Enantioselective Autocatalysis. V. The Spontaneous Resolution of Tri-o-Thymotide

We have attempted to appraise experimentally the allegation that minute chemical and physical differences due to the parity violating energy difference (PVED) between enantiomers are, after suitable autocatalytic amplification, ultimately responsible for the homochirality of contemporary biomolecules. The autocatalytic amplification technique employed involved the spontaneous resolution under racemizing conditions (SRURC) of a conglomerate during crystallization, and the system studied was the known crystallization of P(+)- or M(–)-tri-o-thymotide (TOT) as its optically active inclusion compound (clathrate) with benzene. Our premise was that if a PVED effect were operative, there should be a strong and consistent bias favoring the crystallization of one enantiomer of the TOT-benzene clathrate. Repetitive preparations of the clathrate, however, yielded crystalline products showing random optical activity. These results thus afford no evidence whatsoever for stereoselective bias due to a PVED, and are in accord with earlier statistical studies demonstrating random SRURC in other conglomerate crystallizations, again indicating the inefficacy of PVEDs to promote a preferred chirality in such systems.     

Crystallization behavior and thermal properties of melt-crystallized poly[(R)-3-hydroxybutyric acid-co-6-hydroxyhexanoic acid] films.

Melt-crystallized films of poly[(R)-3-hydroxybutyric acid-co-10mol% 6-hydroxyhexanoic acid] (P[(R)-3HB-co-6HH]) were prepared by isothermal crystallization at various temperatures for 3 days, and subsequently stored at room temperature after the films formed well-developed and volume-filled spherulites. The lamellar morphologies and properties of melt-crystallized films were characterized by means of wide-angle X-ray diffraction, small-angle X-ray scattering, differential scanning calorimetry, transmission electron microscopy, and atomic force microscopy. The melting endotherm of P[(R)-3HB-co-6HH] films was composed of a broad peak starting around room temperature and of a sharper peak starting above the isothermal crystallization temperature. The stacking of flat-on lamellae with lamellar periodicity of 8-10 nm was detected on the surface of P[(R)-3HB-co6HH] films after the primary crystallization at 110 degrees C. On storage at room temperature above the Tg (-5 degrees C) of copolyester, thin crystals of 1-4 nm thickness appeared on the surface of P[(R)-3HB-co-6HH] films crystallized at 110 degrees C. These results suggest that long sequences of (R)-3HB units in a random copolyester form relatively thick P[(R)-3HB] crystalline lamellae during the primary crystallization process at a given crystallization temperature, while shorter sequences of (R)-3HB units, which are incapable of crystallizing at a given crystallization temperature, form relatively thin crystalline lamellae during the subsequent crystallization process at room temperature.     

The use of self-interaction chromatography in stable formulation and crystallization of proteins

This paper reviews the basic principles of the recently developed self-interaction chromatography (SIC) technique with regard to protein solution stability and protein crystallization. It gives experimental protocols for both normal-scale and micro-scale SIC experiments and reviews recent developments and current applications of this novel technique in the biopharmaceutical area. This paper aims to be a benchmark in the further proliferation of this highly effective and fast technology for the rational design of stable aqueous formulations of therapeutic proteins and the determination of solution conditions favoring protein crystallization.     

The Contribution of Polystyrene Nanospheres towards the Crystallization of Proteins

Background

Protein crystallization is a slow process of trial and error and limits the amount of solved protein structures. Search of a universal heterogeneous nucleant is an effort to facilitate crystallizability of proteins.

