Mirror‐symmetric microtubule assembly and cell interactions drive lumen formation in the zebrafish neural rod

By analysing the cellular and subcellular events that occur in the centre of the developing zebrafish neural rod, we have uncovered a novel mechanism of cell polarisation during lumen formation. Cells from each side of the neural rod interdigitate across the tissue midline. This is necessary for localisation of apical junctional proteins to the region where cells intersect the tissue midline. Cells assemble a mirror‐symmetric microtubule cytoskeleton around the tissue midline, which is necessary for the trafficking of proteins required for normal lumen formation, such as partitioning defective 3 and Rab11a to this point. This occurs in advance and is independent of the midline cell division that has been shown to have a powerful role in lumen organisation. To our knowledge, this is the first example of the initiation of apical polarisation part way along the length of a cell, rather than at a cell extremity. Although the midline division is not necessary for apical polarisation, it confers a morphogenetic advantage by efficiently eliminating cellular processes that would otherwise bridge the developing lumen.     

C-terminal actin-binding sites of smooth muscle caldesmon switch actin between conformational states

Caldesmon is a component of the thin filaments of smooth muscles where it is believed to play an essential role in regulating the thin filaments’ interaction with myosin and hence contractility. We studied the effects of caldesmon and two recombinant fragments CaDH1 (residues 506–793) and CaDH2 (residues 683–767) on the structure of actin–tropomyosin by making measurements of the fluorescence polarisation of probes specifically attached to actin. CaDH1, like the parent molecule caldesmon, is an inhibitor of actin–tropomyosin interaction with myosin whilst CaDH2 is an activator. The F-actin in permeabilised and myosin free rabbit skeletal muscle ‘ghost’ fibres was labelled by tetramethyl rhodamine-isothiocyanate (TRITC)–phalloidin or fluorescein-5′-isothiocyanate (FITC) at lysine 61. Fluorescence polarisation measurements were made and the parameters Φ_A, Φ_E, Θ_1/2 and N were calculated. Φ_A and Φ_E are angles between the fiber axis and the absorption and emission dipoles, respectively; Θ_1/2 is the angle between the F-actin filament axis and the fiber axis; N is the relative number of randomly oriented fluorophores. Actin–tropomyosin interaction with myosin subfragment-1 induced changes in the parameters of the polarised fluorescence that are typical of strong binding of myosin to actin and of the ‘on’ conformational state of actin. Caldesmon and CaDH1 (as well as troponin in the absence of Ca²⁺) diminished the effect of S-1, whereas CaDH2 (as well as troponin in the presence of Ca²⁺) enhanced the effect of S1. Thus the structural evidence correlates with biochemical evidence that C-terminal actin-binding sites of caldesmon can modulate the structural transition of actin monomers between ‘off’ (caldesmon and CaDH1) and ‘on’ (S-1 and CaDH2) states in a manner analogous to troponin.     

Changes in cardiac electrophysiology,morphology, tissue biochemistry and vascular reactions in glutathione depleted animals

Human placental syncytiotrophoblast basal membrane plays an important role in transfer of nutrients from the mother to the growing fetus all throughout gestation. The membrane lipid composition together with the bilayer fluidity is found to be the major index in modulation of these transport processes. In the present study, the effects of changing lipid composition on the placental basal membrane fluidity and the modulating influence of the latter on membrane enzyme and transport functions with progress of gestation,were investigated. Steady-state fluorescence analysis using 1,6-diphenyl-1,3,5 hexatriene as the probe, indicated a decrease in fluorescence anisotropy of both labeled native membrane vesicles and liposomes prepared from lipids extracted from the basal membrane vesicles, signifying increased bilayer fluidity with progress of gestation. This in turn, was successfully correlated to the lowering of cholesterol content and enhanced phospholipid concentration with a steady decrease in cholesterol/phospholipid ratio during placental development. Enhanced Na⁺-K⁺-ATPase activity and steady-state glucose uptake across basal membrane with gestational progress suggested modulation of membrane protein functions by the fluidity, which was further corroborated by the increased bilayer fluidity and enzyme activity in benzyl alcohol treated basal membrane in each gestational age group.     

A salt-bridge switch in the molecular recognition between RS receptor and RGD ligand from the ABEEM σπ molecular dynamics simulations

Abstract

How the receptor and ligand recognise each other is a challenging subject in explaining the mechanism of recognition at the molecular level. As a starting point, here, a synthesised RS receptor and its RGD ligand were investigated as a proper model to simulate their recognition process in terms of ABEEMσπ/MM polarisable force field. It is found that a switch of forming up a salt bridge in the ligand triggers the recognition of the receptor and ligand. Through the salt-bridge switch that undergoes several cycles from on-state with parallel hydrogen bonds to off-state with bifurcated hydrogen bonds, the active site of ligand can flex easily to interact with the active site of the receptor. In addition, the water molecules form a decisive bridge connecting the active sites of the bound system. The salt-bridge switch and water-mediated movement are cooperative as the important factors for the receptor-ligand recognition. In addition, the properties, such as binding free energy, conformational flexibility and solvent accessible surface area have been calculated to provide adequate evidence for the whole recognition process. According to the simulation, a detailed mechanism was derived involving diffusion, a switch triggered cooperative water-mediated movement, and conformational folding, for the flexible recognition.     

