All roads lead to Rome (but some may be harder to travel): SRP-independent translocation into the endoplasmic reticulum

Abstract

Translocation into the endoplasmic reticulum (ER) is the first biogenesis step for hundreds of eukaryotic secretome proteins. Over the past 30 years, groundbreaking biochemical, structural and genetic studies have delineated one conserved pathway that enables ER translocation- the signal recognition particle (SRP) pathway. However, it is clear that this is not the only pathway which can mediate ER targeting and insertion. In fact, over the past decade, several SRP-independent pathways have been uncovered, which recognize proteins that cannot engage the SRP and ensure their subsequent translocation into the ER. These SRP-independent pathways face the same challenges that the SRP pathway overcomes: chaperoning the preinserted protein while in the cytosol, targeting it rapidly to the ER surface and generating vectorial movement that inserts the protein into the ER. This review strives to summarize the various mechanisms and machineries which mediate these stages of SRP-independent translocation, as well as examine why SRP-independent translocation is utilized by the cell. This emerging understanding of the various pathways utilized by secretory proteins to insert into the ER draws light to the complexity of the translocational task, and underlines that insertion into the ER might be more varied and tailored than previously appreciated.     

The cysteine 34 residue of A1M/α1-microglobulin is essential for protection of irradiated cell cultures and reduction of carbonyl groups

Abstract

α₁-microglobulin (A1M) is a 26 kDa plasma and a tissue protein belonging to the lipocalin family. The reductase and free radical scavenger A1M has been shown to protect cells and extracellular matrix against oxidative and irradiation-induced damage. The reductase activity was previously shown to depend upon an unpaired cysteinyl side-chain, C34, and three lysyl side-chains, K92, 118, and 130, located around the open end of the lipocalin pocket. The aim of this work was to investigate whether the cell and matrix protection by A1M is a result of its reductase activity by using A1M-variants with site-directed mutations of the C34, K92, K118, and K130 positions. The results show that the C34 side-chain is an absolute requirement for protection of HepG2 cell cultures against alpha-particle irradiation-induced cell death, upregulation of stress response and cell cycle regulation genes. Mutation of C34 also resulted in loss of the reduction capacity toward heme- and hydrogen peroxide-oxidized collagen, and the radical species 2,2´-azino-bis (3-ethyl-benzo-thiazoline-6-sulphonic acid) (ABTS). Furthermore, mutation of C34 significantly suppressed the cell-uptake of A1M. The K92, K118, and K130 side-chains were of minor importance in cell protection and reduction of oxidized collagen but strongly influenced the reduction of the ABTS-radical. It is concluded that antioxidative protection of cells and collagen by A1M is totally dependent on its C34 amino acid residue. A model of the cell protection mechanism of A1M should be based on the redox activity of the free thiolyl group of the C34 side-chain and a regulatory role of the K92, K118, and K130 residues.     

Development and set-up of a portable device to monitor airway exhalation and deposition of particulate matter

The aim of this study was to assess and monitor airway exhalation and deposition of particulate matter (PM). After standardizing inspiratory/expiratory flow and volumes, a novel device was tested on a group of 20 volunteers and in a field study on workers exposed to cristobalite. Both male and female subjects showed a higher percentage of deposition in the 0.5?μm channel than in the 0.3?μm channel on a laser particle counter, but it was higher in the males because of their higher exhaled lung volumes. The device was tested on a wider range of particles (0.3–0.5–1.0–2.5?μm) in the cristobalite productive division. The device has low intrasubject variability and good reproducibility, with geometric mean of %CV?相似文献   

Aquaporin Trafficking in Plant Cells: An Emerging Membrane‐Protein Model

Aquaporins (AQPs) are channel proteins that facilitate the transport of water and small solutes across biological membranes. In plants, AQPs exhibit a high multiplicity of isoforms in relation to a high diversity of sub‐cellular localizations, at the plasma membrane (PM) and in various intracellular compartments. Some members also exhibit a dual localization in distinct cell compartments, whereas others show polarized or domain‐specific expression at the PM or tonoplast, respectively. A diversity of mechanisms controlling the routing of newly synthesized AQPs towards their destination membranes and involving diacidic motifs, phosphorylation or tetramer assembly is being uncovered. Recent approaches using single particle tracking, fluorescence correlation spectroscopy and fluorescence recovery after photobleaching have, in combination with pharmacological interference, stressed the peculiarities of AQP sub‐cellular dynamics in environmentally challenging conditions. A role for clathrin and sterol‐rich domains in cell surface dynamics and endocytosis of PM AQPs was uncovered. These recent advances provide deep insights into the cellular mechanisms of water transport regulation in plants. They also point to AQPs as an emerging model for studying the sub‐cellular dynamics of plant membrane proteins .     