Methodology

The effect of polystyrene nanospheres on protein crystallization were tested with three commercial proteins: lysozyme, xylanase, xylose isomerase, and with five research target proteins: hydrophobins HFBI and HFBII, laccase, sarcosine dimethylglycine N-methyltransferase (SDMT), and anti-testosterone Fab fragment 5F2. The use of nanospheres both in screening and as an additive for known crystallization conditions was studied. In screening, the addition of an aqueous solution of nanosphere to the crystallization drop had a significant positive effect on crystallization success in comparison to the control screen. As an additive in hydrophobin crystallization, the nanospheres altered the crystal packing, most likely due to the amphiphilic nature of hydrophobins. In the case of laccase, nanospheres could be used as an alternative for streak-seeding, which insofar had remained the only technique to produce high-diffracting crystals. With methyltransferase SDMT the nanospheres, used also as an additive, produced fewer, larger crystals in less time. Nanospheres, combined with the streak-seeding method, produced single 5F2 Fab crystals in shorter equilibration times.

Conclusions

All in all, the use of nanospheres in protein crystallization proved to be beneficial, both when screening new crystallization conditions to promote nucleation and when used as an additive to produce better quality crystals, faster. The polystyrene nanospheres are easy to use, commercially available and close to being inert, as even with amphiphilic proteins only the crystal packing is altered and the nanospheres do not interfere with the structure and function of the protein.     

A synergistic approach to protein crystallization: Combination of a fixed‐arm carrier with surface entropy reduction

Protein crystallographers are often confronted with recalcitrant proteins not readily crystallizable, or which crystallize in problematic forms. A variety of techniques have been used to surmount such obstacles: crystallization using carrier proteins or antibody complexes, chemical modification, surface entropy reduction, proteolytic digestion, and additive screening. Here we present a synergistic approach for successful crystallization of proteins that do not form diffraction quality crystals using conventional methods. This approach combines favorable aspects of carrier‐driven crystallization with surface entropy reduction. We have generated a series of maltose binding protein (MBP) fusion constructs containing different surface mutations designed to reduce surface entropy and encourage crystal lattice formation. The MBP advantageously increases protein expression and solubility, and provides a streamlined purification protocol. Using this technique, we have successfully solved the structures of three unrelated proteins that were previously unattainable. This crystallization technique represents a valuable rescue strategy for protein structure solution when conventional methods fail.     

A new generation of sodium chloride porogen for tissue engineering

Porogen leaching is a widely used and simple technique for the creation of porous scaffolds in tissue engineering. Sodium chloride (NaCl) is the most commonly used porogen, but the current grinding and sieving methods generate salt particles with huge size variations and cannot generate porogens in the submicron size range. We have developed a facile method based on the principles of crystallization to precisely control salt crystal sizes down to a few microns within a narrow size distribution. The resulting NaCl crystal size could be controlled through the solution concentration, crystallization temperature, and crystallization time. A reduction in solution temperature, longer crystallization times, and an increase in salt concentration resulted in an increase in NaCl crystal sizes due to the lowered solubility of the salt solution. The nucleation and crystallization technique provides superior control over the resulting NaCl size distribution (13.78 ± 1.18 μm), whereas the traditional grinding and sieving methods produced NaCl porogens 13.89 ± 12.49 μm in size. The resulting NaCl porogens were used to fabricate scaffolds with increased interconnectivity, porous microchanneled scaffolds, and multiphasic vascular grafts. This new generation of salt porogen provides great freedom in designing versatile scaffolds for various tissue-engineering applications.     

Rational design and synthesis of phospholipids for the two-dimensional crystallization of DNA gyrase, a key element in chromosome organization.

Properties required of lipids for two-dimensional crystallization of proteins on lipid layers at the air/water interface are discussed in terms of molecular structure. These properties are related to essential features of the overall system such as (i) the fluidity and stability of the lipid film, (ii) the affinity of the protein to be crystallized for the lipids and (iii) the accessibility of the protein to the ligand in the lipid layer as well as (iv) technical constraints of the crystallization technique. The resulting ideas were tested through the rational design and synthesis of original phospholipid structures linked to novobiocin subsequently used in the production of two-dimensional crystals of DNA gyrase (B subunit), a prokaryotic type II DNA topoisomerase.     

