Infrared Scattering-Type Scanning Near-Field Optical Microscopy of Biomembranes in Water.

Infrared (IR) absorption spectroscopy detects the state and chemical composition of biomolecules solely by their inherent vibrational fingerprints. Major disadvantages like the lack of spatial resolution and sensitivity have lately been overcome by the use of pointed probes as local sensors enabling the detection of quantities as few as hundreds of proteins with nanometer precision. However, the strong absorption of infrared radiation by liquid water still prevents simple access to the measured quantity: the light scattered at the probing atomic force microscope tip. Here we report on the local IR response of biological membranes immersed in aqueous bulk solution. We make use of a silicon solid immersion lens as the substrate and focusing optics to achieve detection efficiencies sufficient to yield IR near-field maps of purple membranes. Finally, we suggest a means to improve the imaging quality by tracing the tip by a laser-scanning approach.

Essay on Biomembrane Structure.

Of all the macromolecular assemblies of life, the least understood is the biomembrane. This is especially true in regard to its atomic structure. Ideas on biomembranes, developed in the last 200 years, culminated in the fluid mosaic model of the membrane. In this essay, I provide a historical outline of how we arrived at our current understanding of biomembranes and the models we use to describe them. A selection of direct experimental findings on the nano-scale structure of biomembranes is taken up to discuss their physical nature, and special emphasis is put on the surprising insights that arise from atomic scale descriptions.

Fast and high-resolution mapping of elastic properties of biomolecules and polymers with bimodal AFM.

Fast, high-resolution mapping of heterogeneous interfaces with a wide elastic modulus range is a major goal of atomic force microscopy (AFM). This goal becomes more challenging when the nanomechanical mapping involves biomolecules in their native environment. Over the years, several AFM-based methods have been developed to address this goal. However, none of these methods combine sub-nanometer spatial resolution, quantitative accuracy, fast data acquisition speed, wide elastic modulus range and operation in physiological solutions. Here, we present detailed procedures for generating high-resolution maps of the elastic properties of biomolecules and polymers using bimodal AFM. This requires the simultaneous excitation of the first two eigenmodes of the cantilever. An amplitude modulation (AM) feedback acting on the first mode controls the tip-sample distance, and a frequency modulation (FM) feedback acts on the second mode. The method is fast because the elastic modulus, deformation and topography images are obtained simultaneously. The method is efficient because only a single data point per pixel is needed to generate the aforementioned images. The main stages of the bimodal imaging are sample preparation, calibration of the instrument, tuning of the microscope and generation of the nanomechanical maps. In addition, with knowledge of the deformation, bimodal AFM enables reconstruction of the true topography of the surface. It takes ~9 h to complete the whole procedure.

Direct observation of rotation and steps of the archaellum in the swimming halophilic archaeon Halobacterium salinarum.

Motile archaea swim using a rotary filament, the archaellum, a surface appendage that resembles bacterial flagella structurally, but is homologous to bacterial type IV pili. Little is known about the mechanism by which archaella produce motility. To gain insights into this mechanism, we characterized archaellar function in the model organism Halobacterium salinarum. Three-dimensional tracking of quantum dots enabled visualization of the left-handed corkscrewing of archaea in detail. An advanced analysis method combined with total internal reflection fluorescence microscopy, termed cross-kymography, was developed and revealed a right-handed helical structure of archaella with a rotation speed of 23 ± 5 Hz. Using these structural and kinetic parameters, we computationally reproduced the swimming and precession motion with a hydrodynamic model and estimated the archaellar motor torque to be 50 pN nm. Finally, in a tethered-cell assay, we observed intermittent pauses during rotation with ∼36° or 60° intervals, which we speculate may be a unitary step consuming a single adenosine triphosphate molecule, which supplies chemical energy of 80 pN nm when hydrolysed. From an estimate of the energy input as ten or six adenosine triphosphates per revolution, the efficiency of the motor is calculated to be ∼6-10%.

Tellurium as a valuable tool for studying the prokaryotic origins of mitochondria.

