Crystalline Patches Research Articles

Growth of Dichalcogenide Layers on TiO2(110)—MoSe2 or TiSe2

Transition‐metal dichalcogenide (TMDC) islands and thin films are grown on TiO2(110) via physical vapor deposition of Mo and Se and are analyzed with electron diffraction, Auger spectroscopy, and scanning tunneling microscopy (STM). Surprisingly, large, crystalline TiSe2 patches develop on the TiO2 surface instead of the expected MoSe2 islands. They are identified by a hexagonal lattice with 3.4 Å periodicity, a unique (2 × 2) superstructure related to charge‐density waves, and an empty conductance doublet in STM spectroscopy. Density‐function‐theory calculations assign the imaging contrast and the conductance doublet to tunneling into the 3p orbitals of the topmost Se layer and Ti 3d‐related electronic states, respectively. Control experiments without Mo deposition confirm that the observed TMDC growth indeed results from a surface reaction between gas‐phase Se and Ti3+ atoms, segregating out of the reduced TiO2 crystal. From the unique shape and orientation of the TiSe2 islands in the low‐coverage regime, a distinct nucleation scheme is proposed, in which the Se(3 × 1) superstructure on TiO2 provides pinning centers for the TMDC. This article aims at increasing the awareness that Mo and Se co‐deposition does not automatically result in MoSe2 formation, but parasitic processes may trigger the growth of other TMDCs.

Artificial Water Channels—Progress Innovations and Prospects

Artificial Water Channels—Progress Innovations and Prospects

Elongation and Contraction of Scallop Sarcoplasmic Reticulum (SR): ATP Stabilizes Ca2+-ATPase Crystalline Array Elongation of SR Vesicles.

The Ca2+-ATPase is an integral transmembrane Ca2+ pump of the sarcoplasmic reticulum (SR). Crystallization of the cytoplasmic surface ATPase molecules of isolated scallop SR vesicles was studied at various calcium concentrations by negative stain electron microscopy. In the absence of ATP, round SR vesicles displaying an assembly of small crystalline patches of ATPase molecules were observed at 18 µM [Ca2+]. These partly transformed into tightly elongated vesicles containing ATPase crystalline arrays at low [Ca2+] (≤1.3 µM). The arrays were classified as ‘’tetramer’’, “two-rail” (like a railroad) and ‘’monomer’’. Their crystallinity was low, and they were unstable. In the presence of ATP (5 mM) at a low [Ca2+] of ~0.002 µM, “two-rail” arrays of high crystallinity appeared more frequently in the tightly elongated vesicles and the distinct tetramer arrays disappeared. During prolonged (~2.5 h) incubation, ATP was consumed and tetramer arrays reappeared. A specific ATPase inhibitor, thapsigargin, prevented both crystal formation and vesicle elongation in the presence of ATP. Together with the second part of this study, these data suggest that the ATPase forms tetramer units and longer tetramer crystalline arrays to elongate SR vesicles, and that the arrays transform into more stable “two-rail” forms in the presence of ATP at low [Ca2+].

Raman-based assay for quantifying how environmental changes affect bR activity

Bacteriorhodopsin (bR) is one of the best studied transport proteins, having been first purified in 1974 by Oesterhelt and Stoeckenius. Acting as a proton pump in halophilic archaea, bR forms crystalline patches in the cell membrane of about 100 nm in size. Despite decades of research into bR, the purpose of these crystalline patches is widely unknown. To determine what benefit patches offer the cell, a method is needed that can measure the activity of bR with sub-diffraction limited resolution.

The crystallization ofPA11,PA12, and their random copolymers at increasing supercooling: From eutectic segregation to mesomorphic solid solutions

The non-isothermal and isothermal crystallization of polyamide 11 (PA11), polyamide 12 (PA12), and their random copolymers was studied over the entire temperature range between the glass transition temperature and the high temperature melting point, using differential scanning calorimetry (DSC) and fast scanning calorimetry (FSC). The DSC and FSC thermal behavior was translated into structural evolutions, relying on earlier gathered X-ray based structural information and theoretical calculations. At low supercooling, the thermal behavior of the copolymers is typical for eutectic systems, involving monomeric segregation and crystallization into separate PA11 and PA12 crystals. Depending on the copolymer composition and the supercooling, the crystals are 4, 5, or 6 monomeric units thick. At very high supercooling, the PA11 and PA12 sequences cocrystallize into mesomorphic solid solutions with isodimorphic characteristics. At intermediate supercooling, the FSC heating traces following isothermal crystallization suggest that crystallization involves the simultaneous, isokinetic production of crystalline and mesomorphic patches. In this temperature range, lamellar crystals are 3 monomeric units thick throughout.

