Enhancing the Cell-Free Expression of Native Membrane Proteins by In Silico Optimization of the Coding Sequence-An Experimental Study of the Human Voltage-Dependent Anion Channel.

Membrane proteins are involved in many aspects of cellular biology; for example, they regulate how cells interact with their environment, so such proteins are important drug targets. The rapid advancement in the field of immune effector cell therapy has been expanding the horizons of synthetic membrane receptors in the areas of cell-based immunotherapy and cellular medicine. However, the investigation of membrane proteins, which are key constituents of cells, is hampered by the difficulty and complexity of their in vitro synthesis, which is of unpredictable yield. Cell-free synthesis is herein employed to unravel the impact of the expression construct on gene transcription and translation, without the complex regulatory mechanisms of cellular systems. Through the systematic design of plasmids in the immediacy of the start of the target gene, it was possible to identify translation initiation and the conformation of mRNA as the main factors governing the cell-free expression efficiency of the human voltage-dependent anion channel (VDAC), which is a relevant membrane protein in drug-based therapy. A simple translation initiation model was developed to quantitatively assess the expression potential for the designed constructs. A scoring function that quantifies the feasibility of the formation of the translation initiation complex through the ribosome-mRNA hybridization energy and the accessibility of the mRNA segment binding to the ribosome is proposed. The scoring function enables one to optimize plasmid sequences and semi-quantitatively predict protein expression efficiencies. This scoring function is publicly available as webservice XenoExpressO at University of Vienna, Austria.

AFM and Fluorescence Microscopy of Single Cells with Simultaneous Mechanical Stimulation via Electrically Stretchable Substrates.

We have developed a novel experimental set-up that simultaneously, (i) applies static and dynamic deformations to adherent cells in culture, (ii) allows the visualization of cells under fluorescence microscopy, and (iii) allows atomic force microscopy nanoindentation measurements of the mechanical properties of the cells. The cell stretcher device relies on a dielectric elastomer film that can be electro-actuated and acts as the cell culture substrate. The shape and position of the electrodes actuating the film can be controlled by design in order to obtain specific deformations across the cell culture chamber. By using optical markers we characterized the strain fields under different electrode configurations and applied potentials. The combined setup, which includes the cell stretcher device, an atomic force microscope, and an inverted optical microscope, can assess in situ and with sub-micron spatial resolution single cell topography and elasticity, as well as ion fluxes, during the application of static deformations. Proof of performance on fibroblasts shows a reproducible increase in the average cell elastic modulus as a response to applied uniaxial stretch of just 4%. Additionally, high resolution topography and elasticity maps on a single fibroblast can be acquired while the cell is deformed, providing evidence of long-term instrumental stability. This study provides a proof-of-concept of a novel platform that allows in situ and real time investigation of single cell mechano-transduction phenomena with sub-cellular spatial resolution.

Baseline correction of AFM force curves in the force-time representation.

This note reports on the proper correction of force data acquired with an atomic force microscope (AFM). The force-time representation is hereby used to obtain the correction factors for the overall offset and slope for a single force-time curve, as the initial force, F0 = F(t0 ), and the rate of change in the force per unit of time, dF/dt, respectively. The report shows that a complete set of force data, including the approach, delay and retraction regions, can be simultaneously corrected in the force-time representation by subtracting the line CLt = F0 + dF/dt·t to the experimental data. The method described here outperforms the one commonly employed in the correction of AFM force curves and highlights the convenience of using the force-time representation for force data processing wherein the artifactual behavior can be expressed as a single, differentiable function of time.

Inward multivesiculation at the basal membrane of adherent giant phospholipid vesicles.

Adherent giant vesicles composed of phosphatidylcholine, phosphatidylserine and biotinylated lipids form clusters of inward spherical buds at their basal membrane. The process is spontaneous and occurs when the vesicles undergo a sequence of osmotic swelling and deswelling. The daughter vesicles have a uniform size (diameter ≈ 2-3 µm), engulf small volumes of outer fluid and remain attached to the region of the membrane from which they generate, even after restoring the isotonicity. A pinning-sealing mechanism of long-wavelength modes of membrane fluctuations is proposed, by which the just-deflated vesicles reduce the surplus of membrane area and avoid excessive spreading and compression via biotin anchors. The work discusses the rationale behind the mechanism that furnishes GUVs with basal endovesicles, and its prospective use to simulate cellular events or to create molecular carriers.

