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Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct on-chip analysis by serial crystallography at room temperature. Nine 'non-model' and diverse biomacromolecules, including seven soluble proteins, a membrane protein and an RNA duplex, were crystallized and treated on-chip with a variety of standard techniques including micro-seeding, crystal soaking with ligands and crystal detection by fluorescence. Furthermore, the crystal structures of four proteins and an RNA were determined based on serial data collected on four synchrotron beamlines, demonstrating the general applicability of this multipurpose chip concept., The following funding is acknowledged: Agence Nationale de la Recherche (contract No. ANR-11-LABX-0057_MITOCROSS to Claude Sauter, Bernard Lorber; contract No. ANR-10-LABX-0036_NETRN to Claude Sauter, Bernard Lorber; contract No. ANR-13-BS07-0007-01 to Eric Girard, Sylvain Engilberge); Ministère des Affaires Etrangères (contract No. PROCOPE Hubert Curien to Claude Sauter, Mario Mörl); Deutsche Forschungsgemeinschaft (contract No. Mo 634/10-1 to Mario Mörl, Heike Betat); Université de Strasbourg [grant No. Initiative d'excellence (IDEX) to Claude Sauter, Raphaël de Wijn]; Centre National de la Recherche Scientifique (grant No. MRCT-2012_PTI_UPR9002 to Claude Sauter).

The preparation of well diffracting crystals and their handling before their X-ray analysis are two critical steps of biocrystallographic studies. We describe a versatile microfluidic chip that enables the production of crystals by the efficient method of counter-diffusion. The convection-free environment provided by the microfluidic channels is ideal for crystal growth and useful to diffuse a substrate into the active site of the crystalline enzyme. Here we applied this approach to the CCA-adding enzyme of the psychrophilic bacterium Planococcus halocryophilus in the presented example. After crystallization and substrate diffusion/soaking, the crystal structure of the enzyme:substrate complex was determined at room temperature by serial crystallography and the analysis of multiple crystals directly inside the chip. The whole procedure preserves the genuine diffraction properties of the samples because it requires no crystal handling. ispartof: JOVE-JOURNAL OF VISUALIZED EXPERIMENTS issue:169 ispartof: location:United States status: published

Over the past two decades small-angle X-ray scattering (SAXS) has become a popular method to characterize solutions of biomolecules including ribonucleic acid (RNA). In an integrative structural approach, SAXS is complementary to crystallography, NMR, and electron microscopy and provides information about RNA architecture and dynamics. This chapter highlights the practical advantages of combining size-exclusion chromatography and SAXS at synchrotron facilities. It is illustrated by practical case studies of samples ranging from single hairpins and tRNA to a large IRES. The emphasis is also put on sample preparation which is a critical step of SAXS analysis and on optimized protocols for in vitro RNA synthesis ensuring the production of mg amount of pure and homogeneous molecules.