Mitochondria are eukaryotic organelles which contain the own genetic material and evolved from free-living Eubacteria, namely hydrogen-producing Alphaproteobacteria. Since 1965, biologists provided, by research at molecular level, evidence for the prokaryotic origins of mitochondria. However, determining the precise origins of mitochondria is challenging due to inherent difficulties in phylogenetically reconstructing ancient evolutionary events. The use of new tools to evidence the prokaryotic origin of mitochondria could be useful to gain an insight into the bacterial endosymbiotic event that resulted in the permanent acquisition of bacteria, from the ancestral cell, that through time were transformed into mitochondria. Electron microscopy has shown that both proteobacterial and yeast cells during their growth in the presence of increasing amount of tellurite resulted in dose-dependent blackening of the culture due to elemental tellurium (Te(0)) that formed large deposits either along the proteobacterial membrane or along the yeast cell wall and mitochondria. Since the mitochondrial inner membrane composition is similar to that of proteobacterial membrane, in the present work we evidenced the black tellurium deposits on both, cell wall and mitochondria of ρ(+) and respiratory deficient ρ(-) mutants of yeast. A possible role of tellurite in studying the evolutionary origins of mitochondria will be discussed.

In-focus electron microscopy of frozen-hydrated biological samples with a Boersch phase plate.

We report the implementation of an electrostatic Einzel lens (Boersch) phase plate in a prototype transmission electron microscope dedicated to aberration-corrected cryo-EM. The combination of phase plate, C(s) corrector and Diffraction Magnification Unit (DMU) as a new electron-optical element ensures minimal information loss due to obstruction by the phase plate and enables in-focus phase contrast imaging of large macromolecular assemblies. As no defocussing is necessary and the spherical aberration is corrected, maximal, non-oscillating phase contrast transfer can be achieved up to the information limit of the instrument. A microchip produced by a scalable micro-fabrication process has 10 phase plates, which are positioned in a conjugate, magnified diffraction plane generated by the DMU. Phase plates remained fully functional for weeks or months. The large distance between phase plate and the cryo sample permits the use of an effective anti-contaminator, resulting in ice contamination rates of <0.6 nm/h at the specimen. Maximal in-focus phase contrast was obtained by applying voltages between 80 and 700 mV to the phase plate electrode. The phase plate allows for in-focus imaging of biological objects with a signal-to-noise of 5-10 at a resolution of 2-3 nm, as demonstrated for frozen-hydrated virus particles and purple membrane at liquid-nitrogen temperature.

Microcalorimetric, spectroscopic and microscopic investigation on the toxic effects of CdTe quantum dots on Halobacterium halobium R1.

The biological effect of CdTe quantum dots (QDs) on Halobacterium halobium R1 (H. halobium R1) growth was analyzed by a microcalorimetric technique. By using a TAM air eight channels microcalorimeter, the thermogenic curves of H. halobium R1 growth were obtained at 37 °C. To analyze the results, the maximum heat power (P(m)) and the growth rate constants (k) were determined, which showed that they were correlated to the concentration of QDs. The addition of quantum dots caused a gradual increase of P(m) and k at low concentrations of QDs, and a conspicuous decrease at high concentrations. For confirmation, the turbidity (OD(600)) and respiratory rate at different concentrations of QDs were studied. The morphology of H. halobium R1 cells both in the absence and presence of QDs was examined by transmission electron microscopy (TEM). The results of these studies were corroborated with ones derived from microcalorimetry. In this work, the mechanism of cytotoxicity of QDs was explored through fluorescence spectroscopy, inductively coupled plasma mass spectrometry (ICP-MS) and microcalorimetry. It was clear that metabolic mechanism of H. halobium R1 growth was changed by the addition of QDs. To the best of our knowledge, the thermokinetics and toxicology of CdTe QDs against H. halobium R1 were obtained for the first time by microcalorimetry.

MALDI-TOF/MS analysis of archaebacterial lipids in lyophilized membranes dry-mixed with 9-aminoacridine.

A method of direct lipid analysis by MALDI mass spectrometry in intact membranes, without prior extraction/separation steps, is described. The purple membrane isolated from the extremely halophilic archaeon Halobacterium salinarum was selected as model membrane. Lyophilized purple membrane were grinded with 9-aminoacridine (9-AA) as dry matrix, and the powder mixture was crushed in a mechanical die press to form a thin pellet. Small pieces of the pellet were then attached to the MALDI target and directly analyzed. In parallel, individual archaebacterial phospholipids and glycolipids, together with the total lipid extract of the purple membrane, were analyzed by MALDI-TOF/MS using 9-AA as the matrix in solution. Results show that 9-AA represents a suitable matrix for the conventional MALDI-TOF/MS analysis of lipid extracts from archaeal microorganisms, as well as for fast and reliable direct dry lipid analysis of lyophilized archaebacterial membranes. This method might be of general application, offering the advantage of quickly gaining information about lipid components without disrupting or altering the membrane matrix.

