Cryocrystallography in capillaries: critical glycerol concentrations and cooling rates

Self-pressurised rapid freezing at arbitrary cryoprotectant concentrations

Self-pressurised rapid freezing (SPRF) has been proposed as a simple alternative to traditional high-pressure freezing (HPF) protocols for vitrification of biological samples in electron microscopy and cryopreservation applications. Both methods exploit the circumstance that the melting point of ice reaches a minimum when subjected to pressure of around 210 MPa, however, in SPRF its precise quantity depends on sample properties and hence, is generally unknown. In particular, cryoprotective agents (CPAs) are expected to be a factor; though eschewed by many SPRF experiments, vitrification of larger samples notably cannot be envisaged without them. Thus, in this study, we address the question of how CPA concentration affects pressure inside sealed capillaries, and how to design SPRF experiments accordingly. By embedding a fibre-optic probe in samples and performing Raman spectroscopy after freezing, we first present a direct assessment of pressure build-up during SPRF, enabled by the large pressure sensitivity of the Raman shift of hexagonal ice. Choosing dimethyl sulphoxide (DMSO) as a model CPA, this approach allows us to demonstrate that average pressure drops to zero when DMSO concentrations of 15 wt% are exceeded. Since a trade-off between pressure and DMSO concentration represents an impasse with regard to vitrification of larger samples, we introduce a sample architecture with two chambers, separated by a partition that allows for equilibration of pressure but not DMSO concentrations. We show that pressure and concentration in the fibre-facing chamber can be tuned independently, and present differential scanning calorimetry (DSC) data supporting the improved vitrification performance of two-chamber designs. Lay version of abstract for 'Self-pressurised rapid freezing at arbitrary cryoprotectant concentrations' Anyone is familiar with pipes bursting in winter because the volume of ice is greater than that of liquid water. Less well known is the fact that inside a thick-walled container, sealed and devoid of air bubbles, this pressure build-up will allow a fraction of water to remain unfrozen if the sample is also cooled sufficiently rapidly far below the freezing point. This phenomenon has already been harnessed for specimen preparation in microscopy, where low temperatures are useful to immobilise the sample, but harmful if ice formation occurs. However, specimen preparation cannot always rely on this pressure-based effect alone, but sometimes requires addition of chemicals to inhibit ice formation. Not enough is known directly about how these chemicals affect pressure build-up: Indeed, rapid cooling below the freezing point is only possible for small sample volumes, typically placed inside sealed capillaries, so that space is generally insufficient to accommodate a pressure sensor. By means of a compact sensor, based on an optical fibre, laser and spectrometer, we present the first direct assessment of pressure inside sealed capillaries. We show that addition of chemicals reduces pressure build-up and present a two-chambered capillary to circumvent the resulting trade-off. Also, we present evidence showing that the two-chambered capillary design can avoid ice formation more readily than a single-chambered one.

Ultra-Rapid Laser Calorimetry for the Assessment of Crystallization in Low-Concentration Cryoprotectants

Cryoprotective agents (CPAs) are routinely used to vitrify, attain an amorphous glass state void of crystallization, and thereby cryopreserve biomaterials. Two vital characteristics of a CPA-loaded system are the critical cooling and warming rates (CCR and CWR), the temperature rates needed to achieve and return from a vitrified state, respectively. Due to the toxicity associated with CPAs, it is often desirable to use the lowest concentrations possible, driving up CWR and making it increasingly difficult to measure. This paper describes a novel method for assessing CWR between the 0.4 × 10⁵ and 10⁷ °C/min in microliter CPA-loaded droplet systems with a new ultrarapid laser calorimetric approach. Cooling was achieved by direct quenching in liquid nitrogen, while warming was achieved by the irradiation of plasmonic gold nanoparticle-loaded vitrified droplets by a high-power 1064 nm millisecond pulsed laser. We assume "apparent" vitrification is achieved provided ice is not visually apparent (i.e., opacity) upon imaging with a camera (CCR) during cooling or highspeed camera (CWR) during warming. Using this approach, we were able to investigate CWRs in single CPA systems such as propylene glycol (PG), glycerol, and Trehalose in water, as well as mixtures of glycerol-trehalose-water and propylene glycol-trehalose-water CPA at low concentrations (20-40 wt %). Further, a phenomenological model for determining the CCRs and CWRs of CPAs was developed which allowed for predictions of CCR or CWR of single component CPA and mixtures (within and outside of the regime their constituents were measured in), providing an avenue for optimizing CCR and CWR and perhaps future CPA cocktail discovery.

