Titanium Dioxide Promotes the Growth and Aggregation of Calcium Phosphate and Monosodium Urate Mixed Crystals
The increased utilization of titanium dioxide (TiO) nanoparticles (TNPs) in various industrial and consumer products has raised concerns regarding its harmful effect due to its accumulation within the different systems of the human body. Here, we focused on the influence of TNPs on the growth and aggregation of two crucial crystalline substances, calcium phosphate (CaP) and monosodium urate (MSU), particularly its implications in gout disease. In this study, we adopted microscopic techniques and generated kinetic models to examine the interactions between TNPs, CaP and MSU, and crystallization, under controlled laboratory conditions. Our findings reveal that TNPs not only facilitate the growth of these crystals but also promote their co-aggregations. Crystal dissolution kinetics also exhibit that an increase in TNPs concentration corresponds to a reduction in the dissolution rate of CaP and MSU crystals in presence of the dissoluting agent hydroxycitrate (Hcit). These observations suggest that TNPs can stabilize CaP+MSU mixed crystals, which underscores the significance of TNPs' exposure in the pathogenesis of gout disease.
Crystal growth and electronic properties of LaSbSe
The ZrSiS-type materials have gained intensive attentions. The magnetic version of the ZrSiS-type materials, SbTe ( = Lanthanide), offers great opportunities to explore new quantum states owing to the interplay between magnetism and electronic band topology. Here, we report the growth and characterization of the non-magnetic LaSbSe of this material family. We found the metallic transport, low magnetoresistance and non-compensated charge carriers with relatively low carrier density in LaSbSe. The specific heat measurement has revealed distinct Sommerfeld coefficient and Debye temperature in comparison to LaSbTe. Such addition of a new SbSe selenide compound could provide the alternative material choices in addition to SbTe telluride materials.
Understanding Cysteine Chemistry Using Conventional and Serial X-Ray Protein Crystallography
Proteins that use cysteine residues for catalysis or regulation are widely distributed and intensively studied, with many biomedically important examples. Enzymes where cysteine is a catalytic nucleophile typically generate covalent catalytic intermediates whose structures are important for understanding mechanism and for designing targeted inhibitors. The formation of catalytic intermediates can change enzyme conformational dynamics, sometimes activating protein motions that are important for catalytic turnover. However, these transiently populated intermediate species have been challenging to structurally characterize using traditional crystallographic approaches. This review describes the use and promise of new time-resolved serial crystallographic methods to study cysteine-dependent enzymes, with a focus on the main (M) and papain-like (PL) cysteine proteases of SARS-CoV-2 as well as other examples. We review features of cysteine chemistry that are relevant for the design and execution of time-resolved serial crystallography experiments. In addition, we discuss emerging X-ray techniques such as time-resolved sulfur X-ray spectroscopy that may be able to detect changes in sulfur charge state and covalency during catalysis or regulatory modification. In summary, cysteine-dependent enzymes have features that make them especially attractive targets for new time-resolved serial crystallography approaches, which can reveal both changes to enzyme structure and dynamics during catalysis in crystalline samples.
Crystal Structure Determination and Hirshfeld Analysis of a New Alternariol Packing Polymorph
A new polymorph of the mycotoxin alternariol is reported and characterized by single crystal X-ray diffraction. Structural data, Hirshfeld surface analysis, and 2D fingerprint plots are used to compare differences in the intermolecular interactions of the orthorhombic 2 Form I (previously reported) and the monoclinic 2/ Form II (herein reported). The polymorphs have small differences in planarity-7.55° and 2.19° between the terminal rings for Form I and Form II, respectively-that brings about significant differences in the crystal packing and O-H … H interactions.
Are Heavy Fermion Strange Metals Planckian?
