A crystal of a typical EF-hand protein grown under microgravity diffracts X-rays beyond 0.9 Å resolution

We report on our recent observation that crystals of a typical EF-hand protein (parvalbumin or Pa; Ca-loaded component from pike muscle with isoelectric point 4.10) grown under microgravity conditions diffract X-rays to a resolution better than 0.9 Å. The crystals were grown in the US space shuttle and characterized at 100 K, using an X-ray synchrotron beam. An effective atomic resolution has been achieved and substates in the conformation of the protein are observed. Large crystals up to 3 mm were also obtained.     

Crystal growth of phosphopantetheine adenylyltransferase,carboxypeptidase t,and thymidine phosphorylase on the international space station by the capillary counter-diffusion method

Crystals of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis, thymidine phosphorylase from Escherichia coli, carboxypeptidase T from Thermoactinomyces vulgaris and its mutant forms, and crystals of complexes of these proteins with functional ligands and inhibitors were grown by the capillary counter-diffusion method in the Japanese Experimental Module Kibo on the International Space Station. The high-resolution X-ray diffraction data sets suitable for the determination of high-resolution three-dimensional structures of these proteins were collected from the grown crystals on the SPring-8 synchrotron radiation facility. The conditions of crystal growth for the proteins and the data-collection statistics are reported. The crystals grown in microgravity diffracted to a higher resolution than crystals of the same proteins grown on Earth.     

Lower dimer impurity incorporation may result in higher perfection of HEWL crystals grown in microgravity: A case study

Crystals of tetragonal hen egg white lysozyme (HEWL) grown on a series of space missions and their terrestrial counterparts were analyzed by gel electrophoresis and X-ray diffraction. The crystals were produced by vapor-diffusion and dialysis methods. The microgravity and terrestrial grown HEWL crystals were found to have effective partitioning coefficients (K_eff) for an oxidatively formed covalent dimer impurity (MW 28 K) of 2 and 9, respectively, i.e. the latter contain 4.5 times more dimers. The microgravity grown crystals allowed the collection of 24% more useful reflections and improved the resolution from 1.6 to 1.35 Å. Other improvements were also noted including lower isotropic B-factors of 16.9, versus 23.8 Å² for their terrestrial counterparts. High-resolution laser interferometry was applied quantitatively to evaluate the influence of dimer impurity on growth kinetics. It is shown that the growth of the (1 0 1) face from solution into which 1% dimers were introduced decelerates with increasing solution flow rate and the growth stops at a flow rate of about 0.2 mm/s. This effect occurs faster than in ultrapure solutions. The covalently bound dimers essentially increase the amplitudes of the striation-inducing growth rate fluctuations. The effect is ascribed to the enhanced transport of growth inhibiting HEWL dimer to the interface. Theoretical analysis shows that a stagnant solution around a growing crystal is strongly depleted with respect to impurity by about 60% for the measured growth parameters as compared to the solution bulk. Thus, a crystal in microgravity grows from essentially purer solution than the ones in the presence of convection flows. Therefore, it traps less stress inducing impurity and should be more perfect. For crystal/impurity systems where K_eff is small enough microgravity should have an opposite effect.     

Protein crystal growth on the Russian segment of the International Space Station

Experiments on protein crystallization on the Russian segment of the International Space Station were started in 2005. These experiments were performed in the Modul’-1 protein crystallization apparatus specially designed for crystal growth by the free-interface-diffusion method. This paper describes experiments on the crystallization of lysozyme, carboxypeptidase B, and recombinant human insulin on Earth and in microgravity using the Modul’-1 protein crystallization apparatus during the ISS-11-ISS-14 space flights. Crystals of all proteins grown in microgravity have larger sizes than those grown on Earth. Space-grown crystals of lysozyme and insulin characterized by X-ray diffraction were shown to diffract to higher resolution than the Earth-grown crystals. The three-dimensional structures of Zn-insulin crystals grown both on Earth and in microgravity were established. The conformation of the Zn-insulin hexamer in the crystalline state is described.     

Synthesis and characterization of large single crystals of NpPd3 by flux method

Synthesis of the active [Ni–Fe]-hydrogenase in prokaryotes requires a series of ancillary maturation factors. Among them, the HypF maturation factor is a multidomain 82 kDa protein, whose N-terminal domain displays sequence and structural similarities to acylphosphatases. Acylphosphatases are small enzymes that are able to catalyze carboxyl-phosphate bond hydrolysis in acylphosphates, as well as in nucleoside di- and tri-phosphates and in arylphosphates. Here, we present a crystallographic comparison between microgravity and earth-grown crystals of the HypF N-terminal domain. Both crystals were of excellent quality, thereby allowing us to collect very high resolution datasets. A detailed analysis of data collection and refinement statistics, together with an analysis of the diffraction pattern showed that microgravity would appear to further improve the internal order of crystals.     