Simple Cryoprotectant-Free Method to Advance Pulsed Dipolar ESR Spectroscopy for Capturing Protein Conformational Ensembles

Double electron-electron resonance (DEER) is a powerful technique for studying protein conformations. To preserve the room-temperature ensemble, proteins are usually shock-frozen in liquid nitrogen prior to DEER measurements. The use of cryoprotectant additives is, therefore, necessary to ensure the formation of a vitrified state. Here, we present a simple modification of the freezing process using a flexible fused silica microcapillary, which increases the freezing rates and thus enables DEER measurement without the use of cryoprotectants. The Bid protein, which is highly sensitive to cryoprotectant additives, is used as a model. We show that DEER with the simple modification can successfully reveal the cold denaturation of Bid, which was not possible with the conventional DEER preparations. The DEER result reveals the nature of Bid folding. Our method advances DEER for capturing the chemically and thermally induced conformational changes of a protein in a cryoprotectant-free medium.

Kinetics of nonisothermal phase change with arbitrary temperature-time history and initial transformed phase distributions

This paper describes the extension of the classic Avrami equation to nonisothermal systems with arbitrary temperature-time history and arbitrary initial distributions of transformed phase. We start by showing that through examination of phase change in Fourier space, we can decouple the nucleation rate, growth rate, and transformed fraction, leading to the derivation of a nonlinear differential equation relating these three properties. We then consider a population balance partial differential equation (PDE) on the phase size distribution and solve it analytically. Then, by relating this PDE solution to the transformed fraction of phase, we are able to derive initial conditions to the differential equation relating nucleation rate, growth rate, and transformed fraction.

High-resolution single-particle cryo-EM of samples vitrified in boiling nitro-gen

Based on work by Dubochet and others in the 1980s and 1990s, samples for single-particle cryo-electron microscopy (cryo-EM) have been vitrified using ethane, propane or ethane/propane mixtures. These liquid cryogens have a large difference between their melting and boiling temperatures and so can absorb substantial heat without formation of an insulating vapor layer adjacent to a cooling sample. However, ethane and propane are flammable, they must be liquified in liquid nitro-gen immediately before cryo-EM sample preparation, and cryocooled samples must be transferred to liquid nitro-gen for storage, complicating workflows and increasing the chance of sample damage during handling. Experiments over the last 15 years have shown that cooling rates required to vitrify pure water are only ∼250 000 K s-1, at the low end of earlier estimates, and that the dominant factor that has limited cooling rates of small samples in liquid nitro-gen is sample precooling in cold gas present above the liquid cryogen surface, not the Leidenfrost effect. Using an automated cryocooling instrument developed for cryocrystallography that combines high plunge speeds with efficient removal of cold gas, we show that single-particle cryo-EM samples on commercial grids can be routinely vitrified using only boiling nitro-gen and obtain apoferritin datasets and refined structures with 2.65 Å resolution. The use of liquid nitro-gen as the primary coolant may allow manual and automated workflows to be simplified and may reduce sample stresses that contribute to beam-induced motion.

Cryopreservation of NK and T Cells Without DMSO for Adoptive Cell-Based Immunotherapy

Dimethylsufoxide (DMSO) being universally used as a cryoprotectant in clinical adoptive cell-therapy settings to treat hematological malignancies and solid tumors is a growing concern, largely due to its broad toxicities. Its use has been associated with significant clinical side effects-cardiovascular, neurological, gastrointestinal, and allergic-in patients receiving infusions of cell-therapy products. DMSO has also been associated with altered expression of natural killer (NK) and T-cell markers and their in vivo function, not to mention difficulties in scaling up DMSO-based cryoprotectants, which introduce manufacturing challenges for autologous and allogeneic cellular therapies, including chimeric antigen receptor (CAR)-T and CAR-NK cell therapies. Interest in developing alternatives to DMSO has resulted in the evaluation of a variety of sugars, proteins, polymers, amino acids, and other small molecules and osmolytes as well as modalities to efficiently enable cellular uptake of these cryoprotectants. However, the DMSO-free cryopreservation of NK and T cells remains difficult. They represent heterogeneous cell populations that are sensitive to freezing and thawing. As a result, clinical use of cryopreserved cell-therapy products has not moved past the use of DMSO. Here, we present the state of the art in the development and use of cryopreservation options that do not contain DMSO toward clinical solutions to enable the global deployment of safer adoptively transferred cell-based therapies.