Surface roughening, premelting and melting of monolayer and bilayer crystals.

Dimensionality often strongly affects material properties and phase transition behaviors, but its effects on crystal surfaces, such as roughening and premelting, have been poorly studied. Our simulation revealed that these surface behaviors are distinct in monolayer and multilayer Lennard-Jones (LJ) crystals. Solid surfaces fluctuate as capillary waves during the roughening process, but complete roughening is preempted by premelting. As the melting temperature is approached, the thickness of the premelted liquid layer approaches a constant (i.e., blocked premelting) for monolayer crystals, but diverges as a power law (i.e., complete premelting) for bilayer and trilayer crystals. The surface liquids of monolayer crystals contain crystalline patches and exhibits rough liquid-vapour and liquid-crystal interfaces, in contrast to the normal surface liquids of bilayer and trilayer crystals. Monolayer crystals melt heterogeneously from the surface without forming a hexatic phase and produce many vacancies.

Through the Lipopolysaccharide Glass: A Potent Antimicrobial Peptide Induces Phase Changes in Membranes.

In the following, molecular simulations are used to reveal unexpected behavior within bacterial membranes. We show that lipopolysaccharide molecules found in these membranes form viscous amorphous solids when they are interlinked with monovalent and divalent cations. The bilayers exhibit both liquid and glassy characteristics, due to the coexistence of both liquid and crystalline domains in the bilayer. Polymyxin B1, a potent antimicrobial peptide, is shown to increase order within the lipopolysaccharide bilayers by inducing the formation of crystalline patches. Crucially we are able to decompose the energetics of insertion into their enthalpic and entropic components. The present coarse-grain molecular dynamics study provides unprecedented insights into the antibacterial action of antimicrobial peptides, thus paving the way for development of novel therapeutic agents to treat multiple drug resistant Gram-negative bacteria.

Structural Changes in Bacteriorhodopsin Caused by Two-Photon-Induced Photobleaching

Bacteriorhodopsin (BR) is the key protein of the halobacterial photosynthetic system. BR assembles into two-dimensional crystalline patches, the so-called purple membranes (PM), and acts as a light-driven proton pump converting light energy into the chemical energy of a proton gradient over the cell membrane. The two-photon absorption (TPA) of BR is so far not fully understood. Astonishingly high TPA cross sections have been reported, but the molecular mechanisms have not been elucidated. In this work, we address structural changes in BR and PM upon TPA, investigating its TPA photochemistry by spectroscopy, small-angle X-ray scattering, as well as electron and atomic force microscopy. We observe that TPA of BR leads to formation of an UV-absorbing N-retinyl-bacterioopsin state, which is accompanied by the loss of crystalline order in PM. FTIR and CD spectroscopy confirm that BR trimers as well as the secondary structure of the BR molecules are preserved. We demonstrate that excitation by TPA results in the photochemical reduction of the retinal Schiff base, which in turn causes a permanent asymmetric shape change of BR, similar to the one transiently observed during the photocycle-related opening and closing of the cytoplasmic proton half channel. This shape change causes PM sheets to merely roll up toward the extracellular side and causes the loss of crystallinity of PM. We present a model for the TPA photoresponse of BR, which also explains the irreversibility of the process in terms of a photochemical reduction of the Schiff base.

Single‐Molecule Tracking of Fibrinogen Dynamics on Nanostructured Poly(ethylene) Films

AbstractUsing fibrinogen (Fg) protein as a probe molecule, mapping using accumulated probe trajectories (MAPT) is performed on nanostructured melt‐drawn high‐density poly(ethylene) (HDPE) films composed of well‐oriented crystalline patches separated by amorphous regions. The spatially grouped molecular trajectories allow for identification of regions with distinct surface properties (i.e., crystalline vs. amorphous) while simultaneously determining the characteristic dynamic protein behavior within those regions. In the presence of solution with a sufficiently high Fg concentration, discrete patches of a dense, ordered protein layer form (presumably on crystalline HDPE regions), leading to a dramatic rise in the surface residence time (by more than two orders of magnitude) of molecules incorporated into the film. Within this ordered Fg layer, individual molecules exhibit slow anisotropic lateral diffusion; the mobility is restricted by the nanostructure boundaries of the underlying HDPE. On HDPE films at low Fg surface coverage, or on films that have been rendered hydrophilic with Ar plasma, short surface residence times and fast, isotropic diffusion are observed. These results demonstrate the ability of spatially resolved single‐molecule tracking to provide mechanistic information about biomolecule‐surface interactions in a highly heterogeneous environment.