Strange metal behavior refers to a linear temperature dependence of the electrical resistivity that is not due to electron-phonon scattering. It is seen in numerous strongly correlated electron systems, from the heavy fermion compounds, via transition metal oxides and iron pnictides, to magic angle twisted bi-layer graphene, frequently in connection with unconventional or "high temperature" superconductivity. To achieve a unified understanding of these phenomena across the different materials classes is a central open problem in condensed matter physics. Tests whether the linear-in-temperature law might be dictated by Planckian dissipation-scattering with the rate -are receiving considerable attention. Here we assess the situation for strange metal heavy fermion compounds. They allow to probe the regime of extreme correlation strength, with effective mass or Fermi velocity renormalizations in excess of three orders of magnitude. Adopting the same procedure as done in previous studies, i.e., assuming a simple Drude conductivity with the above scattering rate, we find that for these strongly renormalized quasiparticles, scattering is much weaker than Planckian, implying that the linear temperature dependence should be due to other effects. We discuss implications of this finding and point to directions for further work.
Ionic Liquids as Protein Crystallization Additives
Among its attributes, the mythical philosopher's stone is supposedly capable of turning base metals to gold or silver. In an analogous fashion, we are finding that protein crystallization optimization using ionic liquids (ILs) often results in the conversion of base protein precipitate to crystals. Recombinant inorganic pyrophosphatases (8 of the 11 proteins) from pathogenic bacteria as well as several other proteins were tested for optimization by 23 ILs, plus a dHO control, at IL concentrations of 0.1, 0.2, and 0.4 M. The ILs were used as additives, and all proteins were crystallized in the presence of at least one IL. For 9 of the 11 proteins, precipitation conditions were converted to crystals with at least one IL. The ILs could be ranked in order of effectiveness, and it was found that ~83% of the precipitation-derived crystallization conditions could be obtained with a suite of just eight ILs, with the top two ILs accounting for ~50% of the hits. Structural trends were found in the effectiveness of the ILs, with shorter-alkyl-chain ILs being more effective. The two top ILs, accounting for ~50% of the unique crystallization results, were choline dihydrogen phosphate and 1-butyl-3-methylimidazolium tetrafluoroborate. Curiously, however, a butyl group was present on the cation of four of the top eight ILs.
Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals
X-ray crystallography remains a powerful method to gain atomistic insights into the catalytic and regulatory functions of RNA molecules. However, the technique requires the preparation of diffraction-quality crystals. This is often a resource- and time-consuming venture because RNA crystallization is hindered by the conformational heterogeneity of RNA, as well as the limited opportunities for stereospecific intermolecular interactions between RNA molecules. The limited success at crystallization explains in part the smaller number of RNA-only structures in the Protein Data Bank. Several approaches have been developed to aid the formation of well-ordered RNA crystals. The majority of these are construct-engineering techniques that aim to introduce crystal contacts to favor the formation of well-diffracting crystals. A typical example is the insertion of tetraloop-tetraloop receptor pairs into non-essential RNA segments to promote intermolecular association. Other methods of promoting crystallization involve chaperones and crystallization-friendly molecules that increase RNA stability and improve crystal packing. In this review, we discuss the various techniques that have been successfully used to facilitate crystal packing of RNA molecules, recent advances in construct engineering, and directions for future research in this vital aspect of RNA crystallography.
Engineering Crystal Packing in RNA-Protein Complexes II: A Historical Perspective from the Structural Studies of the Spliceosome
Cryo-electron microscopy has greatly advanced our understanding of how the spliceosome cycles through different conformational states to conduct the chemical reactions that remove introns from pre-mRNA transcripts. The Cryo-EM structures were built upon decades of crystallographic studies of various spliceosomal RNA-protein complexes. In this review we give an overview of the crystal structures solved in the Nagai group, utilizing many of the strategies to design crystal packing as described in the accompanying paper.
Nuclear Resonance Vibrational Spectroscopy: A Modern Tool to Pinpoint Site-Specific Cooperative Processes
Nuclear resonant vibrational spectroscopy (NRVS) is a synchrotron radiation (SR)-based nuclear inelastic scattering spectroscopy that measures the phonons (i.e., vibrational modes) associated with the nuclear transition. It has distinct advantages over traditional vibration spectroscopy and has wide applications in physics, chemistry, bioinorganic chemistry, materials sciences, and geology, as well as many other research areas. In this article, we present a scientific and figurative description of this yet modern tool for the potential users in various research fields in the future. In addition to short discussions on its development history, principles, and other theoretical issues, the focus of this article is on the experimental aspects, such as the instruments, the practical measurement issues, the data process, and a few examples of its applications. The article concludes with introduction to non-Fe NRVS and an outlook on the impact from the future upgrade of SR rings.