Precipitants and additives for membrane crystallization of lysozyme

Membrane crystallization is a newly developed crystallization technique that has proven to be superior in producing good crystal forms under operating conditions that are not appropriate to perform the crystallization process by other traditional techniques. In this work, static membrane crystallization was carried out on lysozyme, with hollow-fiber microporous hydrophobic membranes. Numerous precipitant and additive types and concentrations were employed in the crystallization processes in order to select the most appropriate precipitant and additive types and to find their corresponding concentration levels that can yield the best crystal forms. The crystallization processes were analyzed in two ways: firstly, by evaluation of the transmembrane fluxes obtained by using different precipitants and additives; secondly, by utilization of the images and results obtained from the micrography and IR spectra in comparisons and evaluations of the crystals formed under all kinds of conditions. Moreover, the size distributions of the crystals yielded under several typical crystallization conditions were analyzed, and turbidity and induction time periods obtained during typical crystallization experiments were also measured. Amongst the numerous precipitants and additives tested, the most appropriate precipitant type and additive were chosen and their concentrations were optimized. Good lysozyme crystals were obtained using a certain precipitant and additive. The obtained results from this work further support the advantages of utilizing the membrane crystallization technique for macromolecule crystallizations.     

Supercritical fluid extractions in biotechnology.

Over the past decade, supercritical fluid (SCF) extraction has been shown to deserve consideration as an alternative to liquid-liquid extraction or distillation. Most current commercial applications of SCF extraction involve biologically produced materials; the technique may be particularly relevant to extraction of biological compounds in cases where there is a requirement for low-temperature processing, high mass-transfer rates and negligible carry over of solvent into the final product. New advances, in which extraction is combined with reaction or crystallization steps, may further increase the attractiveness of SCFs in the bioprocessing industries.     

Conditions of two-dimensional crystallization of cholera toxin B-subunit on lipid films containing ganglioside GM1

A systematic study of the lipid-layer two-dimensional crystallization technique has been carried out on the system composed of cholera toxin B-subunit and monosialoganglioside GM1, by electron microscopy, image analysis, and lipid film surface pressure measurements. Concentrations of protein and lipid components required for two-dimensional crystallization of toxin-GM1 complexes have been determined. Crystals were only obtained in the presence of mixed lipid films, composed of GM1 and of unsaturated lipids, such as dioleoylphosphatidylcholine or dioleoylphosphatidylethanolamine, in agreement with a previous report [D. S. Ludwig et al., (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 8585–8588]. Crystals were obtained with cholera toxin B-subunit concentration as low as 5 μg/ml, as well as in the presence of protein contaminants. They were obtained over a wide range of concentrations of both GM1 and unsaturated lipids. The minimal lipid amount needed for crystallization corresponded to a lipid monolayer at, or near, the maximal spreading pressure (50 mN/m). The use of an excess of lipid resulted in a stabilization of lipid monolayers and in a higher reproducibility or crystallization experiments.     

Metal ion-mediated reduction in surface entropy improves diffraction quality of crystals of the IRAK-4 death domain.

Interleukin-1 receptor-associated kinase-4 (IRAK-4) is an essential component of innate immunity in mice and humans. IRAK-4 is a bipartite protein composed of a death domain (DD) that mediates molecular recognition, and a catalytic kinase domain. Structure determination of the proteolytically stable, soluble IRAK-4 DD was hampered by poor diffraction quality. Addition of manganese (II) chloride to the crystallization solution produced significant improvements in diffraction, and the structure has been determined to 1.7-Angstrom resolution. Examination of the IRAK-4 DD crystal structure reveals a single manganese ion coordinated to surface residues lysine-21 and aspartate-24. Coordination of the manganese ion resulted in a reduction in the surface entropy at this region of the molecule, by generating a contact-forming and conformationally homogenous surface patch. Prior studies have shown that surface entropy reduction by mutation of surface residues with large flexible side chains (i.e., Lys and Glu) to smaller side chains results in the production of diffraction-quality crystals. The intrinsic high surface entropy of Lys residues can also be decreased by reductive methylation. Our results suggest that screening of manganese ions as a crystallization additive may also facilitate ordered crystallization by reduction of surface entropy. Given the quick and inexpensive nature of screening, this technique is likely to be amenable to high-throughput methods such as those employed by Protein Structure Initiatives.     