Solid-state NMR and functional studies on proteorhodopsin

Proteins of the proteorhodopsin (PR) family are found abundantly in many marine bacteria in the photic zone of the oceans. They are colour-tuned to their environment. The green absorbing species has been shown to act as a light-driven proton pump and thus could form a potential source of energy. The pK_a of the primary proton acceptor is close to the pH of seawater which could also indicate a regulatory role. Here, we review and summarize our own recent findings in the context of known data and present some new results. Proton transfer in vitro by PR is shown by a fluorescence assay which confirms a pH dependent vectoriality. Previously reported low diffracting 2D crystal preparations of PR are assessed for their use for solid-state NMR by two dimensional ¹³C-¹³C DARR spectra. ¹⁵N-¹H HETCOR MAS NMR experiments show bound water in the vicinity of the protonated Schiff base which could play a role in proton transfer. The effect of highly conserved H75 onto the properties of the chromophore has been investigated by single site mutations. They do show a pronounced effect onto the optical absorption maximum and the pK_a of the proton acceptor but have only a small effect onto the ¹⁵N chemical shifts of the protonated Schiff base.     

Extended Flip-back Schemes for Sensitivity Enhancement in Multidimensional HSQC-type Out-and-back Experiments

In many NMR experiments, only polarisation of a limited sub-set of all protons is converted into observable coherence. As recently shown by the “longitudinal” TROSY implementation (Pervushin et al. (2002) J. Am. Chem. Soc., 124, 12898–12902) and SOFAST-HMQC (Schanda and Brutscher (2005) J. Am. Chem. Soc., 127, 8014–8015), recovery of unused polarisation can be used indirectly and unspecifically to cool the proton lattice and, thus, accelerate re-equilibration for the selected proton subset. Here we illustrate transfer of this principle to HSQC-based multi-dimensional out-and-back experiments that exploit only polarisation of ¹⁵N-bound protons. The presented modifications to the pulse sequences can be implemented broadly and easily, extending standard flip-back of water polarisation to a much larger pool of protons that may comprise all non−¹⁵N-bound protons. The underlying orthogonal separation of H^N polarisation (selected by the main transfer path) from unused H^u polarisation (flipped-back on the recovery path) is thereby achieved through positive or negative selection by J-coupling, or using band-selective pulses. In practice, H^u polarisation recovery degrades mostly through cumulative pulse imperfections and transverse relaxation; we present, however, strategies to substantially minimise such losses particularly during interim proton decoupling. Depending on the protein’s relaxation properties and the extended flip-back scheme employed, we recovered up to 60% H^u equilibrium polarisation. The concomitant cooling of the proton lattice afforded substantial gains of more than 40%, relative to the water-only flip-back version, in the fast pulsing regime with re-equilibration delays τ much shorter than optimal (τ_opt = 1.25 · T₁(H^N)). These would be typically employed if resolution requirements dominate the total measurement time. Contrarily, if sensitivity is limiting and optimal interscan delays τ_opt can be set (optimal pulsing regime), the best of the presented flip-back schemes may still afford up to ca. 10% absolute sensitivity enhancement.     

How can dragonflies discern bright and dark waters from a distance? The degree of polarisation of reflected light as a possible cue for dragonfly habitat selection

SUMMARY 1. Based on the findings that some dragonflies prefer either ‘dark’ or ‘bright’ water (as perceived by the human eye viewing downwards perpendicularly to the water surface), while others choose both types of water bodies in which to lay their eggs, the question arises: How can dragonflies distinguish a bright from a dark pond from far away, before they get sufficiently close to see it is bright or dark? 2. Our hypothesis is that certain dragonfly species may select their preferred breeding sites from a distance on the basis of the polarisation of reflected light. Is it that waters viewed from a distance can be classified on the basis of the polarisation of reflected light? 3. Therefore we measured, at an angle of view of 20° from the horizontal, the reflection‐polarisation characteristics of several ponds differing in brightness and in their dragonfly fauna. 4. We show that from a distance, at which the angle of view is 20° from the horizontal, dark water bodies cannot be distinguished from bright ones on the basis of the intensity or the angle of polarisation of reflected light. At a similar angle of view, however, dark waters reflect light with a significantly higher degree of linear polarisation than bright waters in any range of the spectrum and in any direction of view with respect to the sun. 5. Thus, the degree of polarisation of reflected light may be a visual cue for the polarisation‐sensitive dragonflies to distinguish dark and bright water bodies from far away. Future experimental studies should prove if dragonflies do indeed use this cue for habitat selection.     

NMR crystallography: The effect of deuteration on high resolution C solid state NMR spectra of a 7-TM protein

The effect of deuteration on the ¹³C linewidths of U-¹³C, ¹⁵N 2D crystalline bacteriorhodopsin (bR) from Halobacterium salinarium, a 248-amino acid protein with seven-transmembrane (7TM) spanning regions, has been studied in purple membranes as a prelude to potential structural studies. Spectral doubling of resonances was observed for receptor expressed in ²H medium (for both 50:50% 1H:2H, and a more highly deuterated form) with the resonances being of similar intensities and separated by < 0.3 ppm in the methyl spectral regions in which they were readily distinguished. Line-widths of the methyl side chains were not significantly altered when the protein was expressed in highly deuterated medium compared to growth in fully protonated medium (spectral line widths were about 0.5 ppm on average for receptor expressed both in the fully protonated and highly deuterated media from the Cδ, Cγ₁, and Cγ₂ Ile ¹³C signals observed in the direct, 21-39 ppm, and indirect, 9-17 ppm, dimensions). The measured ¹³C NMR line-widths observed for both protonated and deuterated form of the receptor are sufficiently narrow, indicating that this crystalline protein morphology is suitable for structural studies. ¹H decoupling comparison of the protonated and deuterated bR imply that deuteration may be advantageous for samples in which low power ¹H decoupling is required.