Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor

Combined quantum mechanical/molecular mechanical (QM/MM) simulations are carried out to analyze factors that dictate the proton transfer in carbonic anhydrase II (CAII), an enzyme that has been used as a prototypical example of long-range proton transfers in biomolecules. In contrast to the long-held conjecture in the experimental literature, the computed potentials of mean force (PMF) suggest that the proton transfer in CAII is not very sensitive to the orientation of the acceptor group (His 64) and, therefore, the number of water molecules that bridge the donor (zinc-water) and acceptor groups. Perturbative analysis indicates that a series of polar and charged residues close to the transfer pathways make the dominant contribution to the barrier and exothermicity of the proton transfer reaction, thus supporting the proposal from previous studies of Warshel and co-workers using a somewhat simpler QM/MM model that electrostatic interactions play a major role in the proton transfer in CAII. The PMF results are in striking contrast to previous analysis using the same QM/MM method but an ensemble of minimum energy path (MEP) calculations, which found a steep dependence of the barrier height on the number of bridging water molecules. Analysis of the configurations sampled in the PMF and MEP simulations suggests that this difference arises because the PMF simulations sample a largely stepwise mechanism while the local MEP calculations artificially favored concerted transfers due to the specific protocol used to generate the initial configurations. Therefore, this study presents a compelling argument for carrying out proper conformational sampling in the study of long-range proton transfers. Finally, we illustrate that Phi analysis, which has been widely used in protein folding studies, can potentially generate new mechanistic information for long-range proton transfers regarding the sequence of events. The results of the perturbation analysis and the Phi analysis provide opportunities for experimentally testing the mechanistic proposals from this study and our recent work in which a stepwise "proton hole" transfer pathway has been proposed.     

Evidence that glucagon stabilizes rather than activates mitochondrial functions in rat liver

The present study is concerned with the question as to whether the acute treatment of intact rats or hepatocytes with glucagon and dibutyryl cAMP, respectively, leads to a stabilization or an activation of mitochondrial functions, such as state-3 respiration, succinate dehydrogenase activity and pyruvate carboxylase activity. For this purpose, the influence of various parameters of mitochondria preparation (isolation medium, washing steps, storage) as well as of phospholipase A inhibitors (cinchocain, chloroquine) on the expression of the hormone effect was examined. With regard to the above mentioned functions, the values displayed by control mitochondria were found to be considerably higher if mannitol instead of sucrose had been used for isolation. Accordingly, only small effects of hormone treatment became apparent. The addition of cinchocain or chloroquine to the sucrose medium yielded results similar to those obtained with mannitol. Furthermore, the hormone effect on state-3 respiration and succinate dehydrogenase activity was only small if the mitochondria had been prepared faster than usual and had been used without washing. Regarding pyruvate carboxylase, a considerably smaller glucagon effect was observed when it was assayed at 25 degrees C and not (as usual) at 37 degrees C. Our results indicate that glucagon application stabilizes rather than activates mitochondrial functions.     

Class I MHC molecules rather than other mouse genes dictate influenza epitope recognition by cytotoxic T cells

Influenza nucleoprotein (NP) is an important target antigen for influenza A virus cross-reactive cytotoxic T cells (Tc). Here we examine the NP epitope recognized by cloned and polyclonal BALB/c Tc and the genetics of this recognition pattern. We can define NP residues 147–161 as the epitope seen in conjunction with K ^d , the only H-2^d class I responder allele for NP restriction. H-2 ^d /H-2 ^b F₁ mice (C57BL × DBA/2) primed by influenza infection lyse only H-2^d target cells treated with peptide 147–161 while H-2^b targets are recognized only after treatment with NP residues 365–379 (previously found to be recognized by D^b restricted Tc cells). Tc cell recognition of NP peptide 147–161 is entirely dictated by expression of K ^d and not by other B10 or OH background genes of congenic mice. Restriction of a unique NP sequence by each responder class I major histocompatibility complex (MHC) allele suggests that antigen and class I MHC interact for Tc recognition.     

