Complex Biological Molecules Research Articles

Evaluating the inter and intra batch variability of protein aggregation behaviour using Taylor dispersion analysis and dynamic light scattering

Biosimilar pharmaceuticals are complex biological molecules that have similar physicochemical properties to the originator therapeutic protein. They are produced by complex multi-stage processes and are not truly equivalent. Therefore, for a biosimilar to be approved for market it is important to demonstrate that the biological product is highly similar to a reference product. This includes its primary and higher order structures and its aggregation behaviour. Representative lots of both the proposed biosimilar and the reference product are analysed to understand the lot-to-lot variability of both drug substances in the manufacturing processes. Whilst it is not easy to characterise every variation of a protein structure at present additional analytical technologies need to be utilised to ensure the safety and efficacy of any potential biosimilar product. We have explored the use of Taylor dispersion analysis (TDA) to analyse such batch to batch variations in the model protein, bovine serum albumin (BSA) and compared the results to that obtained by conventional dynamic light scattering analysis (DLS). Inter and intra batch differences were evident in all grades of BSA analysed. However, the reproducibility of the TDA measurements, enabled the stability and reversibility of BSA aggregates to be more readily monitored. This demonstrates that Taylor dispersion analysis is a very sensitive technique to study higher order protein states and aggregation. The results, here, also indicate a correlation between protein purity and the physical behaviour of the samples after heat shocking. Here, the protein with the highest quoted purity resulted in a reduced increase in the measured hydrodynamic radius after heat stressing, indicating that less unfolding/aggregation had occurred. Whilst DLS was also able to observe the presence of aggregates, its bias towards larger aggregates indicated a much larger increase in hydrodynamic radii and is less sensitive to small changes in hydrodynamic radii. TDA was also able to identify low levels of larger aggregates that were not observed by DLS. Therefore, given the potential for immunogenicity effects that may result from such aggregates it is suggested that TDA may be suitable in the evaluating detailed batch to batch variability and process induced physical changes of biopharmaceuticals and biosimilars.

Adapting and testing a portable Raman spectrometer for SERS analysis of amino acids and small peptides

Surface-Enhanced Raman Spectroscopy (SERS), a powerful spectrochemical technique enabling highly sensitive analysis of organic and biological materials, is investigated for applications in the analysis of archaeological materials including in situ screening. In this work, a compact mobile Raman spectrometer is employed for acquiring Surface-Enhanced Raman spectra from natural amino acids (l-Arg, l-Phe, l-Met) and a tripeptide (Glutathione), adsorbed on silver colloids. The detection limits of the portable Raman spectrometer, together with an optimization of sample preparation and experimental parameters, are reported. The collection and interpretation of SER spectra of amino acids and peptides is a starting point for the optimization of the instrumentation and its application in the study of more complex biological molecules in the context of detection and analysis of archaeological materials and residues.

ChemInform Abstract: Nitrile Oxide/Alkyne Cycloadditions — A Credible Platform for Synthesis of Bioinspired Molecules by Metal‐Free Molecular Clicking

AbstractReview: 101 refs.

Optical imaging with nanoscale resolution using optical nonlinearities and spatiotemporal modulation

We suggest a type of imaging technique that uses optical nonlinearities and spatiotemporal modulation to achieve nanoscale resolution in the far field. The technique utilizes intense laser beams to produce an optical excitation with spatial features that are much smaller than the wavelength of light. Nonlinear mixing with the excitation can then be used to imprint the information contained in high spatial frequencies into the propagating region. As a specific example, we study the implementation of this technique using coherent anti-Stokes Raman scattering (CARS) near maximum molecular coherence. Our simulations suggest that it may be possible to resolve the structure of complex biological molecules at the nanometer scale in the far field using near-infrared light.

Nitrile Oxide/Alkyne Cycloadditions – A Credible Platform for Synthesis of Bioinspired Molecules by Metal‐Free Molecular Clicking

AbstractThe need for precise and flexible synthetic methodology to underpin modern research in chemical biology and materials science has fuelled a resurgence of interest in Huisgen 1,3‐dipolar cycloaddition chemistry. Of late, the in vogue chemistry for the assembly of complex biological molecules and specialist materials has been the copper‐catalysed azide alkyne cycloaddition (CuAAC) reaction. However, in certain circumstances aversion to the copper catalyst flaws this approach and alternatives have been sought. Click chemistry has developed beyond the original triazole‐forming trick and azides are no longer the only dipoles pursued as click cycloaddition partners. This article reviews some of the complications of the CuAAC reaction and evaluates the potential of nitrile oxide/alkyne cycloaddition (NOAC) as a covalent conjugation tool. With a focus on applications in nucleic acid chemistry and materials science it presents the case for a prominent position for nitrile oxides in the catalyst‐free bioconjugation toolbox.