Crystallization of multiple forms of bovine seminal ribonuclease in the liganded and unliganded state

Bovine seminal ribonuclease (BS-RNase) is an intriguing homodimeric enzyme which exists as two conformational isomers, characterized by distinct catalytic and biological properties, referred to as M×M and M=M. Reduction of inter-chain disulfide bridges produces a stable monomeric derivative (M) which is still active. This paper reports the screening and optimization of crystallization conditions for growing single diffraction-quality crystals for the various BS-RNase forms. The crystallization trials were performed using both the vapor diffusion and microbatch methods. The M×M dimer was crystallized in the free form from polyethylene glycol (PEG) 4000 at pH 8.5 and as a complex with the substrate analog uridylyl(2′– 5′)guanosine (UpG) from an unbuffered ammonium sulfate (AS) solution. These two crystal types diffract X-rays to 2.5 and 1.9 Å resolution, respectively. Two different crystal types were obtained both for the M=M dimer and for the monomeric derivative. (M=M)a crystals, grown from PEG 4000 (8% w/v) at pH 5.6, diffract X-rays to 4.0 Å. At higher PEG concentration (15% w/v) a different crystal type was obtained, (M=M)b, which showed a better diffraction limit (2.5 Å). For the monomer, type (M)a and (M)b crystals, diffracting X-rays to 2.5 Å resolution, were obtained from AS at pH 6.5 and from PEG 4000 at pH 8.5, respectively. A comparison with previously crystallized forms of the dimer M×M and its complexes with uridylyl(2′–5′)adenosine and 2′-deoxycytidylyl(3′–5′)-2′-deoxyadenosine is also presented. The three-dimensional structure analysis of (M×M)·UpG and (M=M)b is in progress.     

Determination of the phase diagram for the crystallization of L‐asparaginase II by a turbidity technique ‐ part II. ‐MPD and crystallography studies‐

The phase diagram for the crystallization of L‐asparaginase II including the metastable zone width (MZW), in the presence of PEG₆₀₀₀ and ethanol, respectively, has been studied by an online turbidity technique out of the crystallization in solution (see part I of this work 1 ). Here this paper describes a further investigation on constructing a phase diagram including MZW for the crystallization of L‐asparaginase II with a different precipitant agent of 2‐methyl‐2, 4‐pentandiol (MPD). Along with the phase diagram, the single crystal X‐ray data were successfully collected at 100K from a crystal formed in the presence of 26% (v/v) MPD. The crystals indicate an orthorhombic form and belong to the space group of P2₁2₁2₁ with the unit cell parameters a = 93.9, b = 125.77, c = 151.75Å. The crystal diffracted up to a resolution of 2.88 Å.     

移动加热器法生长碲锌镉晶体的组分输运与界面形貌研究

移动加热器法(THM)生长碲锌镉晶体时,界面稳定性对晶体生长的质量有很大影响。本文基于多物理场有限元仿真软件Comsol建立了THM生长碲锌镉晶体的数值模拟模型,讨论了Te边界层与组分过冷区之间的关系,对不同生长阶段的物理场、Te边界层与组分过冷区进行仿真研究,最后讨论了微重力对物理场分布的影响,并对比了微重力与正常重力下的生长界面形貌。模拟结果表明,Te边界层与组分过冷区的分布趋势是一致的,在不同生长阶段,流场中次生涡旋的位置会发生移动,从而导致生长界面的形貌随着生长的进行发生变化,同时微重力条件下形成的生长界面形貌最有利于单晶生长。因此,在晶体生长的中前期,对次生涡旋位置的控制和对组分过冷的削弱,是THM生长高质量晶体的有效方案。     

Crystalline quality of lysozyme crystals grown in agarose and silica gels studied by X-ray diffraction techniques

The crystalline quality of hen egg white lysozyme (HEWL) crystals grown in agarose gels and in silica gels has been characterized by measuring resolution and mosaic spread. These crystals have been compared to solution grown ones. A quasi-plane-wave X-ray topography study has also been done on some crystals. The study concerns triclinic, monoclinic, orthorhombic and tetragonal forms of HEWL. One observes that the resolution is not really changed by gelling the growth medium, even for rather high gel contents (agarose 0.5% wt/wt). On the contrary, mosaicity, characterized through reflection profile recordings allows to differentiate crystals grown by different techniques: agarose gel grown crystals are, on average, better than solution grown ones but the best crystals are obtained in silica gel. X-ray topography confirms this result.     