Automated setpoint adjustment for biological contact mode atomic force microscopy imaging.

Contact mode atomic force microscopy (AFM) is the most frequently used AFM imaging mode in biology. It is about 5-10 times faster than oscillating mode imaging (in conventional AFM setups), and provides topographs of biological samples with sub-molecular resolution and at a high signal-to-noise ratio. Unfortunately, contact mode imaging is sensitive to the applied force and intrinsic force drift: inappropriate force applied by the AFM tip damages the soft biological samples. We present a methodology that automatically searches for and maintains high resolution imaging forces. We found that the vertical and lateral vibrations of the probe during scanning are valuable signals for the characterization of the actual applied force by the tip. This allows automated adjustment and correction of the setpoint force during an experiment. A system that permanently performs this methodology steered the AFM towards high resolution imaging forces and imaged purple membrane at molecular resolution and live cells at high signal-to-noise ratio for hours without an operator.

Heat-fixation method used in an atomic force microscopy study of cell morphology.

In order to overcome the difficulties with existing methods for sample immobilization in imaging Halobacterium salinarum (H. salinarum) living in a highly salty medium by atomic force microscopy (AFM), a heat-fixation method was, for the first time, used to overcome existing problems in preparing samples for AFM. The effect on the cell morphology of the heat-fixation method was studied by MAC mode AFM, and was compared with the drop-and-dry and the polylysine-adhesion methods. It was found that the heat-fixation method can be successfully used for preparing Gram-negative and Gram-positive bacteria samples for AFM studies. Using this method, high-resolution AFM images of H. salinarum were obtained. Round protrusions on the cell surface and horn-like protrusions only at one pole of H. salinarum were observed.

Microcalorimetric studies of the biological effects of Ho(III) on Halobacterium halobium R1.

The biological effect of Ho3+ on Halobacterium halobium R1 growth was analyzed using the microcalorimetric method. Using the LKB-2277 Bioactivity Monitor with the ampoule method at 37 degrees C, the thermogenic curves of the growth of H. halobium R1 were obtained. Then, the maximum power (P (m)) and the growth rate constants (k) were determined, and the values of P (m) and k were linked to the concentration of Ho3+. In all, the addition of Ho3+ cause a decrease in the maximum heat production and growth rate constants. To confirm the results, the shapes of H. halobium R1 cell addition with Ho3+ using a transmission electron microscope (TEM) were observed. According to the thermogenic curves and TEM photos of H. halobium R1 under different conditions, it is clear that the metabolic mechanism of H. halobium R1 growth has been changed with the addition of Ho3+.

Microcalorimetric study on the effect of Ce3+ on Halobacterium halobium R1.

A microcalorimeric technique was used to evaluate the influence of rare earths Ce3+ on Halobacterium halobium R1 growth. By means of TAM air Thermal Activity Monitor, the thermogenic curves of H. halobium R1 growth were obtained. To analyze the results, the growth rate constant k and IC50 were calculated, indicating that the values of k are linked to the concentration of Ce3+. The growth rate constant k of H. halobium R1 decreased gradually in the low concentration; thus, rare earths restrained the growth of H. halobium R1. On the contrary, as the concentration of Ce3+ became higher, the value of k for H. halobium R1 increased gradually, which showed Ce3+ stimulated the growth of H. halobium R1. When the concentration of rare earths became much higher, the value of k for H. halobium R1 also decreased, and the growth of H. halobium R1 was restrained totally in the end. By using transmission electron microscopy (TEM), it was observed that the transforming of H. halobium R1 in the different concentrations of Ce3+ confirmed the results derived from microcalorimetry. According to the thermogenic curves and TEM photos of H. halobium R1 under various conditions, it showed that there was some special effect about the interaction between rare earths and H. halobium R1 growth.

The flagellar filament structure of the extreme acidothermophile Sulfolobus shibatae B12 suggests that archaeabacterial flagella have a unique and common symmetry and design.