Refinement of RNA Structures Using Amber Force Fields
Atomic models for nucleic acids derived from X-ray diffraction data at low resolution provide much useful information, but the observed scattering intensities can be fit with models that can differ in structural detail. Tradtional geometric restraints favor models that have bond length and angle terms derived from small molecule crystal structures. Here we explore replacing these restraints with energy gradients derived from force fields, including recently developed integral equation models to account for the effects of water molecules and ions that are not part of the explicit model. We compare conventional and force-field based refinements for 22 RNA crystals, ranging in resolution from 1.1 to 3.6 Å. As expected, it can be important to account for solvent screening of charge-charge interactions, especially in the crowded environment of a nucleic acid crystal. The newly refined models can show improvements in torsion angles and hydrogen-bonding interactions, and can significantly reduce unfavorable atomic clashes, while maintaining or improving agreement with observed scattering intensities.
Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing
RNA plays a central role in all organisms and can fold into complex structures to orchestrate function. Visualization of such structures often requires crystallization, which can be a bottleneck in the structure-determination process. To promote crystallization, an RNA-recognition motif (RRM) of the U1A spliceosomal protein has been co-opted as a crystallization module. Specifically, the U1-snRNA hairpin II (hpII) single-stranded loop recognized by U1A can be transplanted into an RNA target to promote crystal contacts and to attain phase information via molecular replacement or anomalous diffraction methods using selenomethionine. Herein, we produced the F37M/F77M mutant of U1A to augment the phasing capability of this powerful crystallization module. Selenomethionine-substituted U1A(F37M/F77M) retains high affinity for hpII ( of 59.7 ± 11.4 nM). The 2.20 Å resolution crystal structure reveals that the mutated sidechains make new S-π interactions in the hydrophobic core and are useful for single-wavelength anomalous diffraction. Crystals were also attained of U1A(F37M/F77M) in complex with a bacterial preQ-II riboswitch. The F34M/F37M/F77M mutant was introduced similarly into a lab-evolved U1A variant (TBP6.9) that recognizes the internal bulged loop of HIV-1 TAR RNA. We envision that this short RNA sequence can be placed into non-essential duplex regions to promote crystallization and phasing of target RNAs. We show that selenomethionine-substituted TBP6.9(F34M/F37M/F77M) binds a TAR variant wherein the apical loop was replaced with a GNRA tetraloop ( of 69.8 ± 2.9 nM), laying the groundwork for use of TBP6.9(F34M/F37M/F77M) as a crystallization module. These new tools are available to the research community.
Crystallization of ApoA1 and ApoE4 nanolipoprotein particles and initial XFEL-based structural studies
Nanolipoprotein particles (NLPs), also called "nanodiscs", are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via HDL and LDL maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics and develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar in characteristics to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment.
Degradation-Induced Actuation in Oxidation-Responsive Liquid Crystal Elastomers
Stimuli-responsive materials that exhibit a mechanical response to specific biological conditions are of considerable interest for responsive, implantable medical devices. Herein, we report the synthesis, processing and characterization of oxidation-responsive liquid crystal elastomers that demonstrate programmable shape changes in response to reactive oxygen species. Direct ink writing (DIW) is used to fabricate Liquid Crystal Elastomers (LCEs) with programmed molecular orientation and anisotropic mechanical properties. LCE structures were immersed in different media (oxidative, basic and saline) at body temperature to measure in vitro degradation. Oxidation-sensitive hydrophobic thioether linkages transition to hydrophilic sulfoxide and sulfone groups. The introduction of these polar moieties brings about anisotropic swelling of the polymer network in an aqueous environment, inducing complex shape changes. 3D-printed uniaxial strips exhibit 8% contraction along the nematic director and 16% orthogonal expansion in oxidative media, while printed LCEs azimuthally deform into cones 19 times their original thickness. Ultimately, these LCEs degrade completely. In contrast, LCEs subjected to basic and saline solutions showed no apparent response. These oxidation-responsive LCEs with programmable shape changes may enable a wide range of applications in target specific drug delivery systems and other diagnostic and therapeutic tools.