Ice in biomolecular cryocrystallography

Diffraction data acquired from cryocooled protein crystals often include diffraction from ice. Analysis of ice diffraction from crystals of three proteins shows that the ice formed within solvent cavities during rapid cooling is comprised of a stacking-disordered mixture of hexagonal and cubic planes, with the cubic plane fraction increasing with increasing cryoprotectant concentration and increasing cooling rate. Building on the work of Thorn and coworkers [Thorn et al. (2017), Acta Cryst. D73, 729-727], a revised metric is defined for detecting ice from deposited protein structure-factor data, and this metric is validated using full-frame diffraction data from the Integrated Resource for Reproducibility in Macromolecular Crystallography. Using this revised metric and improved algorithms, an analysis of structure-factor data from a random sample of 89 827 PDB entries collected at cryogenic temperatures indicates that roughly 16% show evidence of ice contamination, and that this fraction increases with increasing solvent content and maximum solvent-cavity size. By examining the ice diffraction-peak positions at which structure-factor perturbations are observed, it is found that roughly 25% of crystals exhibit ice with primarily hexagonal character, indicating that inadequate cooling rates and/or cryoprotectant concentrations were used, while the remaining 75% show ice with a stacking-disordered or cubic character.

KrioBlast® as a New Technology of Hyper-fast Cryopreservation of Cells and Tissues. Part II. 2. Kinetic Vitrification of Human Pluripotent Stem Cells and Spermatozoa [corrected]

Pilot experiments on kinetic vitrification of human pluripotent stem cells and spermatozoa using a KrioBlast^TM-2 without penetrating cryoprotectants have shown high survival of cells (75-85% in both cases).

Density and electron density of aqueous cryoprotectant solutions at cryogenic temperatures for optimized cryoprotection and diffraction contrast

The glass-phase densities at T = 77 K of aqueous solutions of the common cryoprotective agents (CPAs) methanol, ethanol, 2-propanol, glycerol, 2-methyl-2,4-pentanediol (MPD), ethylene glycol, polyethylene glycol 200 and polypropylene glycol 425 were measured as a function of CPA concentration. Individual drops with volumes as small as ∼65 pl were rapidly cooled to achieve the glass phase, and their densities at T = 77 K were determined by cryoflotation. These densities were used to determine the glass-phase electron density of each solution and its volume thermal contraction between room temperature and 77 K. When combined with data for the critical cooling rates required to achieve the glass phase versus CPA concentration, these yield alternative measures of cryoprotectant effectiveness. These reference data will aid in minimizing sample stresses and mechanical damage in cryocrystallography, in cryogenic temperature X-ray imaging and in vitrification-based cryopreservation protocols, and in maximizing electron-density contrast between cryoprotectant solutions and biomolecules in cryogenic temperature small-angle X-ray scattering experiments and cryo-electron microscopy.

KrioBlast TM as a New Technology of Hyper-fast Cryopreservation of Cells and Tissues. Part I. Thermodynamic Aspects and Potential Applications in Reproductive and Regenerative Medicine

Kinetic (dynamic) vitrification is a promising trend in cryopreservation of biological materials because it allows avoiding the formation of lethal intracellular ice and minimizes harmful effects of highly toxic penetrating cryoprotectants. A uniform cooling protocol and the same instruments can be used for practically all types of cells. In modern technologies, the rate of cooling is essentially limited by the Leidenfrost effect. We describe a novel platform for kinetic vitrification of biological materials KrioBlast ^TM that realizes hyper-fast cooling and allows overcoming the Leidenfrost effect. This opens prospects for creation of a novel technology of cell cryopreservation for reproductive and regenerative medicine.

A standardized technique for high-pressure cooling of protein crystals

Cryogenic temperatures slow down secondary radiation damage during data collection from macromolecular crystals. In 1973, cooling at high pressure was identified as a method for cryopreserving crystals in their mother liquor [Thomanek et al. (1973). Acta Cryst. A29, 263-265]. Results from different groups studying different crystal systems indicated that the approach had merit, although difficulties in making the process work have limited its widespread use. Therefore, a simplified and reliable technique has been developed termed high-pressure cooling (HPC). An essential requirement for HPC is to protect crystals in capillaries. These capillaries form part of new sample holders with SPINE standard dimensions. Crystals are harvested with the capillary, cooled at high pressure (220 MPa) and stored in a cryovial. This system also allows the usage of the standard automation at the synchrotron. Crystals of hen egg-white lysozyme and concanavalin A have been successfully cryopreserved and yielded data sets to resolutions of 1.45 and 1.35 Å, respectively. Extensive work has been performed to define the useful working range of HPC in capillaries with 250 µm inner diameter. Three different 96-well crystallization screens that are most frequently used in our crystallization facility were chosen to study the formation of amorphous ice in this cooling setup. More than 89% of the screening solutions were directly suitable for HPC. This achievement represents a drastic improvement for crystals that suffered from cryoprotection or were not previously eligible for cryoprotection.