Crystallization Mechanism of Hard Sphere Glasses

In supercooled liquids, vitrification generally suppresses crystallization. Yet some glasses can still crystallize despite the arrest of diffusive motion. This ill-understood process may limit the stability of glasses, but its microscopic mechanism is not yet known. Here we present extensive computer simulations addressing the crystallization of monodisperse hard-sphere glasses at constant volume (as in a colloid experiment). Multiple crystalline patches appear without particles having to diffuse more than one diameter. As these patches grow, the mobility in neighboring areas is enhanced, creating dynamic heterogeneity with positive feedback. The future crystallization pattern cannot be predicted from the coordinates alone: Crystallization proceeds by a sequence of stochastic micronucleation events, correlated in space by emergent dynamic heterogeneity.

Sodium Bicarbonate Induces Crystalline Wax Generation, Activates Host-Resistance, and Increases Imazalil Level in Rind Wounds of Oranges, Improving the Control of Green Mold During Storage

Imazalil (IMZ) was quantified in the flavedo and albedo (Citrus fruits outer and inner tissue of the exocarp) of wounded and unwounded Valencia L. Olinda oranges following a 2 min immersion at 25 degrees C in 50, 100, or 250 microg mL(-1) of the fungicide mixture with or without 3% sodium bicarbonate (SBC). The addition of SBC significantly reduced the decay incidence throughout 30 d of storage at 10 degrees C with 95% RH and 6 d of simulated marketing period at 25 degrees C and 75% RH. In unwounded oranges, IMZ uptake was not changed by the coapplication of SBC, and the fungicide was predominantly recovered in the flavedo. To the contrary, in the albedo of wounded fruit, the residue level increased by about 6-fold when the fungicide was applied with SBC. When SBC was coapplied to wounded fruit, the phytoalexin scoparone was induced in the albedo and the accumulation was not affected by IMZ. When fruit was treated with SBC, scanning electron microscopy observations evidenced a production of crystalline wax patches with branched stripes and the magnitude was positively correlated to the salt concentration in the mixture. The generation as fast as 24 h post-treatment, and the different morphology of the new wax suggests a displacement of intracuticular waxes which can affect the fungicide sorption and diffusion coefficient into the rind.

Directed Self-Assembly of Spheres into a Two-Dimensional Colloidal Crystal by Viscoelastic Stresses

Ordering induced by shear flow can be used to direct the assembly of particles in suspensions. Flow-induced ordering is determined by the balance between a range of forces, such as direct interparticle, Brownian, and hydrodynamic forces. The latter are modified when dealing with viscoelastic rather than Newtonian matrices. In particular, 1D stringlike structures of spherical particles have been observed to form along the flow direction in shear thinning viscoelastic fluids, a phenomenon not observed in Newtonian fluids at similar particle volume fractions. Here we report on the formation of freestanding crystalline patches in planes parallel to the shearing surfaces. The novel microstructure is formed when particles are suspended in viscoelastic, wormlike micellar solutions and only when the applied shear rate exceeds a critical value. In spite of the very low volume fraction (less than 0.01), particles arrange themselves in 2D crystalline patches along the flow direction. This is a bulk phenomenon because 2D crystals form throughout the whole gap between plates, with the gap thickness being much larger than the particle size. Shear flow may hence be an easy method to drive particles into crystalline order in suspensions with viscoelastic properties. The crystalline structure reported here could be used to design new materials with special mechanical, optical, thermal, or electric properties.

PH-induced structural change in a sodium/proton antiporter from Methanococcus jannaschii

Na+/H+ antiporters are pH-dependent membrane transport proteins that maintain the homeostasis of H+ and Na+ in living cells. MjNhaP1 from Methanococcus jannaschii, a hyperthermophilic archaeon that grows optimally at 85 degrees C, was cloned and expressed in Escherichia coli. Two-dimensional crystals were obtained from purified protein at pH 4. Electron cryomicroscopy yielded an 8 A projection map. Like the related E. coli antiporter NhaA, MjNhaP1 is a dimer, but otherwise the structures of the two antiporters differ significantly. The map of MjNhaP1 shows elongated densities in the centre of the dimer and a cluster of density peaks on either side of the dimer core, indicative of a bundle of 4-6 membrane-spanning helices. The effect of pH on the structure of MjNhaP1 was studied in situ. A major change in density distribution within the helix bundle, and an approximately 2 A shift in the position of the helix bundle relative to the dimer core occurred at pH 6 and above. The two conformations at low and high pH most likely represent the closed and open states of the antiporter.