Be Cautious with Crystal Structures of Membrane Proteins or Complexes Prepared in Detergents
Membrane proteins are an important class of macromolecules found in all living organisms and many of them serve as important drug targets. In order to understand their biological and biochemical functions and to exploit them for structure-based drug design, high-resolution and accurate structures of membrane proteins are needed, but are still rarely available, e.g., predominantly from X-ray crystallography, and more recently from single particle cryo-EM - an increasingly powerful tool for membrane protein structure determination. However, while protein-lipid interactions play crucial roles for the structural and functional integrity of membrane proteins, for historical reasons and due to technological limitations, until recently, the primary method for membrane protein crystallization has relied on detergents. Bicelle and lipid cubic phase (LCP) methods have also been used for membrane protein crystallization, but the first step requires detergent extraction of the protein from its native cell membrane. The resulting, crystal structures have been occasionally questioned, but such concerns were generally dismissed as accidents or ignored. However, even a hint of controversy indicates that methodological drawbacks in such structural research may exist. In the absence of caution, structures determined using these methods are often assumed to be correct, which has led to surprising hypotheses for their mechanisms of action. In this communication, several examples of structural studies on membrane proteins or complexes will be discussed: Resistance-Nodulation-Division (RND) family transporters, microbial rhodopsins, Tryptophan-rich Sensory Proteins (TSPO), and Energy-Coupling Factor (ECF) type ABC transporters. These analyses should focus the attention of membrane protein structural biologists on the potential problems in structure determination relying on detergent-based methods. Furthermore, careful examination of membrane proteins in their native cell environments by biochemical and biophysical techniques is warranted, and completely detergent-free systems for membrane protein research are crucially needed.
Probing Trace Elements in Human Tissues with Synchrotron Radiation
For the past several decades, synchrotron radiation has been extensively used to measure the spatial distribution and chemical affinity of elements found in trace concentrations (
Anion Influence on the Packing of 1,3-Bis(4-Ethynyl-3-Iodopyridinium)-Benzene Halogen Bond Receptors
Rigid and directional arylethynyl scaffolds have been widely successful across diverse areas of chemistry. Utilizing this platform, we present three new structures of a dicationic 1,3-bis(4-ethynyl-3-iodopyridinium)-benzene halogen bonding receptor with tetrafluoroborate, nitrate, and hydrogen sulfate. Structural analysis focuses on receptor conformation, anion shape, solvation, and long range packing of these systems. Coupled with our previously reported structures, we conclude that anions can be classified as within this family of halogen bonding receptors. Two kinds of antiparallel dimers are observed for these dicationic receptors. An off-centered species is most frequent, present among geometrically diverse anions, and assorted receptor conformations. In contrast, the centered antiparallel dimers are observed with receptors adopting a bidentate conformation in the solid-state. While anions support the solid-state formation of dimers, the molecular geometry and characteristics (planarity, rigidity, and directionality) of arylethynyl systems increases the likelihood of dimer formation by limiting efficient packing arrangements. The significantly larger cation may have considerable influence on the solid-state packing, as similar cationic arylethynyl systems also display these dimers, suggesting.
A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software
The present article describes how to use the computer program to help assemble complete datasets for the solution of macromolecular structures, starting from partial or complete datasets, derived from data collection from multiple crystals. The program is demonstrated on more than two hundred X-ray diffraction datasets obtained from 50 crystals of a complex formed between the SRF transcription factor, its cognate DNA, and a peptide from the SRF cofactor MRTF-A. This structure is currently in the process of being fully solved. While full details of the structure are not yet available, the repeated application of on data from this structure, as they have become available, has made it possible to produce electron density maps clear enough to visualise the potential location of MRTF sequences.