Crystal Dehydration in Membrane Protein Crystallography

Crystal dehydration has been successfully implemented to facilitate the structural solution of a number of soluble and membrane protein structures over the years. This chapter will present the currently available tools to undertake controlled crystal dehydration, focusing on some successful membrane protein cases. Also discussed here will be some practical considerations regarding membrane protein crystals and the relationship between different techniques in order to help researchers to select the most suitable technique for their projects.

Practical macromolecular cryocrystallography

Current methods, reagents and experimental hardware for successfully and reproducibly flash-cooling macromolecular crystals to cryogenic temperatures for X-ray diffraction data collection are reviewed.

Cryocrystallography is an indispensable technique that is routinely used for single-crystal X-ray diffraction data collection at temperatures near 100 K, where radiation damage is mitigated. Modern procedures and tools to cryoprotect and rapidly cool macromolecular crystals with a significant solvent fraction to below the glass-transition phase of water are reviewed. Reagents and methods to help prevent the stresses that damage crystals when flash-cooling are described. A method of using isopentane to assess whether cryogenic temperatures have been preserved when dismounting screened crystals is also presented.

Microfluidic cryofixation for correlative microscopy

Cryofixation yields outstanding ultrastructural preservation of cells for electron microscopy, but current methods disrupt live cell imaging. Here we demonstrate a microfluidic approach that enables cryofixation to be performed directly in the light microscope with millisecond time resolution and at atmospheric pressure. This will provide a link between imaging/stimulation of live cells and post-fixation optical, electron, or X-ray microscopy.

Improved reproducibility of unit-cell parameters in macromolecular cryocrystallography by limiting dehydration during crystal mounting

In macromolecular cryocrystallography unit-cell parameters can have low reproducibility, limiting the effectiveness of combining data sets from multiple crystals and inhibiting the development of defined repeatable cooling protocols. Here, potential sources of unit-cell variation are investigated and crystal dehydration during loop-mounting is found to be an important factor. The amount of water lost by the unit cell depends on the crystal size, the loop size, the ambient relative humidity and the transfer distance to the cooling medium. To limit water loss during crystal mounting, a threefold strategy has been implemented. Firstly, crystal manipulations are performed in a humid environment similar to the humidity of the crystal-growth or soaking solution. Secondly, the looped crystal is transferred to a vial containing a small amount of the crystal soaking solution. Upon loop transfer, the vial is sealed, which allows transport of the crystal at its equilibrated humidity. Thirdly, the crystal loop is directly mounted from the vial into the cold gas stream. This strategy minimizes the exposure of the crystal to relatively low humidity ambient air, improves the reproducibility of low-temperature unit-cell parameters and offers some new approaches to crystal handling and cryoprotection.

Breaking the radiation damage limit with Cryo-SAXS

Small angle x-ray scattering (SAXS) is a versatile and widely used technique for obtaining low-resolution structures of macromolecules and complexes. SAXS experiments measure molecules in solution, without the need for labeling or crystallization. However, radiation damage currently limits the application of SAXS to molecules that can be produced in microgram quantities; for typical proteins, 10-20 μL of solution at 1 mg/mL is required to accumulate adequate signal before irreversible x-ray damage is observed. Here, we show that cryocooled proteins and nucleic acids can withstand doses at least two orders of magnitude larger than room temperature samples. We demonstrate accurate T = 100 K particle envelope reconstructions from sample volumes as small as 15 nL, a factor of 1000 smaller than in current practice. Cryo-SAXS will thus enable structure determination of difficult-to-express proteins and biologically important, highly radiation-sensitive proteins including light-activated switches and metalloenzymes.

