Microplate-based,label-free detection of biomolecular interactions: applications in proteomics

This review describes a new type of label-free optical biosensor that is inexpensively manufactured from continuous sheets of plastic film and incorporated into standard format microplates to enable highly sensitive, high-throughput detection of small molecules, proteins and cells. The biosensor and associated detection instrumentation are applied to review two fundamental limiting issues for assays in proteomics research and drug discovery: requirement for quantitative measurement of protein concentration and specific activity, and measurements made with complex systems in highly parallel measurements. SRU BIosystems, Inc.’s BIND? label-free detection will address these issues using data examples for hybridoma screening, epitope binning and mapping, small-molecule screening, and cell-based functional assays. The review describes several additional applications that are under development for the system, and the key issues that will drive adoption of the technology over the next 5 years.     

Isolation of recombinant proteins from culture broth by co‐precipitation with an amino acid carrier to form stable dry powders

Protein‐coated microcrystals can be generated by co‐precipitation of protein and a water‐soluble crystalline carrier by addition to excess water miscible organic solvent. We have investigated this novel process for its utility in the concentration and partial purification of a recombinant protein exported into the culture broth during expression by Pichia pastoris. Co‐precipitation with a L ‐glutamine carrier selectively isolated the protein content of the culture broth, with a minimal number of steps, and simultaneously removed contaminants including a novel yeast metabolite. This pigment co‐elutes during aqueous chromatography but its elucidation as a benzoylated glycosamine suggested a simple route of removal by partition during the co‐precipitation process. Scale‐up of the process was readily achieved through in‐line mixing and subsequent reconstitution of the dried protein‐coated microcrystals yielded natively folded, bioactive protein. Additional washing of the crystals with saturated L ‐glutamine facilitated further purification of the recombinant protein immobilized on the L ‐glutamine carrier. Thus, we present a novel method for the harvesting of recombinant protein from culture broth as a dry powder, which may be of general applicability to bioprocessing. Biotechnol. Bioeng. 2010;106: 764–773. © 2010 Wiley Periodicals, Inc.     

The foliar micromorphology of Solanum pseudocapsicum

Foliar micromorphology of Solanum pseudocapsicum was investigated by electron microscopical examination. The leaves are characterized by anisocytic stomata which are more abundant on the abaxial surfaces. The leaves have short multicellular glandular trichomes sparsely distributed over the entire leaf surfaces. Crystal deposits were also observed on the surfaces above the stomata. Energy dispersive X-ray spectroscopy-SEM showed that Al, K, Na and Si were the major constituents of the crystals analyzed. The presence of glandular trichomes in this plant could be the source of poisonous compounds that are characteristic of this species.     

Monitoring the stability of crosslinked protein crystals biotemplates: a feasibility study

Protein crystals, routinely prepared for the elucidation of protein 3D structures by X-ray crystallography, present an ordered and highly accurate 3D array of protein molecules. Inherent to the 3D arrangement of the protein molecules in the crystal is a complementary 3D array of voids made of interconnected cavities and exhibiting highly ordered porosity. The permeability of the porosity of chemically crosslinked enzyme protein crystals to low molecular weight solutes, was used for enzyme mediated organic synthesis and size exclusion chromatography. This permeability might be extended to explore new potential applications for protein crystals, for example, their use as bio-templates for the fabrication of novel, nano-structured composite materials. The quality of composites obtained from "filling" of the ordered voids in protein crystals and their potential applications will be strongly dependent upon an accurate preservation of the order in the original protein crystal 3D array during the "filling" process. Here we propose and demonstrate the feasibility of monitoring the changes in 3D order of the protein array by a step-by-step molecular level monitoring of a model system for hydrogel bio-templating by glutaraldehyde crosslinked lysozyme crystals. This monitoring is based on step-by-step comparative analysis of data obtained from (i) X-ray crystallography: resolution, unit cell dimensions and B-factor values and (ii) fluorescence decay kinetics of ultra-fast laser activated dye, impregnated within these crystals. Our results demonstrated feasibility of the proposed monitoring approach and confirmed that the stabilized protein crystal template retained its 3D structure throughout the process.     