Virus-like particles (VLPs) derived from non-enveloped viruses result from the self-assembly of capsid proteins (CPs). They generally display similar structural features to viral particles but are non-infectious and their inner cavity and outer surface can potentially be adapted to serve as nanocarriers of great biotechnological interest. While a VLP outer surface is generally amenable to chemical or genetic modifications, encaging a cargo within particles can be more complex and is often limited to small molecules or peptides. Examples where both inner cavity and outer surface have been used to simultaneously encapsulate and expose entire proteins remain scarce. Here we describe the production of spherical VLPs exposing fluorescent proteins at either their outer surface or inner cavity as a result of the self-assembly of a single genetically modified viral structural protein, the CP of grapevine fanleaf virus (GFLV). We found that the N- and C-terminal ends of the GFLV CP allow the genetic fusion of proteins as large as 27 kDa and the plant-based production of nucleic-acid free VLPs. Remarkably, expression of N- or C-terminal CP fusions, resulted in the production of VLPs with recombinant proteins exposed either to the inner cavity or the outer surface, respectively, while coexpression of both fusion proteins led to the formation hybrid VLP, although rather inefficiently. Such properties are rather unique for a single viral structural protein and open new potential avenues for the design of safe and versatile nanocarriers, particularly for the targeted delivery of bioactive molecules., Particules de type viral (comme VLP s) provenant de virus non enveloppés résultent de l'auto-assemblage des protéines de capside ( CP s). Ils présentent généralement des caractéristiques structurales similaires à des particules virales , mais sont noninfectious et leur cavité intérieure et la surface extérieure peuvent potentiellement être adaptées pour servir nanocarriers d' un grand intérêt biotechnologique. Alors qu'une VLP surface extérieure est généralement prête à des modifications chimiques ou génétiques, encagement une cargaison dans des particules peut être plus complexe et est souvent limité à de petites molécules ou des peptides. Des exemples où les deux cavité intérieure et la surface extérieure ont été utilisées pour encapsuler simultanément et exposer les protéines entières restent rares. Ici, nous décrivons la production de particules sphériques VLP exposant les protéines fluorescentes de soit à leur surface extérieure ou cavité interne à la suite de l'auto-assemblage d'une seule protéine de structure virale génétiquement modifié, le CP du virus grapevine fanleaf ( GFLV ). Nous avons trouvé que les extrémités N- et C-terminales de la GFLV CP permettent à la fusion génétique des protéines aussi grandes que 27 kD a et la production à base de plantes de l' acide nucléique libre- VLP s. De manière remarquable, l' expression de N- ou C-terminaux CP fusion a donné lieu à la production de VLP s avec des protéines recombinantes exposées soit à la cavité intérieure ou sur la surface extérieure, respectivement, tandis que la co - expression des deux protéines de fusion conduit à la formation d'un hybride VLP , mais plutôt inefficacement. De telles propriétés sont plutôt unique pour une seule protéine de structure virale et ouvrent de nouvelles avenues potentielles pour la conception de nanocarriers sûrs et polyvalents, en particulier pour l'administration ciblée de molécules bioactives.

The small icosahedral plant RNA nepovirus Grapevine fanleaf virus (GFLV) is specifically transmitted by a nematode and causes major damage to vineyards worldwide. To elucidate the molecular mechanisms underlying the recognition between the surface of its protein capsid and cellular components of its vector, host and viral proteins synthesized upon infection, the wild type GFLV strain F13 and a natural mutant (GFLV-TD) carrying a Gly297Asp mutation were purified, characterized and crystallized. Subsequently, the geometry and volume of their crystals was optimized by establishing phase diagrams. GFLV-TD was twice as soluble as the parent virus in the crystallization solution and its crystals diffracted X-rays to a resolution of 2.7 A. The diffraction limit of GFLV-F13 crystals was extended from 5.5 to 3 A by growth in agarose gel. Preliminary crystallographic analyses indicate that both types of crystals are suitable for structure determination. Keys for the successful production of GFLV crystals include the rigorous quality control of virus preparations, crystal quality improvement using phase diagrams, and crystal lattice reinforcement by growth in agarose gel. These strategies are applicable to the production of well-diffracting crystals of other viruses and macromolecular assemblies.

Orthorhombic crystals of the enzyme aspartyl-tRNA synthetase (AspRS) were prepared in agarose gel, a chemical alternative to microgravity or nano-volume drops. Besides providing a convection-free medium, the network of the polysaccharide improved the stability of the crystalline lattice during soaking with L-aspartol adenylate, a synthetic and non-hydrolysable analog of the catalytic intermediate aspartyl adenylate. When crystals were embedded in the polysaccharide matrix the ligand reached their surfaces more uniformly. Gel-grown crystals exhibited well defined reflections even at high resolution and low mosaicity values, despite their fairly high solvent content and the relatively harsh flash cooling procedure. By contrast, soaked AspRS crystals prepared in solution broke apart within 10–30 s after the ligand was introduced into the mother liquor, and subsequently these fragments became an amorphous precipitate. A general objection to the use of gels in protein crystallization is that chemical interactions may occur between the polysaccharide matrix and proteins or ligands. The example of AspRS shows that this is not a major concern. This method may be generally applicable to crystal soaking with other small molecules or heavy atoms.

