X-ray Crystallography Research Articles

P1-xTa8+xN13(x = 0.1-0.15): A Phosphorus Tantalum Nitride Featuring Mixed-Valent Tantalum and P/Ta Disorder Visualized by Scanning Transmission Electron Microscopy.

We report on the synthesis, crystal, and electronic structure, as well as the magnetic, and electric properties of the phosphorus-containing tantalum nitride P1-xTa8+xN13 (x = 0.1-0.15). A high-pressure high-temperature reaction (8 GPa, 1400 °C) of Ta3N5 and P3N5 with NH4F as a mineralizing agent yields the compound in the form of black, rod-shaped crystals. Single-crystal X-ray structure elucidation (space group C2/m (no. 12), a = 16.202(3), b = 2.9155(4), c = 11.089(2)Å, β = 126.698(7)°, Z = 2) shows a network of face- and edge-sharing Ta-centered polyhedra that contains small vacant channels and PN6 octahedra strands. Atomic resolution transmission electron microscopy reveals an unusual P/Ta disorder. Mixed-valent tantalum atoms exhibit interatomic distances similar to those in metallic tantalum, however, the electrical resistivity is quite high in the order of 10‑1Ωcm. The density of states and the electron localization function indicate localized electrons in both covalent and ionic bonds between P/Ta and N atoms, combined with less localized electrons that do not contribute to interatomic bonds.

PepBinding: A Workflow for Predicting Peptide Binding Structures by Combining Peptide Docking and Peptide Gaussian Accelerated Molecular Dynamics Simulations.

Predicting protein-peptide interactions is crucial for understanding peptide binding processes and designing peptide drugs. However, traditional computational modeling approaches face challenges in accurately predicting peptide-protein binding structures due to the slow dynamics and high flexibility of the peptides. Here, we introduce a new workflow termed "PepBinding" for predicting peptide binding structures, which combines peptide docking, all-atom enhanced sampling simulations using the Peptide Gaussian accelerated Molecular Dynamics (Pep-GaMD) method, and structural clustering. PepBinding has been demonstrated on seven distinct model peptides. In peptide docking using HPEPDOCK, the peptide backbone root-mean-square deviations (RMSDs) of their bound conformations relative to X-ray structures ranged from 3.8 to 16.0 Å, corresponding to the medium to inaccurate quality models according to the Critical Assessment of PRediction of Interactions (CAPRI) criteria. The Pep-GaMD simulations performed for only 200 ns significantly improved the docking models, resulting in five medium and two acceptable quality models. Therefore, PepBinding is an efficient workflow for predicting peptide binding structures and is publicly available at https://github.com/MiaoLab20/PepBinding.

A New Structural Motif in Aggregation of Methylalumoxanes: Non-hydrolytic Route by the Alkylation of Dicarboxylic Acids.

Alumoxanes are typically produced via controlled hydrolysis of short-chain alkyl aluminium compounds which leads to oligomeric species that are usually difficult to obtain in crystalline form. Simultaneously, various alternative non-hydrolytic approaches to alumoxanes have also been used. In this work, we report on anew methylalumoxane scaffold derived from the alkylation of aseries of dicarboxylic acids: itaconic acid (HO2CCH2C(=CH2)CO2H), succinic acid (HO2CCH2CH2CO2H) and homophthalic acid (HO2CCH2C6H4CO2H). The reactions of AlMe3 with a selected dicarboxylic acid in the molar ratio 4:1 conducted at elevated temperature occur with double methylation of each carboxylic group and provide to the formation of a new methylalumoxane aggregate, Me10Al6O4, flanked by methylaluminium diolate units. We also aimed to obtain dialkylaluminium derivatives of dicarboxylic acids by the controlled reaction of the appropriate acid with AlMe3 in the 1:2 stoichiometry. While the synthesis of organoaluminium derivatives of flexible aliphatic dicarboxylic acids (itaconic and succinic acids) is challenging due to their insolubility, the related homophtalate compound readily forms a molecular tetranuclear cluster, [(homophtalate)(AlMe2)2]2. The molecular and crystal structures of the resulting compounds were determined via NMR spectroscopic analysis and single crystal X-ray diffraction crystallography.

Tetrel bond affects the self-assembly of acetylcholine and its analogues and is an ancillary interaction in protein binding.