Solution behaviors and self-assembly of polyoxometalates as models of macroions and amphiphilic polyoxometalate–organic hybrids as novel surfactants

Large, hydrophilic polyoxoanions with high solubility in water and/or other polar solvents demonstrate unique solution behavior by self-assembling into single layer, hollow, spherical "blackberry" structures, which is obviously different from small, simple ions. These macroions cannot be treated as insoluble colloidal suspensions because they form stable "real solutions". Counterion-mediated attraction is considered as the main driving force for the self-assembly behavior. The size disparity between the macroions and their counterions results in macroion-counterion pairing which leads to the inter-macroanionic attraction. The blackberries, with robust membranes semi-permeable to cations, can adjust their size accurately and reversibly in response to the change of solvent polarity and charge density of individual macroions. The inorganic macroions with well-defined size, shape, mass, charge density, but no intramolecular interactions, are ideal model systems to study the intermolecular interactions in polyelectrolyte and bio-macromolecular solutions. The blackberry structures show certain similarities to spherical viral capsids, from the overall structure to the formation kinetics. More amazingly, these inorganic macroions demonstrate some features usually believed to belong only to complex biological molecules, such as the self-recognition in dilute solutions. Meanwhile, polyoxometalates-based organic-inorganic hybrid materials demonstrate amphiphilic properties by self-assembling into vesicles and reverse vesicles in polar and non-polar solvents, respectively, and form monolayer at the water/air interface. Different from conventional amphiphiles, these hybrids show pH-dependent and counterion-dependent self-assembly behaviors with controllable functionality, e.g. fluorescence and catalytic activity, due to the high and tunable charges and the functionalities of POM polar head groups.

Coral-associated marine fungi form novel lineages and heterogeneous assemblages

Coral stress tolerance is intricately tied to the animal's association with microbial symbionts. The most well-known of these symbioses is that between corals and their dinoflagellate photobionts (Symbiodinium spp.), whose genotype indirectly affects whether a coral can survive cyclical and anthropogenic warming events. Fungi comprise a lesser-known coral symbiotic community whose taxonomy, stability and function is largely un-examined. To assess how fungal communities inside a coral host correlate with water temperature and the genotype of co-occurring Symbiodinium, we sampled Acropora hyacinthus coral colonies from adjacent natural pools with different water temperatures and Symbiodinium identities. Phylogenetic analysis of coral-associated fungal ribosomal DNA amplicons showed a high diversity of Basidiomycetes and Ascomycetes, including several clades separated from known fungal taxa by long and well-supported branches. Community similarity did not correlate with any measured variables, and total fungal community composition was highly variable among A. hyacinthus coral colonies. Colonies in the warmer pool contained more phylogenetically diverse fungal communities than the colder pool and contained statistically significant 'indicator' species. Four taxa were present in all coral colonies sampled, and may represent obligate associates. Messenger RNA sequenced from a subset of these same colonies contained an abundance of transcripts involved in metabolism of complex biological molecules. Coincidence between the taxonomic diversity found in the DNA and RNA analysis indicates a metabolically active and diverse resident marine fungal community.

Biosimilars – Global issues, national solutions

Biotechnology derived medicinal products are presently the best characterized biologicals with considerable production and clinical experience, and have revolutionized the treatment of some of the most difficult-to-treat diseases, prolonging and improving the quality of life and patient care. They are also currently one of the fastest growing segments of the pharmaceutical industry market. The critical challenge that the biopharmaceutical industry is facing is the expiry of patents for the first generation of biopharmaceuticals, mainly recombinant DNA derived products, such as interferons, growth hormone and erythropoetin. The question that immediately arose was how should such copies of the originator products be licensed, bearing in mind that they are highly complex biological molecules produced by equally complex biological production processes with their inherent problem of biological variability. Copying biologicals is much more complex than copying small molecules and the critical issue was how to handle the licensing of products if relying in part on data from an innovator product. Since 2004 there has been considerable international consultation on how to deal with biosimilars and biological copy products. This has led to a better understanding of the challenges in the regulatory evaluation of the quality, safety and efficacy of “biosimilars”, to the exchange of information between regulators, as well as to the identification of key issues. The aim of this article is to provide a brief overview of the scientific and regulatory challenges faced in developing and evaluating similar biotherapeutic products for global use. It is intended as an introduction to the series of articles in this special issue of Biologicals devoted to similar biotherepeutic products.

ChemInform Abstract: Analytical Techniques for Biotechnology

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

High-Speed Nonlinear Interferometric Vibrational Imaging of Biological Tissue With Comparison to Raman Microscopy.