The taxonomic utility of micromorphology in Lepidaploa (Vernonieae: Asteraceae)

Lepidaploa belongs to tribe Vernonieae, one of the most complex tribes of Asteraceae, and the relationships within Lepidaploa and among related genera are poorly understood. Microcharacters may be of taxonomic value and may be used in the identification of taxa at different ranks. To evaluate the reliability of microcharacters as taxonomic markers in this group, we analysed the micromorphology of phyllaries, florets and cypselae in detail in 23 species of Lepidaploa .The species were studied using stereo, light, and scanning electron microscopy. Eight trichome types (eglandular and glandular) were observed on phyllaries, florets and cypselae, in addition to crystals, idioblasts and other microstructures. The results demonstrates that the ocurrence of different combinations of trichome types and crystals, presence of a stylar basal node, idioblasts and glandular apical anther appendages are highly useful to differentiate between related species of Lepidaploa and a diagnostic key using these characters is presented. However, these characters are not of much use to distinguish between closely related genera of Vernonieae since most characters appear homeoplasic and are found in representatives of different genera.     

A new approach for structure analysis of two-dimensional membrane protein crystals using X-ray powder diffraction data

The application of powder diffraction methods to problems in structural biology is generally regarded as intractable because of the large number of unresolved, overlapping X‐ray reflections. Here, we use information about unit cell lattice parameters, space group transformations, and chemical composition as a priori information in a bootstrap process that resolves the ambiguities associated with overlapping reflections. The measured ratios of reflections that can be resolved experimentally are used to refine the position, the shape, and the orientation of low‐resolution molecular structures within the unit cell, in leading to the resolution of the overlapping reflections. The molecular model is then made progressively more sophisticated as additional diffraction information is included in the analysis. We apply our method to the recovery of the structure of the bacteriorhodopsin molecule (bR) to a resolution of 7 Å using experimental data obtained from two‐dimensional purple membrane crystals. The approach can be used to determine the structure factors directly or to provide reliable low‐resolution phase information that can be refined further by the conventional methods of protein crystallography.     

Computer Simulation of Liquid Crystal Films

Abstract

We present the results of extensive Monte Carlo simulations of liquid crystal films of various thicknesses. A simple nearest-neighbour lattice model, the Lebwohl-Lasher model, is employed, with periodic boundaries in two directions and free, planar, surfaces in the third. Particular attention is devoted to locating the temperature of the order-disorder (nematic-isotropic) phase transition. Weak first-order behaviour apparently persists in systems as thin as 8 layers across, but below this the transition cannot be detected. The shift of the transition temperature from its bulk value approaches the expected asymptotic linear dependence on inverse thickness, but significant deviations from this are seen for films of 10 layers thickness and less. These results enable an accurate estimate to be made of the bulk phase transition temperature in the thermodynamic limit, and the result is consistent with that extrapolated from systems with full periodic boundaries.     

Combination of Neutron Scattering and Molecular Dynamics to Determine Internal Motions in Biomolecules

Abstract

The forms and frequencies of atomic dynamics on the pico- and nanosecond timescales are accessible experimentally using incoherent neutron scattering. Molecular dynamics simulations cover the same space and time domains and neutron scattering intensities can be calculated from the simulations for direct comparison with experiment. To illustrate the complementarity of neutron scattering and molecular dynamics we examine measured and simulation-derived elastic incoherent scattering profiles from myoglobin and from the crystalline alanine dipeptide. Elastic incoherent scattering gives information on the geometry of the volume accessible to the atoms in the samples. The simulation-derived dipeptide elastic scattering profiles are in reasonable accord with experiment, deviations being due to the sampling limitations in the simulations and experimental detector normalisation procedures. The simulated dynamics is decomposed, revealing characteristic profiles due to rotational diffusional and translational vibrational motions of the methyl groups. In myoglobin, for which the timescale of the simulation matches more closely that accessible to the experiment, good agreement is seen for the elastic incoherent structure factor. This indicates that the space sampled by the hydrogen atoms in the protein on the timescale <100 ps is well represented by the simulation. Part of the helix atom fluctuations can be described in terms of rigid helix motions.