Crystallizing membrane proteins using lipidic mesophases

A detailed protocol for crystallizing membrane proteins that makes use of lipidic mesophases is described. This has variously been referred to as the lipid cubic phase or in meso method. The method has been shown to be quite general in that it has been used to solve X-ray crystallographic structures of prokaryotic and eukaryotic proteins, proteins that are monomeric, homo- and hetero-multimeric, chromophore-containing and chromophore-free, and alpha-helical and beta-barrel proteins. Its most recent successes are the human-engineered beta(2)-adrenergic and adenosine A(2A) G protein-coupled receptors. Protocols are provided for preparing and characterizing the lipidic mesophase, for reconstituting the protein into the monoolein-based mesophase, for functional assay of the protein in the mesophase and for setting up crystallizations in manual mode. Methods for harvesting microcrystals are also described. The time required to prepare the protein-loaded mesophase and to set up a crystallization plate manually is about 1 h.

High-throughput crystallization: polymorphs, salts, co-crystals and solvates of pharmaceutical solids

The concepts of high-throughput (HT) screening and combinatorial synthesis have been integrated into the pharmaceutical discovery process, but are not yet commonplace in the pharmaceutical development arena. Emerging strategies to speed pharmaceutical development and capture solid form diversity of pharmaceutical substances have resulted in the emergence of HT crystallization technologies. The primary type of diversity often refers to polymorphs, which are different crystal forms of the same chemical composition. However, diverse salt forms, co-crystals, hydrates and solvates are also amenable to study in HT crystallization systems. The impact of form diversity encompasses issues of stability and bioavailability, as well as development considerations such as process definition, formulation design, patent protection and regulatory control. This review highlights the opportunities and challenges of HT crystallization technologies as they apply to pharmaceutical research and development.

Lysine methylation as a routine rescue strategy for protein crystallization

Crystallization remains a critical step in X-ray structure determination. Because it is not generally possible to rationally predict crystallization conditions, commercial screens have been developed which sample a wide range of crystallization space. While this approach has proved successful in many cases, a significant number of proteins fail to crystallize despite being soluble and monodispersed. It is established that chemical modification can facilitate the crystallization of otherwise intractable proteins. Here we describe a method for the reductive methylation of lysine residues which is simple, inexpensive, and efficient, and report on its application to ten proteins. We describe the effect of methylation on the physico-chemical properties of these proteins, and show that it led to diffraction-quality crystals from four proteins and structures for three that had hitherto proved refractory to crystallization. The method is suited to both low- and high-throughput laboratories.

Quartz crystal microbalance (QCM) affinity biosensor for genetically modified organisms (GMOs) detection

A DNA piezoelectric sensor has been developed for the detection of genetically modified organisms (GMOs). Single stranded DNA (ssDNA) probes were immobilised on the sensor surface of a quartz crystal microbalance (QCM) device and the hybridisation between the immobilised probe and the target complementary sequence in solution was monitored. The probe sequences were internal to the sequence of the 35S promoter (P) and Nos terminator (T), which are inserted sequences in the genome of GMOs regulating the transgene expression. Two different probe immobilisation procedures were applied: (a) a thiol-dextran procedure and (b) a thiol-derivatised probe and blocking thiol procedure. The system has been optimised using synthetic oligonucleotides, which were then applied to samples of plasmidic and genomic DNA isolated from the pBI121 plasmid, certified reference materials (CRM), and real samples amplified by the polymerase chain reaction (PCR). The analytical parameters of the sensor have been investigated (sensitivity, reproducibility, lifetime etc.). The results obtained showed that both immobilisation procedures enabled sensitive and specific detection of GMOs, providing a useful tool for screening analysis in food samples.

Manipulation of liquid droplets using amphiphilic, magnetic one-dimensional photonic crystal chaperones

The controlled manipulation of small volumes of liquids is a challenging problem in microfluidics, and it is a key requirement for many high-throughput analyses and microassays. One-dimensional photonic crystals made from porous silicon have been constructed with amphiphilic properties. When prepared in the form of micrometre-sized particles and placed in a two-phase liquid such as dichloromethane/water, these materials will accumulate and spontaneously align at the interface. Here we show that superparamagnetic nanoparticles of Fe(3)O(4) can be incorporated into the porous nanostructure, allowing the materials to chaperone microlitre-scale liquid droplets when an external magnetic field is applied. The optical reflectivity spectrum of the photonic crystal displays a peak that serves to identify the droplet. Two simple microfluidics applications are demonstrated: filling and draining a chaperoned droplet, and combining two different droplets to perform a chemical reaction. The method provides a general means for manipulating and monitoring small volumes of liquids without the use of pumps, valves or a microfluidic container.