Effects of extracellular matrices derived from different cell sources on chondrocyte functions

Cell-derived extracellular matrices (ECMs) are a key factor in regulating cell functions in tissue engineering and regenerative medicine. The fact that cells are surrounded by their specific ECM in vivo elicits the need to elucidate the effects of ECM derived from different cell sources on cell functions. Here, three types of ECM were prepared by decellularizing cultured chondrocytes, fibroblasts, and mesenchymal stem cells (MSC) and used for chondrocyte culture to compare their effects on chondrocyte adhesion, proliferation, and differentiation. Chondrocyte adhesion to the chondrocyte-derived ECM was greater than those to the fibroblast- and MSC-derived ECM. Chondrocyte proliferation on the chondrocyte-derived ECM was lower than those on the fibroblast- and MSC-derived ECM. The ECM showed no evident effect on chondrocyte differentiation. The effects of ECM on cell functions depended on the cell source used to prepare the ECM.     

The thioredoxin homolog YbbN functions as a chaperone rather than as an oxidoreductase

Escherichia coli contains two thioredoxins, Trx1 and Trx2, and a thioredoxin-like protein, YbbN, which presents a strong homology in its N-terminal part with thioredoxins, and possesses a 20 kDa C-terminal part of unknown function. We reported previously that YbbN displays both protein oxido-reductase and chaperone properties in vitro. In this study, we show that an ybbN-deficient strain displays an increased sensitivity to thermal stress but not to oxidative stress, a normal redox state of its cellular proteins but a decreased expression of several cytoplasmic proteins, including EF-Tu, DnaK, GroEL, trigger factor and several Krebs cycle enzymes, suggesting that the chaperone properties of YbbN are more important in vivo than its redox properties. YbbN specifically interacts with DnaK and GroEL, as shown by reverse purification. It increases 4-fold the rate of protein renaturation in vitro by the DnaK chaperone machine, suggesting that it cooperates with DnaK for the optimal expression of several cytoplasmic proteins.     

Ant navigation: one-way routes rather than maps

In recent years, there has been an upsurge of interest and debate about whether social insects-central-place foragers such as bees and ants-acquire and use cognitive maps, which enable the animal to steer novel courses between familiar sites . Especially in honey bees, it has been claimed that these insects indeed possess such "general landscape memories" and use them in a "map-like" way . Here, we address this question in Australian desert ants, Melophorus bagoti, which forage within cluttered environments full of nearby and more distant landmarks. Within these environments, the ants establish landmark-based idiosyncratic routes from the nest to their feeding sites and select different one-way routes for their outbound and inbound journeys. Various types of displacement experiments show that inbound ants when hitting their inbound routes at any particular place immediately channel in and follow these routes until they reach the nest, but that they behave as though lost when hitting their habitual outbound routes. Hence, familiar landmarks are not decoupled from the context within which they have been acquired and are not knitted together in a more general and potentially map-like way. They instruct the ants when to do what rather than provide them with map-like information about their position in space.     

Hippocampal Remapping Is Constrained by Sparseness rather than Capacity

Grid cells in the medial entorhinal cortex encode space with firing fields that are arranged on the nodes of spatial hexagonal lattices. Potential candidates to read out the space information of this grid code and to combine it with other sensory cues are hippocampal place cells. In this paper, we investigate a population of grid cells providing feed-forward input to place cells. The capacity of the underlying synaptic transformation is determined by both spatial acuity and the number of different spatial environments that can be represented. The codes for different environments arise from phase shifts of the periodical entorhinal cortex patterns that induce a global remapping of hippocampal place fields, i.e., a new random assignment of place fields for each environment. If only a single environment is encoded, the grid code can be read out at high acuity with only few place cells. A surplus in place cells can be used to store a space code for more environments via remapping. The number of stored environments can be increased even more efficiently by stronger recurrent inhibition and by partitioning the place cell population such that learning affects only a small fraction of them in each environment. We find that the spatial decoding acuity is much more resilient to multiple remappings than the sparseness of the place code. Since the hippocampal place code is sparse, we thus conclude that the projection from grid cells to the place cells is not using its full capacity to transfer space information. Both populations may encode different aspects of space.     

