy. We incorporated chemically synthesized p7 polypeptides into artificial planar membranes of various lipid compositions. A lipid bilayer composition comprising phosphatidylcholine (PC) and phosphatidylethanolamine (PE) (4:1 PC:PE) led to burst-like patterns in the channel recordings with channel openings lasting up to 0.5 s. The reverse ratio of PC:PE (1:4) gave rise to individual channels continuously opening for up to 8 s. SRCD spectroscopy of p7 embedded into liposomes of corresponding lipid compositions suggests there is a structural effect of the lipid composition on the p7 protein.     

The Persistent Question of Potassium Channel Permeation Mechanisms

Potassium channels play critical roles in many physiological processes, providing a selective permeation route for K⁺ ions in and out of a cell, by employing a carefully designed selectivity filter, evolutionarily conserved from viruses to mammals. The structure of the selectivity filter was determined at atomic resolution by x-ray crystallography, showing a tight coordination of desolvated K⁺ ions by the channel. However, the molecular mechanism of K⁺ ions permeation through potassium channels remains unclear, with structural, functional and computational studies often providing conflicting data and interpretations. In this review, we will present the proposed mechanisms, discuss their origins, and will critically assess them against all available data. General properties shared by all potassium channels are introduced first, followed by the introduction of two main mechanisms of ion permeation: soft and direct knock-on. Then, we will discuss critical computational and experimental studies that shaped the field. We will especially focus on molecular dynamics (MD) simulations, that provided mechanistic and energetic aspects of K⁺ permeation, but at the same time created long-standing controversies. Further challenges and possible solutions are presented as well.     

Bestimmung der Verdaulichkeit der Rohnährstoffe,Basischen und Schwefelhaltigen Aminosäuren von Natürlich und Technisch Getrockneten Rotkleeblättern an Kolostomierten Legehennen

Domesticated animals all over the world are subjected to a wide variety of environmental conditions and challenges. Any deviation from “normal”; may result in adaptive behavior of which changes in feed intake or feed intake pattern is by far the most important. Adaptive behavior may further include influences on passage rate of feed residues through the digestive tract, resulting in changes in digestibility. Adaptive behavior may also result in changes in heat production, either to maintain body temperature constant, or as a result of an elevated body temperature.

Important environmental challenges are infectious diseases. Mild (sub‐clinical) infections usually result in reduced performance, without affecting feed intake or digestibility. Severe infections may disrupt the barriers between the internal metabolism and the respiratory and/or digestive tract, resulting in severe losses of energy and protein. This situation is notably apparent in severe infections with parasites of the gastrointestinal tract and may be associated with severe protein losses. Feeding high protein diets may partly alleviate the negative effects.

Contamination of air, water and feed may occasionally cause problems in farm animals. Such contamination may include pathogenic microbes, toxic secondary fungal metabolites and heavy metals. Negative effects associated with such contamination often show an impaired reproductive efficiency, but their influence on the utilization of energy and nutrients is not well documented.     

Ion channels induced by the prion protein

Prion diseases comprise a group of rapidly progressive and invariably fatal neurodegenerative disorders for which there are no effective treatments. While conversion of the cellular prion protein (PrP^C) to a β-sheet rich isoform (PrP^Sc) is known to be a critical event in propagation of infectious prions, the identity of the neurotoxic form of PrP and its mechanism of action remain unclear. Insights into this mechanism have been provided by studying PrP molecules harboring deletions and point mutations in the conserved central region, encompassing residues 105–125. When expressed in transgenic mice, PrP deleted for these residues (Δ105–125) causes a spontaneous neurodegenerative illness that is reversed by co-expression of wild-type PrP. In cultured cells, Δ105–125 PrP confers hypersensitivity to certain cationic antibiotics and induces spontaneous ion channel activity that can be recorded by electrophysiological techniques. We have utilized these drug-hypersensitization and current-inducing activities to identify which PrP domains and subcellular locations are required for toxicity. We present an ion channel model for the toxicity of Δ105–125 PrP and related mutants and speculate how a similar mechanism could mediate PrP^Sc-associated toxicity. Therapeutic regimens designed to inhibit prion-induced toxicity, as well as formation of PrP^Sc, may prove to be the most clinically beneficial.     