Implementation of Temperature-Controlled Method of Protein Crystallization in Microgravity

An experimental scientific equipment for implementing temperature-controlled protein crystallization in capillaries under microgravity has been developed, fabricated, and tested. This crystallization method, providing on-line separate control of crystal growth both in the stage of nucleation of crystals and during their further growth, requires small amounts of protein solution. The equipment has been tested on board of Foton-M4 spacecraft (growth of lysozyme protein crystals of high structural quality in microgravity) using a cyclogram developed in ground-based experiments. The results obtained have demonstrated efficiency and importance of the developed equipment and method for growing biomacromolecular crystals of high-structural quality.

     

Effect of various precipitants on the nucleation rate of tetragonal hen egg-white lysozyme crystals in an AC external electric field

It was observed that the effect of an external electric field on the nucleation rate of tetragonal hen egg-white lysozyme crystals varied depending on the precipitant used (NaCl, NiCl₂ or YbCl₃) and that the electric double layer (EDL) played an important role in generating an external electric field of the necessary strength to control the nucleation rate. This phenomenon depended on the ionic strength of the precipitant used; that is, a precipitant of greater ionic strength resulted in a thinner EDL and increased the effect of the external electric field as the driving force for nucleation. The dependence of the nucleation rate on the precipitant was attributed to the magnitudes of the external electric fields generated in EDLs of varying thickness which were formed in the presence of different precipitants.     

Three-dimensional structure of Erwinia carotovora L-asparaginase

Three-dimensional structure of Erwinia carotovora L-asparaginase, which has antitumor activity and is used for the treatment of acute lymphoblastic leukemia, was solved at 3 Å resolution and refined to R _cryst = 20% and R _free = 28%. Crystals of recombinant Erwinia carotovora L-asparaginase were grown by the hanging-drop vapor-diffusion method from protein solutions in a HEPES buffer (pH 6.5) and PEG MME 5000 solutions in a cacodylate buffer (pH 6.5) as the precipitant. Three-dimensional X-ray diffraction data were collected up to 3 Å resolution from one crystal at room temperature. The structure was solved by the molecular replacement method using the coordinates of Erwinia chrysanthemi L-asparaginase as the starting model. The coordinates refined with the use of the CNS program package were deposited in the Protein Data Bank (PDB code 1ZCF).     

Batch crystallization of soluble proteins: effect of precipitant, temperature and additive

Although techniques used for protein crystallization have been progressing greatly, successful crystallization is still largely empirical and operatordependent. The crystallization of biological macromolecules is a pretty complicated process involving numerous parameters, thus the detailed understanding of the effect of crystallization conditions on macromolecule crystallization is advantageous. In this study, we have investigated the effect of precipitant, temperature, and additive on the crystallization of lysozyme and chymotrypsinogen A. As the precipitant, sodium chloride is more effective to the crystallization of lysozyme, and ammonium sulfate is more suitable to the crystallization of chymotrypsinogen A. Temperature is found to have no effect on the crystal habit of chymotrypsinogen A, while lysozyme crystallization displays highly sensitive temperature dependence, gradually varied temperature can result in better crystal habit and quality of lysozyme crystals. Furthermore, non-electrolytic additives dimethyl sulfoxide (DMSO) and glycerol are found to not only to increase the protein's solubility, but also decrease the critical supersaturation S_c for explosive nucleation of highly supersaturated protein solution. It is suggested that these additives can affect the interactions between protein molecules, thermodynamic equilibrium, surface energy of the crystal, and nucleation process of protein crystallization.     

PCAM: a multi-user facility-based protein crystallization apparatus for microgravity

A facility-based protein crystallization apparatus for microgravity (PCAM) has been constructed and flown on a series of Space Shuttle Missions. The hardware development was undertaken largely because of the many important examples of quality improvements gained from crystal growth in the diffusion-limited environment in space. The concept was based on the adaptation for microgravity of a commonly available crystallization tray to increase sample density, to facilitate co-investigator participation and to improve flight logistics and handling. A co-investigator group representing scientists from industry, academia, and government laboratories has been established. Microgravity applications of the hardware have produced improvements in a number of structure-based crystallographic studies and include examples of enabling research. Additionally, the facility has been used to support fundamental research in protein crystal growth which has delineated factors contributing to the effect of microgravity on the growth and quality of protein crystals.     

Synthesis and characterization of potassium magnesium sulphate hexahydrate crystals

Potassium magnesium sulphate hexahydrate (picromerite) was synthesized and single crystals were obtained from saturated aqueous solution by slow evaporation method at room temperature. The crystals were bright, colourless and transparent having well defined external faces. The grown crystals were characterized through Fourier Transform Infrared (FTIR) spectral studies and thermal analysis. The FTIR data were used to assign the characteristic vibrational frequencies of the various chemical bonds in the compound. The compound crystallizes in monoclinic lattice with the space group P2₁/c. The thermogravimetry (TG) indicates the removal of only two water molecules around 100 °C. A suitable decomposition pattern was formulated based on the percentage weight losses observed in TG of the compound. The results of differential thermal analysis (DTA) conform to the results of TGA. Differential scanning calorimetry (DSC) analysis carried out at high temperature suggests that the occurrence of two phase transitions in the crystal between 140 and 180 °C. When the crystal was cooled below the room temperature up to –170 °C, no thermal anomaly was observed. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Factorially designed crystallization trials of the full-length P0 myelin membrane glycoprotein. I. Precipitation diagram

