Determination of the phase diagram for soluble and membrane proteins

Droplet-Based Evaporative System for the Estimation of Protein Crystallization Kinetics

Crystallization is a potential cost-effective alternative to chromatography for the purification of biotherapeutic proteins. Crystallization kinetics are required for the design and control of such processes, but only a limited quantity of proteins is available during the initial stage of process development. This article describes the design of a droplet-based evaporative system for the evaluation of candidate crystallization conditions and the estimation of kinetics using only a droplet (on the order of μL) of protein solution. The temperature and humidity of air fed to a flow cell containing the droplet are controlled for evaporation and rehydration of the droplet, which are used for manipulating supersaturation. Dual-angle images of the droplet are taken and analyzed on-line to obtain the droplet volume and crystal sizes. Crystallization kinetics are estimated based on a first-principles process model and experimental data. Tight control of temperature and humidity of the air, fast and accurate image analysis, and accurate estimation of crystallization kinetics are experimentally demonstrated for a model protein lysozyme. The estimated kinetics are suitable for the model-based design and control of protein crystallization processes.

Controllable light-induced droplet evaporative crystallization

Droplet evaporative crystallization is one of the practical tools for clinical diagnosis, environmental monitoring, and pharmaceutical synthesis. Herein, we proposed a controllable and flexible light strategy to manipulate the droplet evaporative crystallization, in which the photothermal effect of a focused infrared laser actuated intense evaporation to attain the droplet evaporative crystallization. Due to the localized heating effect, not only the droplet evaporative crystallization could be promoted, but also the resultant Marangoni-flow enabled the crystals to be concentrated, exhibiting excellent controllability. Besides, a relationship between the crystallization starting time and the solution concentration/laser power was achieved, which benefited the manipulation of the droplet evaporative crystallization. The light strategy proposed in the present study possesses promising potential for future applications.

Recent advances in biophysical studies of rhodopsins - Oligomerization, folding, and structure

Retinal-binding proteins, mainly known as rhodopsins, function as photosensors and ion transporters in a wide range of organisms. From halobacterial light-driven proton pump, bacteriorhodopsin, to bovine photoreceptor, visual rhodopsin, they have served as prototypical α-helical membrane proteins in a large number of biophysical studies and aided in the development of many cutting-edge techniques of structural biology and biospectroscopy. In the last decade, microbial and animal rhodopsin families have expanded significantly, bringing into play a number of new interesting structures and functions. In this review, we will discuss recent advances in biophysical approaches to retinal-binding proteins, primarily microbial rhodopsins, including those in optical spectroscopy, X-ray crystallography, nuclear magnetic resonance, and electron paramagnetic resonance, as applied to such fundamental biological aspects as protein oligomerization, folding, and structure.

A crystallization apparatus for temperature-controlled flow-cell dialysis with real-time visualization

Many instrumentation developments in crystallization have concentrated on massive parallelization assays and reduction of sample volume per experiment to find initial crystallization conditions. Yet improving the size and diffraction quality of the crystals for diffraction studies often requires decoupling of crystal nucleation and growth. This in turn requires the control of variables such as precipitant and protein concentration, equilibration rate, and temperature, which are all difficult parameters to control in the existing setups. The success of the temperature-controlled batch method, originally developed to grow very large crystals for neutron crystallography, demonstrated that the rational optimization of crystal growth has potential in structural biology. A temperature-controlled dialysis button has been developed for our previous device, and a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature-precipitant concentration phase diagrams has been constructed. The presented approach differs from the current paradigm, since it involves serial instead of parallel experiments, exploring multiple crystallization conditions with the same protein sample. The sample is not consumed in the experiment and the conditions can be changed in a reversible fashion, using dialysis with a flowing precipitant reservoir as well as precise temperature control. The control software allows visualization of the crystals, as well as control of the temperature and composition of the crystallization solution. The rational crystallization optimization strategies presented here allow tailoring of crystal size, morphology and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination.

Computational crystallization

Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial and error. In this article, efforts in the field are discussed together with a theoretical underpinning using a solubility phase diagram. Prior knowledge has been used to develop tools that computationally predict the crystallization outcome and define mutational approaches that enhance the likelihood of crystallization. For the most part these tools are based on binary outcomes (crystal or no crystal), and the full information contained in an assembly of crystallization screening experiments is lost. The potential of this additional information is illustrated by examples where new biological knowledge can be obtained and where a target can be sub-categorized to predict which class of reagents provides the crystallization driving force. Computational analysis of crystallization requires complete and correctly formatted data. While massive crystallization screening efforts are under way, the data available from many of these studies are sparse. The potential for this data and the steps needed to realize this potential are discussed.

Solvent compatible microfluidic platforms for pharmaceutical solid form screening

The use of SIFEL in the crystallization fluid layers renders the microfluidic crystallization array compatible with solvents such as tetrahydrofuran, acetonitrile, chloroform, hexane, and toluene.

Crystallization screening: the influence of history on current practice

While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed.