Vibrational contrast imaging of the distribution of complex biological molecules requires the use of techniques that provide broadband spectra with sufficient resolution. Coherent anti-Stokes Raman scattering (CARS) microscopy is currently limited in meeting these requirements due to the presence of a nonresonant background and its inability to target multiple resonances simultaneously. We present nonlinear interferometric vibrational imaging (NIVI), a technique based on CARS that uses femtosecond pump and Stokes pulses to retrieve broadband vibrational spectra over 200 cm(-1) (full-width at half maximum). By chirping the pump and performing spectral interferometric detection, the anti-Stokes pulses are resolved in time. This phase-sensitive detection allows suppression of not only the nonresonant background, but also of the real part of the nonlinear susceptibility χ((3)), improving the spectral resolution and features to make them comparable to those acquired with spontaneous Raman microscopy, as shown for a material sample and mammary tissue.

Myosin XI Is Required for Actin-Associated Movement of Plastid Stromules

Stromules are highly dynamic stroma-filled tubules extending from the surface of plastids and occasionally interconnecting individual plastids, allowing the movement of complex biological molecules between the interconnected plastids. Experiments with inhibitors of cytoskeleton assembly have indicated the involvement of an actin-based system in stromule movement. However, the motor protein associated with the system had not been identified. Here, we present direct evidence that myosin XI is involved in the formation and movement of stromules in tobacco leaves. Application of 2,3-butanedione 2-monoxime, an inhibitor of myosin ATPase activity, resulted in the loss of stromules from tobacco leaf epidermal cells. Transient RNA interference of myosin XI in leaves of Nicotiana benthamiana also resulted in the loss of stromules from epidermal cells, without any effect on transcripts for actin or myosin VIII. Transient expression of a GFP-tagged myosin XI tail domain in tobacco leaf epidermal cells showed that the fusion protein localized to the chloroplast envelope, as well as to mitochondria and other organelles. Our findings identify myosin XI as a key protein involved in the formation and movement of stromules.

Analyzing single‐molecule manipulation experiments

Single-molecule manipulation studies can provide quantitative information about the physical properties of complex biological molecules without ensemble artifacts obscuring the measurements. We demonstrate computational techniques which aim at more fully utilizing the wealth of information contained in noisy experimental time series. The "noise" comes from multiple sources e.g., inherent thermal motion, instrument measurement error, etc. The primary focus of this paper is a methodology that uses time domain based methods to extract the effective molecular friction from single-molecule pulling data. We studied molecules composed of eight tandem repeat titin I27 domains, but the modeling approaches have applicability to other single-molecule mechanical studies. The merits and challenges associated with applying such a computational approach to existing single-molecule manipulation data are also discussed.

In Honor of W.E. Moerner: Confining Molecules for Single‐Molecule Spectroscopy

AbstractSingle‐molecule spectroscopy provides a wealth of information on the dynamics and interactions of complex biological molecules. Yet these measurements are extremely challenging, partly because Brownian motion prevents molecules in free solution from remaining stationary. Here we describe several techniques that our lab has developed for confining single molecules for optical spectroscopy. These alternatives to surface immobilization provide confinement that is gentle enough to minimize perturbations to the molecule, but strong enough to allow long‐time imaging of single fluorescent molecules, often in the presence of a high fluorescent background.

Nanoscale magnetic sensing with an individual electronic spin in diamond

Detection of weak magnetic fields with nanoscale spatial resolution is an outstanding problem in the biological and physical sciences. For example, at a distance of 10 nm, the spin of a single electron produces a magnetic field of about 1 muT, and the corresponding field from a single proton is a few nanoteslas. A sensor able to detect such magnetic fields with nanometre spatial resolution would enable powerful applications, ranging from the detection of magnetic resonance signals from individual electron or nuclear spins in complex biological molecules to readout of classical or quantum bits of information encoded in an electron or nuclear spin memory. Here we experimentally demonstrate an approach to such nanoscale magnetic sensing, using coherent manipulation of an individual electronic spin qubit associated with a nitrogen-vacancy impurity in diamond at room temperature. Using an ultra-pure diamond sample, we achieve detection of 3 nT magnetic fields at kilohertz frequencies after 100 s of averaging. In addition, we demonstrate a sensitivity of 0.5 muT Hz(-1/2) for a diamond nanocrystal with a diameter of 30 nm.

Developing novel biopharmaceutical products through morphogenics

The genomics era has provided valuable information on the content of the human genome, including the structure and chromosomal location of many disease-associated loci. This wealth of information has resulted in the identification of novel targets that are amenable to biopharmaceutical product development, leading to an overall enhanced pace of therapeutic development for a broad array of disease indications. Historically, small chemical entities have been designed as therapies to gene products that are encoded by intracellular proteins, enzymes and channels. With the advent and development of biologically based (protein- and cell-based) entities (BBEs) therapies, it is now possible to create molecules that have exquisite specificity for disease targets and spare unwanted pharmacologic activity against normal tissues. In addition to the specificity, BBEs generally have lower toxicity profiles when compared with small chemical entities, making biologically-based therapeutic approaches even more attractive. One of the difficulties that has been encountered with BBEs is the ability to produce compounds with maximal pharmacologic activity as well as establishing systems that can manufacture these complex biological molecules in sufficient quantities to meet clinical demand. This review discusses a broad enabling platform technology called morphogenics that can rapidly yield robust systems that can overcome present manufacturing shortfalls as well as accelerate the development of highly efficacious BBEs from those with insufficient pharmacological activity.