P0 glycoprotein is the abundant membrane protein of myelin of the peripheral nervous system. We report now the statistical design of the crystallization experiments; based on our belief that important information regarding supersaturation of protein or its solubility nature, as well as metastable state, nucleation or precipitation, are hidden in the trials in which no crystals grow. It is possible to work out this information when the whole set of experiments is designed in such a way as to allow statistical analyses. We selected seven factors, which we believe to be important for crystallization: protein concentration, pH of buffer, nature of precipitant, concentration of precipitant, nature of detergent, additives and temperature. The experimental matrix and detailed work sheet to make 148 solutions having random but balanced combination of these levels were calculated using the program DESIGN. A visual evaluation of crystallization drops was performed using light microscopy. We were able to plot the precipitation boundary diagram. Based on this diagram we have eliminated factors (and levels) that were driving the protein into precipitation. It is known that the precipitation boundary is related to the solubility curves for protein crystals, in the neighborhood of which nucleation and further crystallization is most likely to occur. These conditions are currently being refined to identify important factors (or its levels) that can be crucial in obtaining large and well diffracting crystals. Full-length P0 protein has never been crystallized for structural determination.     

Three-dimensional structure of phosphopantetheine adenylyltransferase from <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> in the apo form and in complexes with coenzyme A and dephosphocoenzyme A

Crystals of phosphopantetheine adenylyltransferase (PPAT) from Mycobacterium tuberculosis in the apo form and in complexes with coenzyme A (PPAT/CoA) and dephosphocoenzyme A (PPAT/dPCoA) were grown in microgravity by the capillary counter-diffusion method. The structures of PPAT Mt in the apo form and in complexes with ligands were solved based on the X-ray diffraction data collected from the grown crystals. The crystal structures were refined at 1.76, 1.59, and 1.59 Å resolution to Rf factors of 0.175, 0.159, and 0.157 and Rfree of 0.224, 0.208, and 0.206 for PPAT, PPAT/CoA, and PPAT/dPCoA, respectively. The atomic coordinates of the structures were deposited in the Protein Data Bank (PDB ID: 3RFF, 3RHS, and 3RBA). In these structures, the ligand-binding sites were determined, the environment of these sites was characterized, and the conformational changes accompanying the ligand binding were analyzed.     

Dewetted growth of CdTe in microgravity (STS‐95)

Two CdTe crystals had been grown in microgravity during the STS‐95 mission. The growth configuration was dedicated to obtain dewetting of the crystals and to achieve high quality material. Background for the performed experiments was based on the theory of the dewetting and previous experience. The after flight characterization of the crystals has demonstrated existance of the dewetting areas of the crystals and their improved quality regarding the earth grown reference sample. The samples had been characterized by EDAX, Synchrotron X‐ray topography, Photoluminescence and Optical and IR microscopy. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Influence of La3+ ions on growth and NLO properties of KDP single crystals

Single crystals of pure and Lanthanum added KDP crystals were grown from aqueous solution. The influence of La³⁺ ions in KDP crystals is studied. Isolated centers are formed by La³⁺ ions in KDP structure along (100) plane. La³⁺ ions incorporated into superficial crystal growth layer and slightly affect the growth process as they generate weak lattice stresses. The creation of these weak lattice stress is confirmed by Vickers's micro hardness test. The HRXRD analysis showed reduced structural defects in the La added KDP in the (100) plane than pure KDP. The incorporation of La in the crystal was confirmed by EDAX analysis. The Kurtz's powder SHG efficiency was found to be 1.5 times that of pure KDP. The UV‐Vis transmission spectra of La added KDP showed excellent transmittance from 1100 nm to 340 nm and did not show any change in lower cutoff wavelength with respect to pure KDP. Laser damage threshold value has been determined using Q‐switched Nd:YAG laser operating at 1064 nm and with 65 ns pulses in single shot mode. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Crystal structure of a mutant of archaeal ribosomal protein L1 from Methanococcus jannaschii

The crystal structure of a mutant of archaeal ribosomal protein L1 from Methanococcus jannaschii with the deletion of a nonconserved positively charged cluster consisting of eight C-terminal amino acid residues is determined by the molecular replacement method at 1.75 Å resolution. This mutant is shown to form more stable and ordered crystals belonging to a space group other than that of the wild-type protein crystals. The positively charged C-terminal region has only a slight effect on the interaction between protein L1 and RNA molecules. Hence, this mutant can be used to prepare protein-RNA complexes and obtain their crystals.