The crystallographic quality of protein crystals that were grown in microgravity has been compared to that of crystals that were grown in parallel on earth gravity under otherwise identical conditions. A goal of this comparison was to assess if a more accurate 3D-structure can be derived from crystallographic analysis of the former crystals. Therefore, the properties of crystals prepared with the Advanced Protein Crystallisation Facility (APCF) on earth and in orbit during the last decade were evaluated. A statistical analysis reveals that about half of the crystals produced under microgravity had a superior X-ray diffraction limit with respect of terrestrial controls. Eleven protein structures could be determined at previously unachieved resolutions using crystals obtained in the APCF. Microgravity induced features of the most relevant structures are reported. A second goal of this study was to identify the cause of the crystal quality enhancement useful for structure determination. No correlations between the effect of microgravity and other system-dependent parameters, such as isoelectric point or crystal solvent content, were found except the reduced convection during the crystallisation process. Thus, crystal growth under diffusive regime appears to be the key parameter explaining the beneficial effect of microgravity on crystal quality. The mimicry of these effects on earth in gels or in capillary tubes is discussed and the practical consequences for structural biology highlighted.

Aspartyl-tRNA synthetases were the model proteins in pilot crystallogenesis experiments. They are homodimeric enzymes of Mr~125 kDa that possess as substrates a transfer RNA, ATP and aspartate. They have been isolated from different sources and were crystallized either as free proteins or in association with their ligands. This review discusses their crystallisability with emphasis to crystal quality and structure determination. Crystallization in low diffusivity gelled media or in microgravity environments is highlighted. It has contributed to prepare high-resolution diffracting crystals with better internal order as reflected by their mosaicity. With AspRS from Thermus thermophilus, the better crystalline quality of the space-grown crystals within APCF is correlated with higher quality of the derived electron density maps. Usefulness for structural biology of targeted methods aimed to improve the intrinsic physical quality of protein crystals is highlighted.

One reason for introducing a gel in the crystallization medium of proteins is its ability to reduce convection in solution. This can lead to better nucleation and growth conditions, and to crystals having enhanced diffraction properties. We report here the X-ray characterization at room temperature of high-quality crystals of the intensely sweet thaumatin prepared in a sodium tartrate solution gelified with 0.15% (m/v) agarose. Using a synchrotron radiation, these crystals diffracted to a previously unachieved resolution. A diffraction dataset was collected from four crystals at a resolution of 1.2 A with a Rsym of 3.6% and a completeness of 99%. Refinement was carried out to a final crystallographic R-factor of 12.0%. The quality of the electron density map allowed for the observation of fine structural details in the protein and its solvation shell. Crystallization in gel might be used more generally to improve the quality of macromolecular crystals. Advantages provided by the gelified medium in the frame of structural studies are emphasized. Proteins 2002;48:146–150. © 2002 Wiley-Liss, Inc.

Two active forms of homodimeric aspartyl-tRNA synthetase from Saccharomyces cerevisiae differing in length at their N-terminus crystallize in the same orthorhombic space group (P4 1 2 1 2) with identical cell parameters. Initial studies were hampered by the poor and anisotropic diffraction of the crystals of enzyme extracted from yeast cells. Isotropic diffraction at higher resolution was obtained when crystals were grown from an engineered protein deprived of its 70 N-terminal amino acids. The present work describes the packing contacts in crystals of the shortened protein whose structure was solved at 2.3 A resolution. Each subunit of the enzyme develops two lattice interactions covering a surface of 670 A 2 , about 7-fold smaller than that of the interface between monomers. The smallest lattice interaction, covering 150 A 2 , brings the anticodon binding domain adjacent to the N-terminus of one monomer in contact with a loop from the active-site domain of a neighboring monomer. Modeling of the extension in the solvent channels shows that the 150 A 2 intermolecular contact is perturbed in protein molecules possessing a floppy appendix while their second and larger 520 A 2 contact area is unaffected. Altogether the packing organization explains the poor diffraction properties of the native enzyme crystals and the enhanced diffraction of the crystals of shortened synthetase.