Critical droplet theory explains the glass formability of aqueous solutions

When pure water is cooled at ~10(6) K / s, it forms an amorphous solid (glass) instead of the more familiar crystalline phase. The presence of solutes can reduce this required (or "critical") cooling rate by orders of magnitude. Here, we present critical cooling rates for a variety of solutes as a function of concentration and a theoretical framework for understanding these rates. For all solutes tested, the critical cooling rate is an exponential function of concentration. The exponential's characteristic concentration for each solute correlates with the solute's Stokes radius. A modification of critical droplet theory relates the characteristic concentration to the solute radius and the critical nucleation radius of ice in pure water. This simple theory of ice nucleation and glass formability in aqueous solutions has consequences for general glass-forming systems, and in cryobiology, cloud physics, and climate modeling.

Effect of common cryoprotectants on critical warming rates and ice formation in aqueous solutions

Ice formation on warming is of comparable or greater importance to ice formation on cooling in determining survival of cryopreserved samples. Critical warming rates required for ice-free warming of vitrified aqueous solutions of glycerol, dimethyl sulfoxide, ethylene glycol, polyethylene glycol 200 and sucrose have been measured for warming rates of order 10-10⁴ K/s. Critical warming rates are typically one to three orders of magnitude larger than critical cooling rates. Warming rates vary strongly with cooling rates, perhaps due to the presence of small ice fractions in nominally vitrified samples. Critical warming and cooling rate data spanning orders of magnitude in rates provide rigorous tests of ice nucleation and growth models and their assumed input parameters. Current models with current best estimates for input parameters provide a reasonable account of critical warming rates for glycerol solutions at high concentrations/low rates, but overestimate both critical warming and cooling rates by orders of magnitude at lower concentrations and larger rates. In vitrification protocols, minimizing concentrations of potentially damaging cryoprotectants while minimizing ice formation will require ultrafast warming rates, as well as fast cooling rates to minimize the required warming rates.

Crystalline ice as a cryoprotectant: theoretical calculation of cooling speed in capillary tubes

It is generally assumed that vitrification of both cells and the surrounding medium provides the best preservation of ultrastructure of biological material for study by electron microscopy. At the same time it is known that the cell cytoplasm may provide substantial cryoprotection for internal cell structure even when the medium crystallizes. Thus, vitrification of the medium is not essential for good structural preservation. By contrast, a high cooling rate is an essential factor for good cryopreservation because it limits phase separation and movement of cellular components during freezing, thus preserving the native-like state. Here we present calculations of freezing rates that incorporate the effect of medium crystallization, using finite difference methods. We demonstrate that crystallization of the medium in capillary tubes may increase the cooling rate of suspended cells by a factor of 25-300 depending on the distance from the centre. We conclude that crystallization of the medium, for example due to low cryoprotectant content, may actually improve cryopreservation of some samples in a near native state.

Slow cooling and temperature-controlled protein crystallography

In cryocrystallography, rapid sample cooling is generally deemed essential to prevent solvent crystallization and associated sample damage. We show that by carefully and completely removing all external solvent, many protein crystals can be successfully cooled to T = 100 K at only 0.1 K/s without additional penetrating cryoprotectants. Slow cooling provides an alternative when flash cooling fails, and enables diffraction studies of protein structure and function at all temperatures between T = 300 K and T = 100 K.

Slow cooling of protein crystals

Cryoprotectant-free thaumatin crystals have been cooled from 300 to 100 K at a rate of 0.1 K s(-1) - 10(3)-10(4) times slower than in conventional flash cooling - while continuously collecting X-ray diffraction data, so as to follow the evolution of protein lattice and solvent properties during cooling. Diffraction patterns show no evidence of crystalline ice at any temperature. This indicates that the lattice of protein molecules is itself an excellent cryoprotectant, and with sodium potassium tartrate incorporated from the 1.5 M mother liquor ice nucleation rates are at least as low as in a 70% glycerol solution. Crystal quality during slow cooling remains high, with an average mosaicity at 100 K of 0.2 degrees . Most of the mosaicity increase occurs above approximately 200 K, where the solvent is still liquid, and is concurrent with an anisotropic contraction of the unit cell. Near 180 K a crossover to solid-like solvent behavior occurs, and on further cooling there is no additional degradation of crystal order. The variation of B factor with temperature shows clear evidence of a protein dynamical transition near 210 K, and at lower temperatures the slope dB/dT is a factor of 3-6 smaller than has been reported for any other protein. These results establish the feasibility of fully temperature controlled studies of protein structure and dynamics between 300 and 100 K.