Ultra-thin membranes aid microscopy and have potential use in filtration applications

Carbon membranes recently created by scientists at Germany's Max Planck Institute for Solid State Research are only one atom thick. For electrons, such membranes are almost completely transparent, and using an electron microscope researchers may be able to examine absorbed individual molecules on the membranes and image the atomic structure of complex biological molecules. The ultra-thin membranes also may be used in filtration applications. This feature article briefly looks at their development.

Organization and mobility of water in amorphous and crystalline trehalose

The disaccharide trehalose is accumulated by microorganisms, such as yeasts, and multicellular organisms, such as tardigrades, when conditions of extreme drought occur. In this way these organisms can withstand dehydration through the formation of an intracellular carbohydrate glass, which, with its high viscosity and hydrogen-bonding interactions, stabilizes and protects the integrity of complex biological structures and molecules. This property of trehalose can also be harnessed in the stabilization of liposomes, proteins and in the preservation of red blood cells, but the underlying mechanism of bioprotection is not yet fully understood. Here we use positron annihilation lifetime spectroscopy to probe the free volume of trehalose matrices; specifically, we develop a molecular picture of the organization and mobility of water in both amorphous and crystalline states. Whereas in amorphous matrices, water increases the average intermolecular hole size, in the crystalline dihydrate it is organized as a confined one-dimensional fluid in channels of fixed diameter that allow activated diffusion of water in and out of the crystallites. We present direct real-time evidence of water molecules unloading reversibly from these channels, thereby acting as both a sink and a source of water in low-moisture systems. We postulate that this behaviour may provide the overall stability required to keep organisms viable through dehydration conditions.

Mechanical unfolding revisited through a simple but realistic model

Single-molecule experiments and their application to probe the mechanical resistance and related properties of proteins provide a new dimension in our knowledge of these important and complex biological molecules. Single-molecule techniques may not have yet overridden solution experiments as a method of choice to characterize biophysical and biological properties of proteins, but have stimulated a debate and contributed considerably to bridge theory and experiment. Here we demonstrate this latter contribution by illustrating the reach of some theoretical findings using a solvable but nontrivial molecular model whose properties are analogous to those of the corresponding experimental systems. In particular, we show the relationship between the thermodynamic and the mechanical properties of a protein. The simulations presented here also illustrate how forced and spontaneous unfolding occur through different pathways and that folding and unfolding rates at equilibrium cannot in general be obtained from forced unfolding experiments or simulations. We also study the relationship between the energy surface and the mechanical resistance of a protein and show how a simple analysis of the native state can predict much of the mechanical properties of a protein.

Tangible Interfaces for Structural Molecular Biology

The evolving technology of computer autofabrication makes it possible to produce physical models for complex biological molecules and assemblies. Augmented reality has recently developed as a computer interface technology that enables the mixing of real-world objects and computer-generated graphics. We report an application that demonstrates the use of autofabricated tangible models and augmented reality for research and communication in molecular biology. We have extended our molecular modeling environment, PMV, to support the fabrication of a wide variety of physical molecular models, and have adapted an augmented reality system to allow virtual 3D representations to be overlaid onto the tangible molecular models. Users can easily change the overlaid information, switching between different representations of the molecule, displays of molecular properties, or dynamic information. The physical models provide a powerful, intuitive interface for manipulating the computer models, streamlining the interface between human intent, the physical model, and the computational activity.

Recent developments in the use of transgenic plants for the production of human therapeutics and biopharmaceuticals.

In recent years there has been a dramatic increase in the application of plant biotechnology for the production of a variety of commercially valuable simple and complex biological molecules (biologics) for use in human and animal healthcare. Transgenic whole plants and plant cell culture systems have been developed that have the capacity to economically produce large-scale quantities of antibodies and antibody fragments, antigens and/or vaccine epitopes, metabolic enzymes, hormones, (neuro)peptides and a variety of biologically active complexes and secondary metabolites for direct use as therapeutic agents or diagnostic tools in the medical healthcare industry. As the products of genetically modified plants make their way from concept to commercialization the associated risks and acceptance by the public has been become a focal point. In this paper, we summarize the recent advances made in the use of transgenic plants and plant cell cultures as biological factories for the production of human therapeutics and biopharmaceuticals and discuss the long-term potential of `molecular farming' as a low-cost, efficient method for the production of biological materials with demonstrated utility to the pharmaceutical industry or medical community.