A microgravity protein crystallization experiment is described in which the existence of a supersaturation wave traveling across a diffusion-reaction system is experimentally demonstrated for the first time. The self-organized dynamics of the experimental setup were used to implement a crystallization technique able to search automatically through the crystallization parameter space for optimum nucleation and growth conditions. The crystals obtained by this automatic optimization produced the highest quality X-ray diffraction data ever collected from the model protein used in the experiment.

Quasi-planar wave reflection profile and X-ray topography studies have been done to characterize the mosaicity of solution- and gel-grown crystals of three proteins, turkey egg-white (TEW) lysozyme, thaumatin, and a bacterial aspartyl-tRNA synthetase (AspRS) as well as of one virus, tomato bushy stunt virus (TBSV). These materials are representative of a large range of molecular weight, overall particle shapes, crystals habits, packings, and solvent contents. Measurements of the full-width at half-maximum (FWHM) of reflections show that these different crystals have all a weak mosaicity. Topographs display the same features as those of the well-studied hen egg-white (HEW) lysozyme crystals: misorientation generated at the seed level for TEW lysozyme or thaumatin crystals and/or strains at growth sector boundaries for AspRS crystals. No growth defects are evidenced for TBSV crystals. For the study of crystals diffracting at lower resolution (AspRS and virus), a less absorbant sample holder, which facilitates crystal positioning in the X-ray beam, has been developed. The results obtained for solution- and gel-grown crystals do not show important differences. However, for TEW lysozyme and thaumatin crystals, one notices a larger dispersion of results in the solution case and an overall tendency for improved reproducibility of quality for gel-grown crystals.

Numerous molecules have been described in literature as additives that were indispensable either for nucleation or growth of macromolecular crystals. In some cases, such additives were shown to improve the quality of the X-ray diffraction and to extend diffraction limits. We have investigated the effects of more than fifty compounds, belonging to several chemical families, on the crystallization of four model proteins (hen and turkey egg-white lysozymes, thaumatin, and aspartyl-tRNA synthetase from Thermus thermophilus). In addition, we have studied the crystallization of a ribonucleic acid from yeast, the transfer RNA specific for phenylalanine in the presence of synthetic polyamines. Crystals grown in the presence of the additives were optically evaluated and X-ray diffraction analyses were performed on selective crystals to compare their space group, cell parameters, and diffraction limit with those of controls. Whereas no changes in space group nor cell parameters were observed for the model proteins, significant improvements in diffraction limit were found when the transfer RNA was crystallized with certain synthetic polyamines.

Microfluidic technology has opened new possibilities for the crystallization of biological macromolecules during the past decade. Microfluidic systems offer numerous advantages over conventional crystal growth methods. They enable easy handling of nanovolumes of solutions, extreme miniaturization, and parallelization of crystallization assays, especially for high-throughput screening applications. Our goal was to design a versatile, low cost, and easy-to-use crystallization chip based on counter-diffusion that is compatible with on-chip crystallographic characterization. The ChipX is a microfluidic chip made of cyclic olefin copolymer. It was used to grow crystals of biomolecules and perform complete X-ray diffraction analyses on synchrotron sources. Our results demonstrate that accurate crystallographic data can be collected at room temperature directly from ChipX microfluidic devices for both experimental single-wavelength anomalous dispersion phasing and structure refinement.