A new automatic contact point detection algorithm for AFM force curves.

A new method for estimating the contact point in AFM force curves, based on a local regression algorithm, is presented. The main advantage of this method is that can be easily implemented as a computer algorithm and used for a fully automatic detection of the contact points in the approach force curves on living cells. The estimated contact points have been compared to those obtained by other published methods, which were applied either for materials with an elastic response to indentation forces or for experiments at high loading rates. We have found that the differences in the values of the contact points estimated with three different methods were not statistically significant and thus the algorithm is reliable. Also, we test the convenience of the algorithm for batch-processing by computing the contact points of a force curve map of 625 (25×25) curves.

Nanostructure of polysaccharide complexes.

The interaction of gum arabic (GA) with chitosan (Ch) of different degree of deacetylation was studied by turbidity measurements, dynamic light scattering and atomic force microscopy. The structure of the complexes was found to be directly related to the charge density of chitosan molecules. Gum arabic and chitosan with a degree of deacetylation of 75% form soluble complexes with a loosely globular structure of about 250 nm, at weight ratios up to 1.2, if the concentrations are kept low (total biopolymer concentration up to 0.06%). If chitosan has a higher charge density (degree of deacetylation of 93%), colloidal particles are formed, independently of the polymer concentration or ratio. At low concentrations and GA/Ch ratios of 1 or 1.2, the particles have diameters of 200-250 nm. The formation of soluble complexes is attributed to a chitosan lower charge density and the presence of non-charged monomers, which prevent the efficient self-assembly of the macromolecules.

Stress relaxation and creep on living cells with the atomic force microscope: a means to calculate elastic moduli and viscosities of cell components.

In this work we present a unified method to study the mechanical properties of cells using the atomic force microscope. Stress relaxation and creep compliance measurements permitted us to determine, the relaxation times, the Young moduli and the viscosity of breast cancer cells (MCF-7). The results show that the mechanical behaviour of MCF-7 cells responds to a two-layered model of similar elasticity but differing viscosity. Treatment of MCF-7 cells with an actin-depolymerising agent results in an overall decrease in both cell elasticity and viscosity, however to a different extent for each layer. The layer that undergoes the smaller decrease (36-38%) is assigned to the cell membrane/cortex while the layer that experiences the larger decrease (70-80%) is attributed to the cell cytoplasm. The combination of the method presented in this work, together with the approach based on stress relaxation microscopy (Moreno-Flores et al 2010 J. Biomech. 43 349-54), constitutes a unique AFM-based experimental framework to study cell mechanics. This methodology can also be extended to study the mechanical properties of biomaterials in general.

Rationalized approach to the determination of contact point in force-distance curves: application to polymer brushes in salt solutions and in water.

In this work, we present two methods to determine the contact point in force-distance curves obtained with the atomic force microscope. These procedures are compared with the typical determination of contact point by a visual assessment of the data. One method, based on the assumption that the sample shows linear elastic behavior, provides results similar to those obtained by a visual assessment of the data, and will be suitable for determining the contact point in cases where ionic repulsion is not significant. The second method is based on a series of measurements in which the sample deformation is measured at increasing values of applied load; the contact point is determined by extrapolation to zero load. Because this method is based on extrapolation of measurements made in the contact regime, it is not subject to long-range repulsion. It is thus suitable for the analyses of the contact point even in cases where ionic repulsions will affect the point at which individual force curves deviate from the baseline or zero-force regime. The methods described here are demonstrated with a glycopolymer brush compressed with a colloidal silica particle on the tip of the AFM cantilever.

Surface dependence of protein nanocrystal formation.