温度影响蛋白质结晶的研究现状

温度控制作为调控蛋白质结晶过程的手段,在结晶实验中被广泛采用。热历史效应作为蛋白质结晶实验中新的影响因素,已被越来越多的科学家所重视。控制温度可以改变蛋白质的溶解度,进一步改变溶液的过饱和度,从而影响结晶过程。我们简要总结了温度对蛋白质结晶的影响及应用温度技术控制蛋白质晶体生长的各种技术,为蛋白质结晶工作提供理论和实验依据。     

(NZ)CH...O Contacts assist crystallization of a ParB-like nuclease

Background

The major bottleneck for determination of 3 D structures of proteins using X-rays is the production of diffraction quality crystals. Often proteins are subjected to chemical modification to improve the chances of crystallization

Results

Here, we report the successful crystallization of a nuclease employing a reductive methylation protocol. The key to crystallization was the successful introduction of 44 new cohesive (NZ) CH...O contacts (3.2 – 3.7 Å) by the addition of 2 methyl groups to the side chain amine nitrogen (NZ) of 9 lysine residues of the nuclease. The new contacts dramatically altered the crystallization properties of the protein, resulting in crystals that diffracted to 1.2 Å resolution. Analytical ultracentrifugation analysis and thermodynamics results revealed a more compact protein structure with better solvent exclusion of buried Trp residues in the folded state of the methylated protein, assisting crystallization.

Conclusion

In this study, introduction of novel cohesive (NZ)CH...O contacts by reductive methylation resulted in the crystallization of a protein that had previously resisted crystallization in spite of extensive purification and crystallization space screening. Introduction of (NZ)CH...O contacts could provide a solution to crystallization problems for a broad range of protein targets.     

Systematic Improvement of Protein Crystals by Determining the Supersolubility Curves of Phase Diagrams

A systematic approach for improving protein crystals by growing them in the metastable zone using the vapor diffusion technique is described. This is a simple technique for optimization of crystallization conditions. Screening around known conditions is performed to establish a working phase diagram for the crystallization of the protein. Dilutions of the crystallization drops across the supersolubility curve into the metastable zone are then carried out as follows: the coverslips holding the hanging drops are transferred, after being incubated for some time at conditions normally giving many small crystals, over reservoirs at concentrations which normally yield clear drops. Fewer, much larger crystals are obtained when the incubation times are optimized, compared with conventional crystallization at similar conditions. This systematic approach has led to the structure determination of the light-harvesting protein C-phycocyanin to the highest-ever resolution of 1.45 Å.     

New techniques for membrane protein crystallization tested on photosystem II core complex of Pisum sativum

The crystallization of a given protein is a hard task being even more complicated when the protein shows a hydrophobic behavior. In the case of photosynthetic proteins, the difficulty of the experiments increased due to the high light sensitivity. Aqueous solutions of photosystem II core complex (OEC PSII) of Pisum sativum were screened for crystallization conditions using standard crystallization methods. Crystal improvement was achieved by counter-diffusion technique in single capillaries of 0.2 mm inner diameter with a three-layer configuration. The use of this advanced crystallization technique—for the first time applied to the crystallization of membrane proteins—improves the reproducibility of the experiments allowing the initial crystal characterization, and facilitates the manipulation under light protection.     