The outcome of protein crystallization attempts is often uncertain due to inherent features of the protein or to the crystallization process that are not fully under control of the experimentalist. The aim of this contribution is to propose user-friendly tools that can increase the success rate of a protein crytallization project. Different bioinformatic approaches to predict the crystallization feasibility (before any crystallization attempts are undertaken) are discussed and a novel approach to assess the nucleation process of a given protein is proposed. Practical examples illustrate these two points.

International audience; Medium-sized single crystals with perfect habits and no defect producing intense and well-resolved diffraction patterns are the dream of every protein crystallographer. Crystals of biological macromolecules possessing these characteristics can be prepared within a medium in which mass transport is restricted to diffusion. Chemical gels (like polysiloxane) and physical gels (such as agarose) provide such an environment and are therefore suitable for the crystallisation of biological macromolecules. Instructions for the preparation of each type of gel are given to urge crystal growers to apply diffusive media for enhancing crystallographic quality of their crystals. Examples of quality enhancement achieved with silica and agarose gels are given. Results obtained with other substances forming gel-like media (such as lipidic phases and cellulose derivatives) are presented. Finally, the use of gels in combination with capillary tubes for counter-diffusion experiments is discussed. Methods and techniques implemented with proteins can also be applied to nucleic acids and nucleoprotein assemblies such as viruses.

International audience; Microfluidic devices were designed to perform on micromoles of biological macromolecules and viruses the search and the optimization of crystallization conditions by counter-diffusion, as well as the on-chip analysis of crystals by X-ray diffraction. Chips composed of microchannels were fabricated in poly-dimethylsiloxane (PDMS), poly-methyl-methacrylate (PMMA) and cyclo-olefin-copolymer (COC) by three distinct methods, namely replica casting, laser ablation and hot embossing. The geometry of the channels was chosen to ensure that crystallization occurs in a convection-free environment. The transparency of the materials is compatible with crystal growth monitoring by optical microscopy. The quality of the protein 3D structures derived from on-chip crystal analysis by X-ray diffraction using a synchrotron radiation was used to identify the most appropriate polymers. Altogether the results demonstrate that for a novel biomolecule, all steps from the initial search of crystallization conditions to X-ray diffraction data collection for 3D structure determination can be performed in a single chip.

International audience; This review presents the goals and principles of microfluidic technologies applied to the crystallization of biological macromolecules. A comparison of the devices that are available commercially or described in the literature summarizes the current state-of-the-art in microfluidics. A novel chip based on the counter-diffusion of solute molecules playing the role of crystallization agents is described. Inside the microfluidic channels composing the chip mass transport essentially occurs by diffusion. The chip is made of a rigid polymer that is impermeable to gases and compatible with crystal examination and monitoring in polarized light. The selected material is also transparent to X-rays, and three-dimensional protein structures can be determined from crystals contained inside this device using X-ray diffraction data collected on a synchrotron source. The outstanding quality of the electron-density maps demonstrates that on-chip crystal analysis is feasible. The replacement of conventional crystallization setups by inexpensive microfluidic chips for screening best crystallization agents and automated crystal diffraction analysis is discussed.

The preparation of well diffracting crystals is a crucial step of any crystallographic project. This chapter defines the nature of biomacromolecular crystals, sketches the theoretical background of crystallogenesis and describes the practical approaches currently available for crystal growth in structural biology. Chemical, biochemical and physical parameters that affect crystallization are discussed. Emphasis is given to the importance of purity and of structural homogeneity. The classical crystallization methodologies are described, such as the favoured vapour-phase equilibration, batch and dialysis techniques, and the less widely used but powerful counter-diffusion methods, and the new trends for their miniaturization and automation are outlined. Advanced methodologies are also covered such as growth methods in convection-free media (i.e. in microfluidic devices or in gels). Furthermore, the behaviour of macromolecules during the prenucleation, nucleation and growth steps is discussed from the physics viewpoint, and ways to enhance crystal perfection are given. In a practical perspective, strategies to efficiently prepare crystals for structural biology and to overcome crystallization bottlenecks are proposed. Keywords: batch methods of crystallization; crystal growth; crystal quality; crystal seeding; crystallization; crystallizing agents; dialysis methods of crystallization; gel acupuncture method; crystallization in gels; interface diffusion method of crystallization; microgravity; nucleation; prenucleation; vapour-diffusion methods of crystallization