The self-assembly kinetics and nanocrystal formation of the bacterial surface-layer-protein SbpA are studied with a combination of quartz crystal microbalance with dissipation monitoring (QCM-D) and atomic force microscopy (AFM). Silane coupling agents, aminopropyltriethoxysilane (APTS) and octadecyltrichlorosilane (OTS), are used to vary the protein-surface interaction in order to induce new recrystallization pathways. The results show that the final S-layer crystal lattice parameters (a = b = 14 nm, gamma = 90 degrees ), the layer thickness (15 nm), and the adsorbed mass density (1700 ng cm(-2)) are independent of the surface chemistry. Nevertheless, the adsorption rate is five times faster on APTS and OTS than on SiO(2,) strongly affecting protein nucleation and growth. As a consequence, protein crystalline domains of 0.02 microm(2) for APTS and 0.05 microm(2) for OTS are formed, while for silicon dioxide the protein domains have a typical size of about 32 microm(2). In addition, more-rigid crystalline protein layers are formed on hydrophobic substrates. In situ AFM experiments reveal three different kinetic steps: adsorption, self-assembly, and crystalline-domain reorganization. These steps are corroborated by frequency-dissipation curves. Finally, it is shown that protein adsorption is a diffusion-driven process. Experiments at different protein concentrations demonstrate that protein adsorption saturates at 0.05 mg mL(-1) on silane-coated substrates and at 0.07 mg mL(-1) on hydrophilic silicon dioxide.

Physical attachment of fluorescent protein particles to atomic force microscopy probes in aqueous media: implications for surface pH, fluorescence, and mechanical properties studies.

Transfer of a fluorescently labeled protein particle from a surface to a microsized scanning probe has been induced by repetitive scanning in aqueous medium. The so-attached particle can in turn act as a probing tool to study particle-substrate and particle-particle interactions. Attachment of the fluorescent particle occurs at the apical region of an atomic force microscope (AFM) cantilever tip and it endures repetitive loading-unloading cycles against the sample surface. Fluorescence microscopy has been used to address the exact location of the attached particle in the cantilever and to identify the moment when the particle contacts the sample. Moreover, we have observed that fluorescence intensity at the contact point is lower when the probing particle contacts another fluorescent particle than when it contacts the nonfluorescent substrate. The change in fluorescence is attributed to local changes of pH and interparticle-quenching of fluorophores in the contact region. These findings are promising since they constitute a chemical-free way to attach bioparticles to AFM probes under physiological conditions. The atomic force microscopy combined with fluorescence microscopy provides a straight forward method to study particle/particle and particle/substrate interactions, as well as to investigate mechanical properties of biocolloids.

Stress relaxation microscopy: imaging local stress in cells.

Biomechanics is gaining relevance as complementary discipline to structural and cellular biology. The response of cells to mechanical stimuli determines cell type and function, while the spatial distribution of mechanical forces within the cells is crucial to understand cell activity. The experimental methodologies to approach cell mechanics are diverse but either they are effective in few cases or they rule out the innate cell complexity. In this regard, we have developed a simple scanning probe-based methodology that overcomes the limitations of the available methods. Stress relaxation, the decay of the force exerted by the cell surface at constant deformation, has been used to extract relaxational responses at each cellular sublocalisation and generate maps. Surprisingly, decay curves exerted by test cells are fully described by a generalized viscoelastic model that accounts for more than one simultaneously occurring relaxations. Within the range of applied forces (0.5-4nN) a slow and a fast relaxation with characteristic times of 0.1 and 1s have been detected and assigned to rearrangements of cell membrane and cytoskeleton, respectively. Relaxation time mapping of entire cells is thus promising to simultaneously detect non-uniformities in membrane and cytoskeleton and as identifying tool for cell type and disease.

Quantitative characterization of nanoadhesion by dynamic force spectroscopy.

We present a method for the characterization of adhesive bonds formed in nanocontacts. Using a modified atomic force microscope, the nanoadhesion between a silicon nitride tip and a self-assembled monolayer of 1-nonanethiol on gold(111) was measured at different loading rates. Adhesion force-versus-loading rate curves could be fitted with two logarithmic terms, indicating a two step (two energy barrier) process. The application of the Bell-Evans model and classical contact mechanics allows the extraction of quantitative information about the effective adhesion potential and characterization of the different components contributing to nanoadhesion.