Effects of extracellular matrix proteins in chondrocyte‐derived matrices on chondrocyte functions

Loss of cartilaginous phenotype during in vitro expansion culture of chondrocytes is a major barrier to the application of chondrocytes for tissue engineering. In previous study, we showed that dedifferentiation of chondrocytes during the passage culture was delayed by matrices formed by primary chondrocytes (P0‐ECM). In this study, we investigated bovine chondrocyte functions when being cultured on isolated extracellular matrix (ECM) protein‐coated substrata and P0‐ECM. Low chondrocyte attachment was observed on aggrecan‐coated substratum and P0‐ECM. Cell proliferation on aggrecan‐ and type II collagen/aggrecan‐coated substrata and P0‐ECM was lower than that on the other ECM protein (type I collagen and type II collagen)‐coated substrata. When chondrocytes were subcultured on aggrecan‐coated substratum, decline of cartilaginous gene expression was delayed, which was similar to the cells subcultured on P0‐ECM. These results indicate that aggrecan plays an important role in the regulation of chondrocyte functions and P0‐ECM may be a good experimental control for investigating the role of each ECM protein in cartilage ECM. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:1331–1336, 2013     

Role of the extracellular matrix in cell-cell signalling: paracrine paradigms

The plant extracellular matrix (ECM) is complex and diverse, and is involved in cell-cell communication in a wide range of developmental, reproductive and pathogenic processes. Characterisation of integral ECM components is leading to improved understanding of their roles in signalling. Interactions between the extracellular domains of plant plasma membrane receptor kinases and their ligands are potentially regulated by the properties of the ECM. Several of these interactions, for example those involving the S-locus receptor kinase, are being characterised in some detail. Non-protein constituents are also implicated in regulating the movement of signalling molecules in the ECM, which is associated with developmental patterning. In contrast to the situation in animal cells, cytoskeleton-integrin-ECM signalling complexes appear not to be dominant features of signal transduction in plant cells. Nevertheless, structural adhesions between the plasma membrane and cell wall are important for a variety of functions.     

Immune response to leishmania: paradox rather than paradigm

The leishmaniases are a group of diseases caused by protozoan parasites of the genus Leishmania. Various Leishmania species can cause human infection, producing a spectrum of clinical manifestations. It is estimated that 350 million people are at risk, with a global yearly incidence of 1-1.5 million for cutaneous and 500,000 for visceral leishmaniasis (VL). VL is a major cause of morbidity and mortality in East Africa and the Indian subcontinent. Coinfection with HIV enhances the risk of the disease. The only control measure currently available in India is case detection and treatment with antimonial drugs, which are expensive, not always available and cannot be self-administered. Newer drugs like oral miltefosine have not become widely available. Vector and reservoir control is difficult due to the elusive nature of the vector and the diversity of the animal reservoir. A detailed knowledge of immune response to the parasite would help in designing prophylactic and therapeutic strategies against this infection.     

Binding of extracellular matrix molecules by probiotic bacteria

AIMS: The aim of this study was to investigate extracellular matrix (ECM) and mucin binding of selected bacterial isolates with probiotic features in comparison with commercially used probiotic bacteria. METHODS AND RESULTS: ECM molecules were immobilized in microtitre plates (mucin and fetuin) or on the surface of latex beads. Porcine mucin was bound by all 13 probiotic strains tested with important inter-strain differences; however, fetuin binding was similar (weak) for all 14 strains tested. Strongly positive (three) binding of bovine fibrinogen was expressed by strains from fermented food (Lactobacillus rhamnosus GG, L. casei Shirota and L. johnsonii La1) as well as by L. casei L.c., Lactobacillus sp. 2I3 and by L. plantarum LP. The other strains expressed moderate (2) or weakly positive (1) binding of bovine fibrinogen. Strongly positive (3) binding of porcine fibronectin was observed only with two strains; however, all other strains also bound this molecule. Bovine lactoferrin was bound to a higher extent than transferrins. SIGNIFICANCE AND IMPACT OF THE STUDY: Some animal strains (at least L. casei L.c. and Lactobacillus sp. 2I3) are comparable with the commercially used strains with respect to their ECM binding ability. As this feature is important for probiotic bacteria to be able to colonize intestine, these strains should be considered for their wider use in fermented feed (or probiotic preparations) for animals.     