Although macromolecular purity is thought to be essential for the growth of flawless protein crystals, only a few studies have investigated how contaminants alter the crystallization process and crystal quality. Likewise, the outcome of a crystallization process may vary with the crystallization method. Here, it is reported how these two variables affect the crystallogenesis of aspartyl-tRNA synthetase from the eubacterium Thermus thermophilus. This homodimeric enzyme (M r = 130 000) possesses a multi-domain architecture and crystallizes either in a monoclinic or an orthorhombic habit. Minute amounts of protein impurities alter to a different extent the growth of each crystal form. The best synthetase crystals are only obtained when the crystallizing solution is either enclosed in capillaries or immobilized in agarose gel. In these two environments convection is reduced with regard to that existing in an unconstrained solution.

Gellified media prevent convection and crystal sedimentation, and provide an attractive growth environment for optimising biological crystals. Agarose gels are particularly easy to use and they are compatible with most of the common crystallization methods. They also offer new possibilities like counter-diffusion techniques. This paper gives a brief overview of their general properties and presents an application of a counter-diffusion setup combining agarose gel and capillaries to the crystallization of proteins and protein / nucleic acid complexes.

Very high quality crystals of tetragonal hen egg-white lysozyme were grown in the Advanced Protein Crystallization Facility (APCF) on board the Space Shuttle using a modified free-interface diffusion (FID) reactor designed ad hoc to have a longer diffusion path. This design allows the performance of true counter-diffusion experiments. Crystals were obtained under the classical chemical conditions defined 50 y ago with NaCl as a crystallizing agent and acetate pH 4.5 as a buffer. Counter-diffusion crystallization allows a "physical" instead of chemical optimization of growth conditions: indeed, this method screens for the best supersaturation conditions in a single trial and yields crystals of very high quality. A complete diffraction data set was collected at atomic resolution from one of these crystals using synchrotron radiation at the DESY-EMBL beamlines. The overall R(merge) on intensities in the resolution range 31-0.94 A was 5.2% and the data were 98.9% complete. Refinement was carried out with the programs CNS and SHELX97 to a final crystallographic R factor of 12.26% for 72 390 reflections. A mean standard uncertainty in the atomic positions of 0.024 A was estimated from inversion of blocked least-squares matrices. 22 side chains show alternate conformations and the loop 59-75 adopts in the same crystal packing two conformations that were observed for either triclinic or tetragonal lysozyme in previous high-resolution studies. In addition to 255 water molecules, the crystallizing agent (one hexacoordinated sodium ion and five chloride anions) participates in the ordered lysozyme hydration shell.

International audience; Aspartyl-tRNA synthetase (AspRS) extracted from yeast is heterogeneous owing to proteolysis of its positively charged N-terminus; its crystals are of poor quality. To overcome this drawback, a rational strategy was developed to grow crystals of sufficient quality for structure determination. The strategy is based on improvement of the protein homogeneity and optimization of crystallization, taking advantage of predictions from crystal-growth theories. An active mutant lacking the first 70 residues was produced and initial crystallization conditions searched. The shape and habit of initial crystals were improved by establishing a phase diagram of protein versus crystallizing-agent concentrations. Growth of large well faceted crystals takes place at low supersaturations near the isochronic supersolubility curve. Further refinement led to reproducible growth of two crystalline forms of bipyramidal (I) or prismatic (II) habit. Both diffract X-­rays better than crystals previously obtained with native AspRS. Complete data sets were collected at 3 Å resolution for form I (space group P41212) and form II (space group P3221) and molecular-replacement solutions were found in both space groups.