Selective Area Growth and Structural Characterization of GaN Nanostructures on Si(111) Substrates
Selective area growth (SAG) of GaN nanowires and nanowalls on Si(111) substrates with AlN and GaN buffer layers grown by plasma-assisted molecular beam epitaxy was studied. For N-polar samples filling of SAG features increased with decreasing lattice mismatch between the SAG and buffer. Defects related to Al-Si eutectic formation were observed in all samples, irrespective of lattice mismatch and buffer layer polarity. Eutectic related defects in the Si surface caused voids in N-polar samples, but not in metal-polar samples. Likewise, inversion domains were present in N-polar, but not metal-polar samples. The morphology of Ga-polar GaN SAG on nitride buffered Si(111) was similar to that of homoepitaxial GaN SAG.
Characterization of Sub-Monolayer Contaminants at the Regrowth Interface in GaN Nanowires Grown by Selective-Area Molecular Beam Epitaxy
While GaN nanowires (NWs) offer an attractive architecture for a variety of nanoscale optical, electronic, and mechanical devices, defects such as crystal polarity inversion domains (IDs) can limit device performance. Moreover, the formation of such defects during NW growth is not fully understood. In this study, we use transmission electron microscopy (TEM) and atom probe tomography (APT) to investigate the effects of sub-monolayer contamination at the regrowth interface in GaN NWs grown by selective-area molecular beam epitaxy (MBE). TEM energy dispersive X-ray spectroscopy (EDS) and APT independently identified Al and O contamination localized at the regrowth interface in two of the three growth runs examined. The Al and O concentrations were each estimated to be on the order of 11% of an ideal -plane monolayer in the most severely contaminated case. The amount of contamination correlated with the number of crystal polarity inversion domain defects (IDs) across the growth runs. A growth run in which the pre-regrowth HF vapor etch step was replaced by HCl immersion showed the smallest quantity of O and no measurable Al. In addition, many of the NWs examined from the HCl-treated growth run turned out to be free of IDs. These results suggest that sub-monolayer contamination introduced during processing contributes to defect formation in MBE-grown GaN NWs.
Effect of Type I Antifreeze Proteins on the Freezing and Melting Processes of Cryoprotective Solutions Studied by Site-Directed Spin Labeling Technique
Antifreeze proteins (AFPs) protect organisms living in subzero environments from freezing injury, which render them potential applications for cryopreservation of living cells, organs, and tissues. Cryoprotective agents (CPAs), such as glycerol and propylene glycol, have been used as ingredients to treat cellular tissues and organs to prevent ice crystal's formation at low temperatures. To assess AFP's function in CPA solutions, we have the applied site-directed spin labeling technique to a Type I AFP. A two-step process to prevent bulk freezing of the CPA solutions was observed by the cryo-photo microscopy, i.e., (1) thermodynamic freezing point depression by the CPAs; and (2) inhibition to the growth of seed ice crystals by the AFP. Electron paramagnetic resonance (EPR) experiments were also carried out from room temperature to 97 K, and vice versa. The EPR results indicate that the spin labeled AFP bound to ice surfaces, and inhibit the growths of ice through the bulk freezing processes in the CPA solutions. The ice-surface bound AFP in the frozen matrices could also prevent the formation of large ice crystals during the melting processes of the solutions. Our study illustrates that AFPs can play an active role in CPA solutions for cryopreservation applications.
Isotropic Nature of the Metallic Kagome Ferromagnet FeSn at High Temperatures
Anisotropy and competing exchange interactions have emerged as two central ingredients needed for centrosymmetric materials to exhibit topological spin textures. FeSn is thought to have these ingredients as well, as it has recently been discovered to host room temperature skyrmionic bubbles with an accompanying topological Hall effect. We present small-angle inelastic neutron scattering measurements that unambiguously show that FeSn is an isotropic ferromagnet below to at least 480 K - the lower temperature threshold of our experimental configuration. FeSn is known to have competing magnetic exchange interactions, correlated electron behavior, weak magnetocrystalline anisotropy, and lattice anisotropy; all of these features are thought to play a role in stabilizing skyrmions in centrosymmetric systems. Our results reveal that at elevated temperatures, there is an absence of magnetocrystalline anisotropy and that the system behaves as a typical exchange ferromagnet with a spin stiffness .