Crystal Structures of Sodium-Bound Annexin A4

Annexin A4 (Anx4) possesses four repeat domains with one Ca²⁺-binding site (CBS) in each domain. In this study, we resolved two crystal structures of the Na⁺-bound form at high resolution (1.58 and 1.35 Å). This is the first report that Anx4 binds the Na⁺ ion in CBSs. Electron density maps, valence screening, and atomic absorbance spectrometry confirmed that Anx4 bound the Na⁺ ion. One structure (1.58 Å) bound the Na⁺ ion in CBS I, whereas another structure (1.35 Å) bound the Na⁺ ion in CBS II and CBS III. We compared the two Na⁺-bound forms by superimposing their C^α traces. The C^α atoms of CBS III largely moved by coordination of the Na⁺ ion. In the C^α atoms of CBS I, however, little change resulted from Na⁺-coordination. Only the side chain of Glu71 was moved by Na⁺-coordination in CBS I. These results indicate that Anx4 also binds not only Ca²⁺ but also Na⁺ ion in the CBS.     

Life‐history constraints in grassland plant species: a growth‐defence trade‐off is the norm

Plant growth can be limited by resource acquisition and defence against consumers, leading to contrasting trade‐off possibilities. The competition‐defence hypothesis posits a trade‐off between competitive ability and defence against enemies (e.g. herbivores and pathogens). The growth‐defence hypothesis suggests that strong competitors for nutrients are also defended against enemies, at a cost to growth rate. We tested these hypotheses using observations of 706 plant populations of over 500 species before and following identical fertilisation and fencing treatments at 39 grassland sites worldwide. Strong positive covariance in species responses to both treatments provided support for a growth‐defence trade‐off: populations that increased with the removal of nutrient limitation (poor competitors) also increased following removal of consumers. This result held globally across 4 years within plant life‐history groups and within the majority of individual sites. Thus, a growth‐defence trade‐off appears to be the norm, and mechanisms maintaining grassland biodiversity may operate within this constraint.     

Does rock chemistry affect periphyton accrual in streams?

Stones of different rock types often accrue different amounts of periphytic algae. Although algal biomass may be positively related to stone roughness, the confounding role of rock chemistry is unclear. This independent effect of rock chemistry on benthic algae was tested using the nutrient-diffusing technique, by incorporating powdered stone, rather than nutrients, into the agar matrix. Rocks tested were sandstone, obsidian, schist, greywacke, pumice, gypsum, limestone, serpentine, and phosphorite. Petri-dishes containing powdered rock and agar, and covered with a permeable cellulose filter, were incubated in eight pools in a granitic stream. Algal biomass did not differ among any of the nine rock types and plain agar control, whereas biomass differed among the concurrently placed nutrient diffusing substrates (the stream was phosphorus-limited). Algal composition was more related to an upstream-downstream gradient (for filamentous algae) and pool-specific effects (deposition of fine sediment for diatoms) than rock chemistry. This minimal effect of rock chemistry may be caused by the low dissolution rate of stones. Handling editor: J. Padisak     

Fitness of resprouters versus seeders in relation to nutrient availability in two Plantago species

Two contrasting strategies of plants from disturbed areas are reported to depend on nutrient availability. Resprouters, investing into storage and capable of vegetative regeneration after disturbance, are predicted to be enhanced in nutrient poor environments. This contrasts to seeders, which invest preferentially into seed production and regenerating only from seeds, and are thought to prevail in nutrient rich environments. To test such predicted dichotomy, we set up an experiment with two facultative resprouters with contrasting nutrient demands and assessed the fitness of individuals regenerated from seeds and root fragments in differently productive environments. We hypothesized that 1) plants with higher nutrient demands have a higher fitness as seeders irrespectable of nutrient availability and/or 2) both species will have a higher fitness as resprouters under lower nutrient availability and as seeders when nutrient availability is higher. Nutrient availability was also manipulated prior to and after disturbance to evaluate the impact of changing nutrient availability on the strategy of resprouting. The results of our pot experiment with Plantago lanceolata and Plantago media supported the first but not the second hypothesis. Moreover, high nutrient availability prior to disturbance negatively affected resprouting success, but the growth and fitness of successfully regenerated individuals were enhanced under higher nutrient availability. We concluded that resprouting from roots after disturbance is affected by nutrient availability, but this effect considerably differs between individual life-history stages.