Placing molecules with Bohr radius resolution using DNA origami

Molecular self-assembly with nucleic acids can be used to fabricate discrete objects with defined sizes and arbitrary shapes. It relies on building blocks that are commensurate to those of biological macromolecular machines and should therefore be capable of delivering the atomic-scale placement accuracy known today only from natural and designed proteins. However, research in the field has predominantly focused on producing increasingly large and complex, but more coarsely defined, objects and placing them in an orderly manner on solid substrates. So far, few objects afford a design accuracy better than 5 nm, and the subnanometre scale has been reached only within the unit cells of designed DNA crystals. Here, we report a molecular positioning device made from a hinged DNA origami object in which the angle between the two structural units can be controlled with adjuster helices. To test the positioning capabilities of the device, we used photophysical and crosslinking assays that report the coordinate of interest directly with atomic resolution. Using this combination of placement and analysis, we rationally adjusted the average distance between fluorescent molecules and reactive groups from 1.5 to 9 nm in 123 discrete displacement steps. The smallest displacement step possible was 0.04 nm, which is slightly less than the Bohr radius. The fluctuation amplitudes in the distance coordinate were also small (±0.5 nm), and within a factor of two to three of the amplitudes found in protein structures.

Self-assembled polymeric solid films with temperature-induced large and reversible photonic-bandgap switching

In aqueous solutions the response of polymers and biological matter to external conditions, such as temperature and pH, is typically based on the hydrophobic/hydrophilic balance and its effects on the polymer conformation. In the solid state, related concepts using competing interactions could allow novel functions. In this work we demonstrate that polymeric self-assembly, reversibility of hydrogen bonding, and polymer-additive phase behaviour allow temperature response in the solid state with large and reversible switching of an optical bandgap. A complex of polystyrene-block-poly(4-vinylpyridinium methanesulphonate) and 3-n-pentadecylphenol leads to the supramolecular comb-shaped architecture with a particularly long lamellar period. The sample is green at room temperature, as an incomplete photonic bandgap due to a dielectric reflector is formed. On heating, hydrogen bonds are broken and 3-n-pentadecylphenol additionally becomes soluble in polystyrene, leading to a sharp and reversible transition at approximately 125 degrees C to uncoloured material due to collapse of the long period. This encourages further developments, for example, for functional coatings or sensors in the solid state.

Design and synthesis of self-ordered mesoporous nanocomposite through controlled in-situ crystallization

Mesoporous materials are of technological interest because of their applications ranging from catalysts, molecular sieves, separation technology and gas sensors, to batteries and electronics. Here we demonstrate a synthetic methodology that allows us to create an ordered mesoporous nanocomposite with a crystalline oxide framework. We design a 'nanocrystal-glass' configuration to build a nanoarchitecture by means of surfactant-templated self-assembly followed by the controlled in-situ crystallization of materials. Functional nanocrystals are used as the building blocks of ordered mesopores, and the glass phase can act both as the 'glue' between nanocrystals and as a functionalized component in the composites. Specifically, we demonstrate this methodology for ordered mesoporous nanocomposites consisting of electrochemically active nanocrystals and semiconductive glass in the TiO2-P2O5-M(x)O(y) systems (where M is a metal ion). This approach could be applied to many other multicomponent oxides to fabricate mesoporous nanocomposites for numerous uses.

Microfluidics in structural biology: smaller, faster em leader better

Microfluidic technologies promise unprecedented savings in cost and time through the integration of complex chemical and biological assays on a microfabricated chip. Recent advances are making elements of this vision a reality, facilitating the first large-scale integration of microfluidic plumbing with biological assays. The power of miniaturization lies not only in achieving an economy of scale, but also in exploiting the unusual physics of fluid flow and mass transport on small length scales to realize precise and efficient assays that are not accessible with macroscopic tools. Diverse applications ranging from time-resolved studies of protein folding to highly efficient protein crystal growth suggest that microfluidics may become an indispensable tool in biology.