Assembly of Human Immunodeficiency Virus Precursor Gag Proteins

To investigate the mechanism by which human immunodeficiency virus (HIV) precursor Gag (PrGag) proteins assemble to form immature virus particles, we examined the in vitro assembly of MACANC proteins, composed of the PrGag matrix, capsid, and nucleocapsid domains. In the absence of other components, MACANC proteins assembled efficiently at physiological temperature but inefficiently at lower temperatures. However, the addition of RNA reduced the temperature sensitivity of assembly reactions. Assembly of MACANC proteins also was affected by pH because the proteins preferentially formed tubes at pH 6.0, whereas spheres were obtained at pH 8.0. Because neither tubes nor spheres were amenable to analysis of protein-protein contacts, we also examined the membrane-bound assemblies of MACANC proteins. Interestingly, MACANC proteins organized on membranes in tightly packed hexameric rings. The observed hexamer spacing of 79.7 A is consistent with the notion that more PrGag proteins assemble into virions than are needed to provide capsid proteins for mature virus cores. Our data are also consistent with a model for PrGag contacts in immature virions where capsid hexamers are tightly packed, where nucleocapsid domains align beneath capsid C-terminal domains, and where matrix domains form trimers at the nexus of three neighbor hexamers.

Direct observation of different surface structures on high-resolution images of native halorhodopsin

Halorhodopsin (HR) was investigated with atomic force microscopic techniques (AFM) in aqueous solution. Two-dimensional (2D) crystals of HR were obtained by purifying an HR membrane fraction with the same buoyant density as the purple membrane (HR-PM) from the overexpressing strain Halobacterium salinarum D2. The membrane patches of HR were immobilized on mica. Images with a resolution up to 14 Å were recorded. Crystals showed an orthogonal structure and the orientation of the molecules showed p42 12 symmetry; thus, alternate tetramers are inverted in the membrane. The crystal surface was found to display different structures depending on the imaging force used, indicating that some parts of the HR molecule are more rigid but others more compressible. From samples with single tetramers missing in the crystalline patches dimensions of the unit cell could be determined. Helix-connecting loops in single molecules of halorhodopsin were assigned. The images indicate that the large extracellular BC loop covers the whole molecule and is very flexible.

The S-layer Protein of Lactobacillus acidophilus ATCC 4356: Identification and Characterisation of Domains Responsible for S-protein Assembly and Cell Wall Binding

Lactobacillus acidophilus, like many other bacteria, harbors a surface layer consisting of a protein (S A-protein) of 43 kDa. S A-protein could be readily extracted and crystallized in vitro into large crystalline patches on lipid monolayers with a net negative charge but not on lipids with a net neutral charge. Reconstruction of the S-layer from crystals grown on dioleoylphosphatidylserine indicated an oblique lattice with unit cell dimensions ( a=118 Å; b=53 Å, and γ=102 °) resembling those determined for the S-layer of Lactobacillus helveticus ATCC 12046. Sequence comparison of S A-protein with S-proteins from L. helveticus , Lactobacillus crispatus and the S-proteins encoded by the silent S-protein genes from L. acidophilus and L. crispatus suggested the presence of two domains, one comprising the N-terminal two-thirds (SAN), and another made up of the C-terminal one-third (SAC) of S A-protein. The sequence of the N-terminal domains is variable, while that of the C-terminal domain is highly conserved in the S-proteins of these organisms and contains a tandem repeat. Proteolytic digestion of S A-protein showed that SAN was protease-resistant, suggesting a compact structure. SAC was rapidly degraded by proteases and therefore probably has a more accessible structure. DNA sequences encoding SAN or Green Fluorescent Protein fused to SAC (GFP-SAC) were efficiently expressed in Escherichia coli. Purified SAN could crystallize into mono and multi-layered crystals with the same lattice parameters as those found for authentic S A-protein. A calculated S A-protein minus SAN density-difference map revealed the probable location, in projection, of the SAC domain, which is missing from the truncated SAN peptide. The GFP-SAC fusion product was shown to bind to the surface of L. acidophilus , L. helveticus and L. crispatus cells from which the S-layer had been removed, but not to non-stripped cells or to Lactobacillus casei.