Archaea, constituting a third domain of life between Eubacteria and Eukarya, characteristically inhabit extreme environments. They swim by rotating flagellar filaments that are phenomenologically and functionally similar to those of eubacteria. However, biochemical, genetic and structural evidence has pointed to significant differences but even greater similarity to eubacterial type IV pili. Here we determined the three-dimensional symmetry and structure of the flagellar filament of the acidothermophilic archaeabacterium Sulfolobus shibatae B12 using transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM). Processing of the cryo-negatively stained filaments included analysis of their helical symmetry and subsequent single particle reconstruction. Two filament subunit packing arrangements were identified: one has helical symmetry, similar to that of the extreme halophile Halobacterium salinarum, with ten subunits per 5.3 nm repeat and the other has helically arranged stacked disks with C(3) symmetry and 12 subunits per repeat. The two structures are related by a slight twist. The S. shibatae filament has a larger diameter compared to that of H. salinarum, at the opposite end of the archaeabacterial phylogenetic spectrum, but the basic three-start symmetry and the size and arrangement of the core domain are conserved and the filament lacks a central channel. This similarity suggests a unique and common underlying symmetry for archaeabacterial flagellar filaments.

Microcalorimetric studies of the biological effect of holmium (III) on Halobacterium halobium R1 growth.

The biological effect of Ho3+ on Halobacterium halobium R1 growth was analyzed by a microcalorimetric technique. By means of LKB-2277 Bioactivity Monitor, ampoule method at 37 degrees C, we obtained the thermogenic curves of H. halobium R1 growth. To analyze the results, the maximum power (Pm) and the growth rate constants (k) were determined, which show that values of Pm and k are linked to the concentration of Ho3+. In all, the addition of Ho3+ causes a decrease of the maximum heat production and growth rate constants. For comparison, we observed the shapes of H. halobium R1 cell by means of transmission electron microscope (TEM). According to the thermogenic curves and TEM photos of H. halobium R1 under different conditions, it is clear that metabolic mechanism of H. halobium R1 growth has been changed with the addition of Ho3+.

[Multicomponent nature of Halobacterium salinarum flagella].

Filaments of the flagellum of the halophilic archaeon Halobacterium salinarum consist of five flagellins: A1, A2, B1, B2, and B3, which are encoded by five genes localized in tandem in twoflgA and flgB operons. While the role of flagellins A1 and A2 has been determined, the role of the proteins, B operon products, is still unclear. A mutant strain of H. salinarum with deleted A and B flagellin genes (deltaflgAdeltaflgB) has been obtained for the first time. This strain has been used to create and analyze the strains carrying only individual B1 or B3 flagellin genes. Cells of the deltaflgAdeltaflgB strain were shown to have short filamentous formations, 7-8 nm thick, which we have named as X-filaments. It has been shown that X-filaments consist of a protein immunologically related to flagellins A and B. Expression of the B1 and B3 genes is suppressed in the absence of A1, A2, and B2. It has been shown that flagellins B1 and B3 cannot be substituted for flagellin B2 upon the formation of a curved hook-like structure, which serves as a connecting element between the flagellar filament and the motor axis. The multicomponent nature of flagella is discussed in the light of their possible involvement in other cell processes besides providing motility.

The archaeabacterial flagellar filament: a bacterial propeller with a pilus-like structure.

Common prokaryotic motility modes are swimming by means of rotating internal or external flagellar filaments or gliding by means of retracting pili. The archaeabacterial flagellar filament differs significantly from the eubacterial flagellum: (1) Its diameter is 10-14 nm, compared to 18-24 nm for eubacterial flagellar filaments. (2) It has 3.3 subunits/turn of a 1.9 nm pitch left-handed helix compared to 5.5 subunits/turn of a 2.6 nm pitch right-handed helix for plain eubacterial flagellar filaments. (3) The archaeabacterial filament is glycosylated, which is uncommon in eubacterial flagella and is believed to be one of the key elements for stabilizing proteins under extreme conditions. (4) The amino acid composition of archaeabacterial flagellin, although highly conserved within the group, seems unrelated to the highly conserved eubacterial flagellins. On the other hand, the archaeabacterial flagellar filament shares some fundamental properties with type IV pili: (1) The hydrophobic N termini are largely homologous with the oligomerization domain of pilin. (2) The flagellin monomers follow a different mode of transport and assembly. They are synthesized as pre-flagellin and have a cleavable signal peptide, like pre-pilin and unlike eubacterial flagellin. (3) The archaeabacterial flagellin, like pilin, is glycosylated. (4) The filament lacks a central channel, consistent with polymerization occurring at the cell-proximal end. (5) The diameter of type IV pili, 6-9 nm, is closer to that of the archaeabacterial filament, 10-14 nm. A large body of data on the biochemistry and molecular biology of archaeabacterial flagella has accumulated in recent years. However, their structure and symmetry is only beginning to unfold. Here, we review the structure of the archaeabacterial flagellar filament in reference to the structures of type IV pili and eubacterial flagellar filaments, with which it shares structural and functional similarities, correspondingly.