The new future of scanning probe microscopy: Combining atomic force microscopy with other surface-sensitive techniques, optical microscopy and fluorescence techniques.

Atomic force microscopy (AFM) is in its thirties and has become an invaluable tool for studying the micro- and nanoworlds. As a stand-alone, high-resolution imaging technique and force transducer, it defies most other surface instrumentation in ease of use, sensitivity and versatility. Still, the technique has limitations to overcome. A promising way is to integrate the atomic force microscope into hybrid devices, a combination of two or three complementary techniques in one instrument. In this way, a comprehensive description of molecular processes is at hand; morphological, (electro)chemical, mechanical and kinetic information are simultaneously obtained in one experiment. Hereby we review the recent efforts towards such development, describing the aim and the applications resulting from the combination of AFM with spectroscopic, optical, mechanical or electrochemical techniques. Interesting possibilities include using AFM to bring optical microscopies beyond the diffraction limit and also bestowing spectroscopic capabilities on the atomic force microscope.

Structure, surface interactions, and compressibility of bacterial S-layers through scanning force microscopy and the surface force apparatus.

Two-dimensional crystalline bacterial surface layers (S-layers) are found in a broad range of bacteria and archaea as the outermost cell envelope component. The self-assembling properties of the S-layers permit them to recrystallize on solid substrates. Beyond their biological interest as S-layers, they are currently used in nanotechnology to build supramolecular structures. Here, the structure of S-layers and the interactions between them are studied through surface force techniques. Scanning force microscopy has been used to study the structure of recrystallized S-layers from Bacillus sphaericus on mica at different 1:1 electrolyte concentrations. They give evidence of the two-dimensional organization of the proteins and reveal small corrugations of the S-layers formed on mica. The lattice parameters of the S-layers were a=b=14 nm, gamma=90 degrees and did not depend on the electrolyte concentration. The interaction forces between recrystallized S-layers on mica were studied with the surface force apparatus as a function of electrolyte concentration. Force measurements show that electrostatic and steric interactions are dominant at long distances. When the S-layers are compressed they exhibit elastic behavior. No adhesion between recrystallized layers takes place. We report for the first time, to our knowledge, the value of the compressibility modulus of the S-layer (0.6 MPa). The compressibility modulus is independent on the electrolyte concentration, although loads of 20 mN m-1 damage the layer locally. Control experiments with denatured S-proteins show similar elastic properties under compression but they exhibit adhesion forces between proteins, which were not observed in recrystallized S-layers.

Chemical and thermal denaturation of crystalline bacterial S-layer proteins: an atomic force microscopy study.

Crystalline monomolecular cell surface layers, S-layers, are one of the most common outermost cell envelope components of the prokaryotic organisms (bacteria and archaeda) that protects them from competitive habitats. Since isolated S-protein subunits are able to re-assemble into crystalline arrays on lipid films and solid supports making biomimetic surfaces, S-layer technology is currently used in nanobiotechnology. An important aspect of the biomimetic surfaces built with S-layers is their stability under extreme solvent conditions or temperature. Chemical (pH, alcohol) and physical (thermal) denaturant conditions were employed to test the stability of S-layers. Recrystallized bacterial surface layers from Bacillus sphaericus (SbpA) on hydrophilic silicon wafers loses the crystalline structure at 80% ethanol/water mixtures, the change in structure being reversible after treating the surface with buffer solution. SbpA on silicon supports denatures at pH 3 and at 70 degrees C, and the process is irreversible. Cross-linking of SbpA enhances the stability for high ethanol and acidic conditions, but it does not improve thermal stability. Recrystallized SbpA on secondary cell wall polymer (SCWP), a natural environment for the protein layer, is more resistant to ethanol and pH exposure than recrystallized SbpA on hydrophilic silicon supports. Atomic force microscopy (AFM) was used to monitor the loss of stability and the changes in protein layer conformation.