Continuous synthesis of amorphous carbonated apatites

Amorphous carbonated hydroxyapatite was prepared by rapid mixing of aqueous solutions of a continuous computer-controlled reactor. The variation of the carbonate content in the solid product is possible by adjustment of the ratios of phosphate to carbonate in the initial solution. The principal reaction parameters (temperature, pH, stirrer speed, solution composition and supersaturation) are controlled and monitored. By controlling these processing parameters, a non-stoichiometric hydroxyapatite with fine-tuned crystallinity, morphology, and carbonate content can be reproducibly prepared. The higher solubility under the conditions of osteoclastic resorption was tested in vitro at constant pH (4.4).

MASSIF-1: a beamline dedicated to the fully automatic characterization and data collection from crystals of biological macromolecules

MASSIF-1 (ID30A-1) is an ESRF undulator beamline operating at a fixed wavelength of 0.969 Å (12.8 keV) that is dedicated to the completely automatic characterization of and data collection from crystals of biological macromolecules. The first of the ESRF Upgrade MASSIF beamlines to be commissioned, it has been open since September 2014, providing a unique automated data collection service to academic and industrial users. Here, the beamline characteristics and details of the new service are outlined.

Porous substrates for label-free molecular level detection of nonresonant organic molecules

We report on the design of practical surface enhanced Raman scattering (SERS) substrate based upon 3D alumina membranes with cylindrical nanopores chemically modified with polyelectrolyte coating and loaded with gold nanoparticle clusters. These substrates allow for a molecular-level, label-free detection of common plastic explosive materials (TNT, DNT) down to 5-10 zeptograms or 15-30 molecules and a common liquid explosive (HMTD) down to 1 picogram. Such a sensitive detection of organic molecules by utilizing efficient SERS substrates opens the path for affordable and label-free detection of trace amount of practically important chemical compounds.

Reproducible, high-throughput synthesis of colloidal nanocrystals for optimization in multidimensional parameter space

While colloidal nanocrystals hold tremendous potential for both enhancing fundamental understanding of materials scaling and enabling advanced technologies, progress in both realms can be inhibited by the limited reproducibility of traditional synthetic methods and by the difficulty of optimizing syntheses over a large number of synthetic parameters. Here, we describe an automated platform for the reproducible synthesis of colloidal nanocrystals and for the high-throughput optimization of physical properties relevant to emerging applications of nanomaterials. This robotic platform enables precise control over reaction conditions while performing workflows analogous to those of traditional flask syntheses. We demonstrate control over the size, size distribution, kinetics, and concentration of reactions by synthesizing CdSe nanocrystals with 0.2% coefficient of variation in the mean diameters across an array of batch reactors and over multiple runs. Leveraging this precise control along with high-throughput optical and diffraction characterization, we effectively map multidimensional parameter space to tune the size and polydispersity of CdSe nanocrystals, to maximize the photoluminescence efficiency of CdTe nanocrystals, and to control the crystal phase and maximize the upconverted luminescence of lanthanide-doped NaYF(4) nanocrystals. On the basis of these demonstrative examples, we conclude that this automated synthesis approach will be of great utility for the development of diverse colloidal nanomaterials for electronic assemblies, luminescent biological labels, electroluminescent devices, and other emerging applications.

In situ macromolecular crystallography using microbeams

Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams.

Low-dose fixed-target serial synchrotron crystallography

The development of serial crystallography has been driven by the sample requirements imposed by X-ray free-electron lasers. Serial techniques are now being exploited at synchrotrons. Using a fixed-target approach to high-throughput serial sampling, it is demonstrated that high-quality data can be collected from myoglobin crystals, allowing room-temperature, low-dose structure determination. The combination of fixed-target arrays and a fast, accurate translation system allows high-throughput serial data collection at high hit rates and with low sample consumption.