A microprobe analysis of inorganic elements in Halobacterium salinarum.

Halobacterium salinarum were grown on peptone agar containing 4.28 M NaCl, 0.036 M K and other salts. Stationary phase organisms were lifted onto carbon planchets, freeze-dried, carbon coated and examined in a scanning electron microscope equipped with an X-ray spectrometer. Intracellular element concentrations (mol/kg H(2)O) were determined using a bulk analysis program with appropriate standards. The cell K concentration was 110 times that of the medium. For Na this value was 0.3 and for Cl, 1.1. When Rb was present in the medium, its intracellular concentration was 77 times higher than the external value. The cation minus anion value suggests a high fixed negative charge, 0.72 equivalents. Intracellular apparent dielectric constants were calculated using cellular EMFs derived from the literature, and sodium concentration. The determined values ranged from 22-28 (vs 80 for normal water) suggesting phases of structured cell water. Ionic distributions in these extremophiles are treated according to the classical principles elucidated by Willard Gibbs and represents a heterogeneous system in thermodynamic equilibrium with the hypersaline environment. Factors to be considered are: (1) composition of Halobacterium and its immobile negative charge; (2) the physicochemical properties of the individual ions (charge, ionic radius, hydration energy, standard chemical potential); (3) the dielectric constant of the dispersion medium (water); and (4) the binding of ions, particularly potassium.

Microcalorimetric studies of the action of Er3+ on Halobacterium halobium R1 growth.

A microcalorimetric technique was used to evaluate the influence of Er3+ on Halobacterium halobium R1 growth. By means of a LKB-2277 Bioactivity Monitor ampoule method, we obtained the thermogenic curves of H. halobium R1 growth at 37 degrees C. In order to analyze the results, the relationship between k and C was obtained. The addition of Er3+ in low concentration cause a decrease of the maximum heat production Pmax and growth rate constants k; however, Er3+ in a high concentration might promote growth of H. halobium R1. When Er3+ is in a much higher concentration, the growth of H. halobium R1 is inhibited completely. For comparison, the shapes of H. halobium R1 cells were observed by means of transmission electron microscope (TEM). According to the thermogenic curves and TEM photos of H. halobium R1 under different conditions, it is clear that the metabolic mechanism of H. halobium R1 growth has been changed with the addition of Er3+.

Integration of cell membranes and nanotube transistors.

We report the integration of a complex biological system and a nanoelectronic device, demonstrating that both components retain their functionality while interacting with each other. As the biological system, we use the cell membrane of Halobacterium salinarum. As the nanoelectronic device, we use a nanotube network transistor, which incorporates many individual nanotubes in such a way that entire patches of cell membrane are contacted by nanotubes. We demonstrate that the biophysical properties of the membrane are preserved, that the nanoelectronic devices still function as transistors, and that the two systems interact. Further, we use the interaction to study the charge distribution in the biological system, finding that the electric dipole of the membrane protein bacteriorhodopsin is located 2/3 of the way from the extracellular to the cytoplasmic side.

Refining the structure of the Halobacterium salinarum flagellar filament using the iterative helical real space reconstruction method: insights into polymorphism.

The eubacterial flagellar filament is an external, self-assembling, helical polymer approximately 220 A in diameter constructed from a highly conserved monomer, flagellin, which polymerizes externally at the distal end. The archaeal filament is only approximately 100 A in diameter, assembles at the proximal end and is constructed from different, glycosylated flagellins. Although the phenomenology of swimming is similar to that of eubacteria, the symmetry of the archebacterial filament is entirely different. Here, we extend our previous study on the flagellar coiled filament structure of strain R1M1 of Halobacterium salinarum. We use strain M175 of H.salinarum, which forms poly-flagellar bundles at high yield which, under conditions of relatively low ionic-strength (0.8 M versus 5 M) and low pH ( approximately 2.5 versus approximately 6.8), form straight filaments. We demonstrated previously that a single-particle approach to helical reconstruction has many advantages over conventional Fourier-Bessel methods when dealing with variable helical symmetry and heterogeneity. We show here that when this method is applied to the ordered helical structure of the archebacterial uncoiled flagellar filament, significant extensions in resolution can be obtained readily when compared to applying traditional helical techniques. The filament population can be separated into classes of different morphologies, which may represent polymorphic states. Using cryo-negatively stained images, a resolution of approximately 10-15 A has been achieved. Single alpha-helices can be fit into the reconstruction, supporting the proposed similarity of the structure to that of type IV bacterial pili.