Coil fraction-dependent phase behaviour of a model globular protein-polymer diblock copolymer

The self-assembly of the model globular protein-polymer block copolymer mCherry-b-poly(N-isopropyl acrylamide) is explored across a range of polymer coil fractions from 0.21 to 0.82 to produce a phase diagram for these materials as a function of molecular composition. Overall, four types of morphologies were observed: hexagonally packed cylinders, perforated lamellae, lamellae, and disordered nanostructures. Across all coil fractions and morphologies, a lyotropic re-entrant order-disorder transition in water was observed, with disordered structures below 30 wt% and above 70 wt% and well-ordered morphologies at intermediate concentrations. Solid state samples prepared by solvent evaporation show moderately ordered structures similar to those observed in 60 wt% solutions, suggesting that bulk structures result from kinetic trapping of morphologies which appear at lower concentrations. While highly ordered cylindrical nanostructures are observed around a bioconjugate polymer volume fraction of 0.3 and well-ordered lamellae are seen near a volume fraction of 0.6, materials at lower or higher coil fractions become increasingly disordered. Notable differences between the phase behaviour of globular protein-polymer block copolymers and coil-coil diblock copolymers include the lack of spherical nanostructures at either high or low polymer coil fractions as well as shifted phase boundaries between morphologies which result in an asymmetric phase diagram.

A microfluidic platform for evaporation-based salt screening of pharmaceutical parent compounds

We describe a microfluidic platform to screen for salt forms of pharmaceutical compounds (PCs) via controlled evaporation. The platform enables on-chip combinatorial mixing of PC and salt former solutions in a 24-well array (~200 nL/well), which is a drastic reduction in the amount of PC needed per condition screened compared to traditional screening approaches that require ~100 μL/well. The reduced sample needs enable salt screening at a much earlier stage in the drug development process, when only limited quantities of PCs are available. Compatibility with (i) solvents commonly used in the pharmaceutical industry, and (ii) Raman spectroscopy for solid form identification was ensured by using a hybrid microfluidic platform. A thin layer of elastomeric PDMS was utilized to retain pneumatic valving capabilities. This layer is sandwiched between layers of cyclic-olefin copolymer, a material with low air and solvent permeability and low Raman background to yield a physically rigid and Raman compatible chip. A solvent-impermeable thiolene layer patterned with evaporation channels permits control over the rate of solvent evaporation. Control over the rate of solvent evaporation (2-15 nL h(-1)) results in consistent, known rates of increase in the supersaturation levels attained on-chip, and increases the probability for crystalline solids to form. The modular nature of the platform enables on-chip Raman and birefringence analysis of the solid forms. Model compounds, tamoxifen and ephedrine, were used to validate the platform's ability to screen for salts. On-chip Raman analysis helped to identify six different salts each of tamoxifen and ephedrine.

Fabrication of X-ray compatible microfluidic platforms for protein crystallization

This paper reports a method for fabricating multilayer microfluidic protein crystallization platforms using different materials to achieve X-ray transparency and compatibility with crystallization reagents. To validate this approach, three soluble proteins, lysozyme, thaumatin, and ribonuclease A were crystallized on-chip, followed by on-chip diffraction data collection. We also report a chip with an array of wells for screening different conditions that consume a minimal amount of protein solution as compared to traditional screening methods. A large number of high quality isomorphous protein crystals can be grown in the wells, after which slices of X-ray data can be collected from many crystals still residing within the wells. Complete protein structures can be obtained by merging these slices of data followed by further processing with crystallography software. This approach of using an x-ray transparent chip for screening, crystal growth, and X-ray data collection enables room temperature data collection from many crystals mounted in parallel, which thus eliminates crystal handling and minimizes radiation damage to the crystals.

Iterative operations on microdroplets and continuous monitoring of processes within them; determination of solubility diagrams of proteins

We demonstrate a technique for controlling the content of multiple microdroplets in time. We use this system to rapidly and quantiatively determine the solubility diagrams of two model proteins (lysozyme and ribonuclease A).

Generic pathways to stability in concentrated protein mixtures

We present a series of experimental results that disclose the crucial role of ionic strength and partial volume fractions in the control of the phase behaviour of binary protein mixtures. Our findings can be understood as that the ionic strength determines the relative contribution of the entropy of the protein counter-ions to the overall thermodynamics of the system. Associative phase separation and crystallization observed at, respectively, low and high ionic strength are suppressed at intermediate salt concentrations, where the entropy gain upon releasing the counter-ions from the double layer of the proteins is negligible and the entropy loss upon confining the counter-ions within the protein crystal phase significant. Moreover, we find that the partial volume fraction of the protein prone to crystallize determines the crystallization boundary and that the presence of other proteins strongly delays crystallization, leading to temporarily stable mixtures. These findings suggest that stability in more complex protein mixtures, such as the cytosol, relates to the ionic strength and protein composition rather than to protein specific properties.

A Stochastic Model for Nucleation Kinetics Determination in Droplet-Based Microfluidic Systems

The measured induction times in droplet-based microfluidic systems are stochastic and are not described by the deterministic population balances or moment equations commonly used to model the crystallization of amino acids, proteins, and active pharmaceutical ingredients. A stochastic model in the form of a Master equation is formulated for crystal nucleation in droplet-based microfluidic systems for any form of nucleation rate expression under conditions of time-varying supersaturation. An analytical solution is provided to describe the (1) time evolution of the probability of crystal nucleation, (2) the average number of crystals that will form at time t for a large number of droplets, (3) the induction time distribution, and (4) the mean, most likely, and median induction times. These expressions are used to develop methods for determining the nucleation kinetics. Nucleation kinetics are determined from induction times measured for paracetamol and lysozyme at high supersaturation in an evaporation-based high-throughput crystallization platform, which give low prediction errors when the nucleation kinetics were used to predict induction times for other experimental conditions. The proposed stochastic model is relevant to homogeneous and heterogeneous crystal nucleation in a wide range of droplet-based and microfluidic crystallization platforms.