Advances in carbon-nanotube assembly

Iijima's observation in 1991 of fullerene-like materials by high-resolution transmission electron microscopy heralded the beginning of the carbon nanotube (CNT) era. A wealth of theoretical predictions and experimental verifications about CNTs have disclosed remarkable size- and structure-dependent properties that are attractive for various potential applications, ranging from conducting wires in molecular devices to fillers in nanocomposites. Many of these applications require assembly (alignment and/or patterning) of CNTs into hierarchical arrays over large-scale areas with controllable shape, location, orientation, and density of the nanotubes. Efforts from both the scientific and engineering points of view have been made to address this issue, beginning shortly after the discovery of CNTs. We review here the development of CNT-assembly techniques under the two rubrics of synthetic assembly and post-synthetic assembly, with emphasis given to the post-synthetic approach. Preliminary to the survey of assembly techniques, we also discuss the characterization techniques that have been widely used for the challenging tasks of visualizing and quantifying CNT assembly.

High-kappa oxide nanoribbons as gate dielectrics for high mobility top-gated graphene transistors

Deposition of high-kappa dielectrics onto graphene is of significant challenge due to the difficulties of nucleating high quality oxide on pristine graphene without introducing defects into the monolayer of carbon lattice. Previous efforts to deposit high-kappa dielectrics on graphene often resulted in significant degradation in carrier mobility. Here we report an entirely new strategy to integrate high quality high-kappa dielectrics with graphene by first synthesizing freestanding high-kappa oxide nanoribbons at high temperature and then transferring them onto graphene at room temperature. We show that single crystalline Al(2)O(3) nanoribbons can be synthesized with excellent dielectric properties. Using such nanoribbons as the gate dielectrics, we have demonstrated top-gated graphene transistors with the highest carrier mobility (up to 23,600 cm(2)/V x s) reported to date, and a more than 10-fold increase in transconductance compared to the back-gated devices. This method opens a new avenue to integrate high-kappa dielectrics on graphene with the preservation of the pristine nature of graphene and high carrier mobility, representing an important step forward to high-performance graphene electronics.

Microfluidic assembly of monodisperse multistage pH-responsive polymer/porous silicon composites for precisely controlled multi-drug delivery

We report an advanced drug delivery platform for combination chemotherapy by concurrently incorporating two different drugs into microcompoistes with ratiometric control over the loading degree. Atorvastatin and celecoxib were selected as model drugs due to their different physicochemical properties and synergetic effect on colorectal cancer prevention and inhibition. To be effective in colorectal cancer prevention and inhibition, the produced microcomposite contained hypromellose acetate succinate, which is insoluble in acidic conditions but highly dissolving at neutral or alkaline pH conditions. Taking advantage of the large pore volume of porous silicon (PSi), atorvastatin was firstly loaded into the PSi matrix, and then encapsulated into the pH-responsive polymer microparticles containing celecoxib by microfluidics in order to obtain multi-drug loaded polymer/PSi microcomposites. The prepared microcomposites showed monodisperse size distribution, multistage pH-response, precise ratiometric controlled loading degree towards the simultaneously loaded drug molecules, and tailored release kinetics of the loaded cargos. This attractive microcomposite platform protects the payloads from being released at low pH-values, and enhances their release at higher pH-values, which can be further used for colon cancer prevention and treatment. Overall, the pH-responsive polymer/PSi-based microcomposite can be used as a universal platform for the delivery of different drug molecules for combination therapy.

Strategies for sample delivery for femtosecond crystallography

Highly efficient data-collection methods are required for successful macromolecular crystallography (MX) experiments at X-ray free-electron lasers (XFELs). XFEL beamtime is scarce, and the high peak brightness of each XFEL pulse destroys the exposed crystal volume. It is therefore necessary to combine diffraction images from a large number of crystals (hundreds to hundreds of thousands) to obtain a final data set, bringing about sample-refreshment challenges that have previously been unknown to the MX synchrotron community. In view of this experimental complexity, a number of sample delivery methods have emerged, each with specific requirements, drawbacks and advantages. To provide useful selection criteria for future experiments, this review summarizes the currently available sample delivery methods, emphasising the basic principles and the specific sample requirements. Two main approaches to sample delivery are first covered: (i) injector methods with liquid or viscous media and (ii) fixed-target methods using large crystals or using microcrystals inside multi-crystal holders or chips. Additionally, hybrid methods such as acoustic droplet ejection and crystal extraction are covered, which combine the advantages of both fixed-target and injector approaches.