Efficient optimization of crystallization conditions by manipulation of drop volume ratio and temperature

An efficient optimization method for the crystallization of biological macromolecules has been developed and tested. This builds on a successful high-throughput technique for the determination of initial crystallization conditions. The optimization method takes an initial condition identified through screening and then varies the concentration of the macromolecule, precipitant, and the growth temperature in a systematic manner. The amount of sample and number of steps is minimized and no biochemical reformulation is required. In the current application a robotic liquid handling system enables high-throughput use, but the technique can easily be adapted in a nonautomated setting. This method has been applied successfully for the rapid optimization of crystallization conditions in nine representative cases.     

Characterization of lipid matrices for membrane protein crystallization by high-throughput small angle X-ray scattering

The lipidic cubic phase (LCP) has repeatedly proven to serve as a successful membrane-mimetic matrix for a variety of difficult-to-crystallize membrane proteins. While monoolein has been the predominant lipid of choice, there is a growing need for the characterization and use of other LCP host lipids, allowing exploration of a range of structural parameters such as bilayer thickness and curvature for optimal insertion, stability and crystallogenesis of membrane proteins. Here, we describe the development of a high-throughput (HT) pipeline to employ small angle X-ray scattering (SAXS) - the most direct technique to identify lipid mesophases and measure their structural parameters - to interrogate rapidly a large number of lipid samples under a variety of conditions, similar to those encountered during crystallization. Leveraging the identical setup format for LCP crystallization trials, this method allows the quickly assessment of lipid matrices for their utility in membrane protein crystallization, and could inform the tailoring of lipid and precipitant conditions to overcome specific crystallization challenges. As proof of concept, we present HT LCP-SAXS analysis of lipid samples made of monoolein with and without cholesterol, and of monovaccenin, equilibrated with solutions used for crystallization trials and LCP fluorescence recovery after photobleaching (FRAP) experiments.     

Application of hybrid LRR technique to protein crystallization

LRR family proteins play important roles in a variety of physiological processes. To facilitate their production and crystallization, we have invented a novel method termed "Hybrid LRR Technique". Using this technique, the first crystal structures of three TLR family proteins could be determined. In this review, design principles and application of the technique to protein crystallization will be summarized. For crystallization of TLRs, hagfish VLR receptors were chosen as the fusion partners and the TLR and the VLR fragments were fused at the conserved LxxLxLxxN motif to minimize local structural incompatibility. TLR-VLR hybridization did not disturb structures and functions of the target TLR proteins. The Hybrid LRR Technique is a general technique that can be applied to structural studies of other LRR proteins. It may also have broader application in biochemical and medical application of LRR proteins by modifying them without compromising their structural integrity.     

Crystals of luciferase from Vibrio harveyi. A preliminary characterization

Bacterial luciferase from Vibrio harveyi, the 77,000-dalton light-emitting enzyme of the marine bacterium, has been crystallized into a two million cubic Angstrom cell with P212121 symmetry. The cell constants are a = 59.6 +/- 0.4 A, b = 112 +/- 0.7 A, and c = 302 +/- 2 A. The reflections corresponding to the 302-A cell edge can be resolved by suitable collimation of the incident beam, without resorting to focusing mirrors. The crystals diffract to better than 3-A resolution and are large enough (0.7 mm) for data collection. The crystallization conditions are presented and general crystallization characteristics are discussed.     

Nobel lecture. The photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis.

In our lectures we first describe the history and methods of membrane protein crystallization, before we show how the structure of the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis was solved. Then the structure of this membrane protein complex is correlated with its function as a light-driven electron pump across the photosynthetic membrane. Finally we draw conclusions on the structure of the photosystem II reaction centre from plants and discuss the aspects of membrane protein structure. Sections 1 (crystallization), 4 (conclusions on the structure of photosystem II reaction centre and evolutionary aspects) and 5 (aspects of membrane protein structure) were presented and written by H.M., Sections 2 (determination of the structure) and 3 (structure and function) by J.D. We have arranged the paper in this way in order to facilitate continuous reading.