Accelerated Mineralization of Prosthetic Heart Valves

The most common cause of prosthetic heart valve failure is severe regurgitation due to rupture of one or more valve cusps that have become mineralized and rigid. To assess the role of stress and strain in the mineralization initiation, in vitro, reference-grade, essentially lipid-free, glutaraldehyde-tanned bovine pericardium (developed as a standard reference material for bioprosthetic device testing) was exposed to a supersaturated calcium phosphate solution in a high-speed valve tester. The pericardium was tested as sheets constructed into tricuspid valves and dumbbell-shaped tensile-test specimens, and then tested at 720 cycles/min. for up to 18 million cycles. Mineralization was followed using X-ray photography, energy-dispersive X-ray analysis, field-emission scanning electron microscopy, and multiple-attenuated internal reflection infrared spectroscopy. Tensile strength of the tissue was determined using a chemomechanical testing apparatus. Phosphate-based tissue mineralization, first concentrated superficially in an annular distribution at the valve cusp bases, was followed by minimal diffuse calcification within the valve cusps. Small crystalline patches also appeared in the tissue compressed by the valve support rings. Mineralization occurred in a distribution similar to that found in clinically explanted prosthetic heart valves, in areas of maximal tensile and compressive stress and maximal strain. Infrared and tensile test data combine to show that tissue fatigue due to cyclic loading most likely caused breakage of collagen cross-links. Exposure of superficial broken cross-link sites, and unmasking of hydroxyproline binding sites, of the tissue collagen are thus implicated as the main factors in phosphate-radical nucleation events leading to valve mineralization, overshadowing previously cited contributions from tissue lipids and membranes. Mineralization first occurs at the surface regions subjected to the greatest stress and strain, and begins as amorphous phosphate-rich rather than crystalline calcium-rich deposits.

Structure of the bacteriorhodopsin mutant F219L N intermediate revealed by electron crystallography.

Bacteriorhodopsin is a light-driven proton pump in halobacteria that forms crystalline patches in the cell membrane. Isomerization of the bound retinal initiates a photocycle resulting in the extrusion of a proton. An electron crystallographic analysis of the N intermediate from the mutant F219L gives a three-dimensional view of the large conformational change that occurs on the cytoplasmic side after deprotonation of the retinal Schiff base. Helix F, together with helix E, tilts away from the center of the molecule, causing a shift of approximately 3 A at the EF loop. The top of helix G moves slightly toward the ground state location of helix F. These movements open a water-accessible channel in the protein, enabling the transfer of a proton from an aspartate residue to the Schiff base. The movement of helix F toward neighbors in the crystal lattice is so large that it would not allow all molecules to change conformation simultaneously, limiting the occupancy of this state in the membrane to 33%. This explains photocooperative phenomena in the purple membrane.

Cryo-electron crystallography of small and mosaic 2-D crystals: an assessment of a procedure for high-resolution data retrieval

We describe a procedure to obtain structural data of biological macromolecules from small 2-D crystals using cryo-electron crystallography. The procedure has been applied to a membrane-embedded multi-protein complex (photosystem II). This complex, under certain conditions, forms 2-D crystals in its native membrane which are composed of many small mosaic patches and therefore represents an ideal test specimen. By averaging in reciprocal space over more than 50 crystalline patches, it was possible to calculate a projection map using data approaching 1.3 nm resolution while in the Fourier transforms of individual patches only reflections up to the 4th order were readily identifiable. The efficiency of the procedure was evaluated by examining the fidelity of (i) the rotational alignment of patches prior to merging, (ii) the space group assignment, (iii) phase and amplitude extraction, and (iv) the correction of the structure factors for the effects of the contrast transfer function (CTF).

Characterization of the Growth of 2D Protein Crystals on a Lipid Monolayer by Ellipsometry and Rigidity Measurements Coupled to Electron Microscopy

We present here some sensitive optical and mechanical experiments for monitoring the process of formation and growth of two-dimensional (2D) crystals of proteins on a lipid monolayer at an air-water interface. The adsorption of proteins on the lipid monolayer was monitored by ellipsometry measurements. An instrument was developed to measure the shear elastic constant (in plane rigidity) of the monolayer. These experiments have been done using cholera toxin B subunit (CTB) and annexin V as model proteins interacting with a monosialoganglioside (GM1) and dioleoylphosphatidylserine (DOPS), respectively. Electron microscopy observations of the protein-lipid layer transferred to grids were systematically used as a control. We found a good correlation between the measured in-plane rigidity of the monolayer and the presence of large crystalline domains observed by electron microscopy grids. Our interpretation of these data is that the crystallization process of proteins on a lipid monolayer passes through at least three successive stages: 1) molecular recognition between protein and lipid-ligand, i.e., adsorption of the protein on the lipid layer; 2) nucleation and growth of crystalline patches whose percolation is detected by the appearance of a non-zero in-plane rigidity; and 3) annealing of the layer producing a slower increase of the lateral or in-plane rigidity.