The nature of stem cells: state rather than entity

Stem cells are endowed with self-renewal and multipotential differentiation capacities. Contrary to the expectation that stem cells would selectively express specific genes, these cells have a highly promiscuous gene-expression pattern. Here, I suggest that the transient stem cell state, termed the 'stem state', may be assumed by any cell and that the search for specific genes expressed by all stem cells, which would characterize the stem cell as a cell type, might be futile.     

Modular extracellular matrices: solutions for the puzzle

The common technique of growing cells in two-dimensions (2-D) is gradually being replaced by culturing cells on matrices with more appropriate composition and stiffness, or by encapsulation of cells in three-dimensions (3-D). The universal acceptance of the new 3-D paradigm has been constrained by the absence of a commercially available, biocompatible material that offers ease of use, experimental flexibility, and a seamless transition from in vitro to in vivo applications. The challenge-the puzzle that needs a solution-is to replicate the complexity of the native extracellular matrix (ECM) environment with the minimum number of components necessary to allow cells to rebuild and replicate a given tissue. For use in drug discovery, toxicology, cell banking, and ultimately in reparative medicine, the ideal matrix would therefore need to be highly reproducible, manufacturable, approvable, and affordable. Herein we describe the development of a set of modular components that can be assembled into biomimetic materials that meet these requirements. These semi-synthetic ECMs, or sECMs, are based on hyaluronan derivatives that form covalently crosslinked, biodegradable hydrogels suitable for 3-D culture of primary and stem cells in vitro, and for tissue formation in vivo. The sECMs can be engineered to provide appropriate biological cues needed to recapitulate the complexity of a given ECM environment. Specific applications for different sECM compositions include stem cell expansion with control of differentiation, scar-free wound healing, growth factor delivery, cell delivery for osteochondral defect and liver repair, and development of vascularized tumor xenografts for personalized chemotherapy.     

Interaction against different environmental dynamics during a leg extension task is controlled by temporal rather than amplitude scaling of muscular activity

Force exertion against different mechanical environments can affect motor control strategies in order to account for the altered environmental dynamics and to maintain the ability to produce force. Here, we investigated the change of muscular activity of selected muscles of the lower extremities while the participants interacted with an external mechanical device of variable stability. Twenty-five healthy participants exerted force against the device by performing a unilateral ballistic leg extension task under 1 or 3 degrees of freedom (DoF). Directional force data and electromyographic responses from four leg muscles (TA, VM, GM, PL) were recorded. Muscle responses to the altered experimental conditions were analyzed by calculating time to peak electrical activity (TTP), peak electrical activity (PEA), slope of EMG-signal and muscle activity. It was found that neuromuscular system adjustments to the task are expressed mainly by temporal (TTP) rather than amplitude (PEA) scaling of muscular activity. This change was specific for the investigated muscles. Moreover, a selective increase of muscle activity occurred while increasing external DoF. This scheme was accompanied by a significant reduction of applicable force against the device in the unstable 3 DoF condition. The findings suggest that orchestration of movement control is linked to environmental dynamics also affecting the ability to produce force under dynamic conditions. The adjustments of the neuromuscular system are rather temporal in nature being consistent with the impulse timing hypothesis of motor control.     

DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization

The effect of secondary structure on DNA duplex formation is poorly understood. Using oxDNA, a nucleotide level coarse-grained model of DNA, we study how hairpins influence the rate and reaction pathways of DNA hybridzation. We compare to experimental systems studied by Gao et al. (1) and find that 3-base pair hairpins reduce the hybridization rate by a factor of 2, and 4-base pair hairpins by a factor of 10, compared to DNA with limited secondary structure, which is in good agreement with experiments. By contrast, melting rates are accelerated by factors of ∼100 and ∼2000. This surprisingly large speed-up occurs because hairpins form during the melting process, and significantly lower the free energy barrier for dissociation. These results should assist experimentalists in designing sequences to be used in DNA nanotechnology, by putting limits on the suppression of hybridization reaction rates through the use of hairpins and offering the possibility of deliberately increasing dissociation rates by incorporating hairpins into single strands.