Fabrication,Operation and Flow Visualization in Surface-acoustic-wave-driven Acoustic-counterflow Microfluidics

Surface acoustic waves (SAWs) can be used to drive liquids in portable microfluidic chips via the acoustic counterflow phenomenon. In this video we present the fabrication protocol for a multilayered SAW acoustic counterflow device. The device is fabricated starting from a lithium niobate (LN) substrate onto which two interdigital transducers (IDTs) and appropriate markers are patterned. A polydimethylsiloxane (PDMS) channel cast on an SU8 master mold is finally bonded on the patterned substrate. Following the fabrication procedure, we show the techniques that allow the characterization and operation of the acoustic counterflow device in order to pump fluids through the PDMS channel grid. We finally present the procedure to visualize liquid flow in the channels. The protocol is used to show on-chip fluid pumping under different flow regimes such as laminar flow and more complicated dynamics characterized by vortices and particle accumulation domains.     

Dissipative particle dynamics simulation of the soft micro actuator using polymer chain displacement in electro-osmotic flow

ABSTRACT

In this research, the numerical simulation of a soft polymer micro actuator performance has been investigated using the dissipative particle dynamics method in electro-osmotic flow. Effective factors including electro-osmotic flow and polymer chain parameters have been studied. First of all, considering a wide range of electro-osmotic parameters, the validation of analytical results is carried out in a simple micro channel. The electric field and zeta potential changes are linearly related to the flow rate, and the kh parameter behaves nonlinearly to around the kh?=?10. In the following, a convergent–divergent channel is used for the soft micro actuator simulation in which a polymer chain as a heart of actuation is embedded in the middle. As the main control parameter, the direction of the electric field is changed every 4?s, and it leads to a reciprocating motion. The numerical results indicate that the displacement of the soft polymer chain will be increased by enhancing the electric field, the number of beads, decreasing the harmonic bond coefficient and also exposing more length of a polymer chain in front of fluid flow. The results of this study may be useful for some future applications such as artificial fibres and muscles.     

On the Application of Widom's Test Particle Method to Homogeneous and Inhomogeneous Fluids

Abstract

Chemical potentials of a homogeneous and an inhomogeneous Lennard-Jones fluid have been determined by molecular dynamics simulations on the vector computer CYBER 205 by applying essentially the fictitious test particle method of Widom. For the homogeneous fluid we find, contrary to the previous result of Guillot and Guissani, that the simulated chemical potential is independent of the particle number. The crucial point, however, is a sufficiently large cut-off radius in the evaluation of the Boltzmann factor. Comparing with our WCA-type perturbation theory, we get agreement in the chemical potentials within 0.1 kT up to the density n[sgrave]³ = 0.80 and a difference of 0.2 kT at n[sgrave]³ = 0.85. For the inhomogeneous case we consider a fluid in a cylindrical pore and integrate Widom's equation over a certain probe volume as suggested earlier by us. Chemical potentials are then calculated independently in five different probe volumes, which are cylindrical shells. The results agree well from the second to the fourth shell. Inaccuracies in the innermost cylinder can be easily explained by bad statistics. In the shell close to the wall the extremely high local density is responsible for the inaccuracies. Extending the probe volume over all cylindrical shells besides the one closest to the wall is thought to yield rather reliable results for the chemical potential. As a by-product of the simulations we also obtained diffusion coefficients, which are given in an appendix.     

Dissipative particle dynamics of non-spherical particles using a Gaussian density model

The Gaussian density molecular model has been adapted for dissipative particle dynamics. The model, when combined with a soft potential, is shown to be a very flexible mesoscale model exhibiting a wide range of phase behaviour. The soft potential allows relatively large time steps to be used and hence a more rapid equilibration. In addition, the model can be used to study both uniaxial and biaxial systems. We have undertaken a number of pilot studies and have demonstrated that the Gaussian model is able to identify nematic–isotropic phase transitions in liquid crystals and the formation of ordered discotic phases.     

Dissipative particle dynamics simulation on the meso-scale structure of diblock copolymer under cylindrical confinement

The meso-scale structure of symmetric diblock copolymer under cylindrical confinement is studied by dissipative particle dynamics (DPD). The simulation results show that coiled cylindrical geometry is favored in the presence of larger cylinder radius (R/L ₀>～1.5), and the number of rings depends on the cylinder radius. Because of the cylinder wall's selectivity, each block can form the central core, but only the preferential block forms the outmost layer. An approximately linear relationship exists between structure transition point, which is approximately in proportion to the 3/5 exponential of chain length of copolymer and number of layers. As the cylinder radius is decreased, a helical morphology is found. Lamellae parallel to the underside of the cylinder appear when the cylinder radius is made smaller (R/L ₀ < ～1.1).     

Heat transfer simulation using energy conservative dissipative particle dynamics

Dissipative particle dynamics with energy conservation (eDPD) was used to investigate conduction heat transfer in two dimensions under steady-state condition. Various types of boundary condition were implemented to the conduction domain. Besides, 2D conduction with internal heat generation was studied and the heat generation term was used to measure the thermal conductivity and diffusivity of the eDPD system. The boundary conditions used include both the Neumann and Dirichlet boundary conditions. The Neumann boundary condition was applied via adiabatic surfaces and surfaces exposed to convection heat transfer. The DPD simulations were compared to analytical solutions and finite-difference techniques. It was found that DPD appropriately predicts the temperature distribution in the conduction regime. Details of boundary condition implementation and thermal diffusivity measurement are also described in this paper.