Bioseparations

Here we review key applications of separation technology in applied biology. We first sketch out the field as a whole, but then narrow our scope to the processing of fermentation products, particularly to high-value biologicals such as proteins and nucleotides. We go on to provide a qualitative overview describing the importance and general nature of this large field, major trends, and the strategies that have proven most fruitful in evolving effective separation and purification processes. We then give a detailed description of individual separations equipment and the principles governing their operation. We concentrate throughout on making the available literature accessible to the reader; we provide what is hoped to be a representative set of basic references. However, these references, in turn, include some that suggest promising new developments as well as a number of more specialized reviews. We hope that our overall result provides the reader with access to the most relevant literature.

Gentle, fast and effective crystal soaking by acoustic dispensing

The steady expansion in the capacity of modern beamlines for high-throughput data collection, enabled by increasing X-ray brightness, capacity of robotics and detector speeds, has pushed the bottleneck upstream towards sample preparation. Even in ligand-binding studies using crystal soaking, the experiment best able to exploit beamline capacity, a primary limitation is the need for gentle and nontrivial soaking regimens such as stepwise concentration increases, even for robust and well characterized crystals. Here, the use of acoustic droplet ejection for the soaking of protein crystals with small molecules is described, and it is shown that it is both gentle on crystals and allows very high throughput, with 1000 unique soaks easily performed in under 10 min. In addition to having very low compound consumption (tens of nanolitres per sample), the positional precision of acoustic droplet ejection enables the targeted placement of the compound/solvent away from crystals and towards drop edges, allowing gradual diffusion of solvent across the drop. This ensures both an improvement in the reproducibility of X-ray diffraction and increased solvent tolerance of the crystals, thus enabling higher effective compound-soaking concentrations. The technique is detailed here with examples from the protein target JMJD2D, a histone lysine demethylase with roles in cancer and the focus of active structure-based drug-design efforts.

Optimization of crystallization conditions for biological macromolecules

For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that can be grown. The quality of an X-ray structure determination is directly correlated with the size and the perfection of the crystalline samples; thus, refinement of conditions should always be a primary component of crystal growth. The improvement process is referred to as optimization, and it entails sequential, incremental changes in the chemical parameters that influence crystallization, such as pH, ionic strength and precipitant concentration, as well as physical parameters such as temperature, sample volume and overall methodology. It also includes the application of some unique procedures and approaches, and the addition of novel components such as detergents, ligands or other small molecules that may enhance nucleation or crystal development. Here, an attempt is made to provide guidance on how optimization might best be applied to crystal-growth problems, and what parameters and factors might most profitably be explored to accelerate and achieve success.

Multiparameter screening on SlipChip used for nanoliter protein crystallization combining free interface diffusion and microbatch methods

This paper describes two SlipChip-based approaches to protein crystallization: a SlipChip-based free interface diffusion (FID) method and a SlipChip-based composite method that simultaneously performs microbatch and FID crystallization methods in a single device. The FID SlipChip was designed to screen multiple reagents, each at multiple diffusion equilibration times, and was validated by screening conditions for crystallization of two proteins, enoyl-CoA hydratase from Mycobacterium tuberculosis and dihydrofolate reductase/thymidylate synthase from Babesia bovis, against 48 different reagents at five different equilibration times each, consuming 12 microL of each protein for a total of 480 experiments using three SlipChips. The composite SlipChip was designed to screen multiple reagents, each at multiple mixing ratios and multiple equilibration times, and was validated by screening conditions for crystallization of two proteins, enoyl-CoA hydratase from Mycobacterium tuberculosis and dihydrofolate reductase/thymidylate synthase from Babesia bovis. To prevent cross-contamination while keeping the solution in the neck channels for FID stable, the plates of the SlipChip were etched with a pattern of nanowells. This nanopattern was used to increase the contact angle of aqueous solutions on the surface of the silanized glass. The composite SlipChip increased the number of successful crystallization conditions and identified more conditions for crystallization than separate FID and microbatch screenings. Crystallization experiments were scaled up in well plates using conditions identified during the SlipChip screenings, and X-ray diffraction data were obtained to yield the protein structure of dihydrofolate reductase/thymidylate synthase at 1.95 A resolution. This free-interface diffusion approach provides a convenient and high-throughput method of setting up gradients in microfluidic devices and may find additional applications in cell-based assays.