The -N+(CH3)3 residue is present in acetylcholine (ACh) and in many of its analogues which are used as selective ACh agonist or antagonists for human therapy. The X-ray structures of four ACh derivatives show the presence of short and linear contacts between the C atoms of -N+(CH3)3 groups and lone pair possessing atoms. These contacts can be rationalized as tetrel bonds (TtBs) thanks to their geometric features. Interrogation of the Protein Data Bank suggests that similar -N+‒C···nucleophile contacts affect the details of the binding of ACh and its derivatives to proteins. Quantum theory of atoms in molecules, noncovalent interaction plot, and natural bond orbital analyses consistently confirm that the -N+‒C···nucleophile contacts observed in small molecule crystals and in substrate/protein complexes are attractive in nature and can be rationalized as TtBs. TtBs involving methyl groups of the -N+(CH3)3 moiety can be proposed as a new item in the palette of interactions allowing the compounds containing this pharmacophoric unit to bind to their target protein and/or to express their biological/pharmacological properties.

Layer-Ordered Organooxotin Clusters for Extreme-Ultraviolet Photolithography.

Extreme-ultraviolet (EUV) photolithography, which enables the high-throughput production of well-defined patterns with critical dimensions on the scale of several nanometers, is essential for the fabrication of a highly integrated semiconductor. The full exploitation of EUV lithographic techniques necessitates the development of photoresist (PR) materials with both high EUV sensitivity and a long shelf-life. However, despite notable advances, the available library of EUV PR materials remains limited. Here we report EUV PRs capable of forming preorganized layers consisting of ladder-structured tetranuclear stannoxanes. Single-crystal X-ray structure analyses reveal a close interlayer distance of 8.5 Å through interdigitation of the pseudoaxial butyl chains. The developed EUV PR materials exhibit high solubility in organic solvents commonly used in semiconductor processing, enabling the preparation of PR solutions with superior wettability and uniform film-forming ability on Si wafer substrates. These PR solutions also demonstrate notable resistance to hydrolytic decomposition for as long as 1 month, indicating a long shelf-life. Our PR materials enabled negative-tone patterning processes that involved a solubility decrease upon irradiation. The presence of chromophoric ligands makes our PR materials compatible with conventional UV photolithography, through photochemical reactions involving carbonyl units. In addition, e-beam and EUV lithography could produce fine line patterns of our PRs, with critical dimensions of 20 and 15 nm, respectively. Our research showcases the potential of layer-ordered organooxotin clusters for EUV PR applications.

Rapid aminations of functionalized aryl fluorosulfatesin water.

Aryl fluorosulfates of varying complexities have been used in amination reactions in water using a new Pd oxidative addition complex (OAC-1) developed specifically to match the needs of the fine chemicals industry, not only in terms of functional group tolerance, but also reflecting time considerations associated with these important C-N couplings. Also especially noteworthy is that they replace both PFAS-related triflates and nonaflates, which are today out of favor due to recent government regulations. The new complex based on the BippyPhos ligand is used at low loadings and under aqueous micellar conditions. Moreover, it is easily prepared and stable to long term storage. DFT calculations on the OAC precatalyst compare well with the X-ray structure of the crystals withπ-complexation to the aromatic system of the ligand and also confirm the NMR data showing a mixture of conformers in solution that differ from the X-ray structure in rotation of the phenyl andt-butyl ligand substituents. An extensive variety of coupling partners, including pharmaceutically relevant APIs, readily participate under mild and environmentally responsible reaction conditions.

AQuaRef: Machine learning accelerated quantum refinement of protein structures.

Cryo-EM and X-ray crystallography provide crucial experimental data for obtaining atomic-detail models of biomacromolecules. Refining these models relies on library-based stereochemical restraints, which, in addition to being limited to known chemical entities, do not include meaningful noncovalent interactions relying solely on nonbonded repulsions. Quantum mechanical (QM) calculations could alleviate these issues but are too expensive for large molecules. We present a novel AI-enabled Quantum Refinement (AQuaRef) based on AIMNet2 neural network potential mimicking QM at substantially lower computational costs. By refining 41 cryo-EM and 30 X-ray structures, we show that this approach yields atomic models with superior geometric quality compared to standard techniques, while maintaining an equal or better fit to experimental data.

Probing Short-Range Interactions in Isostructural Hydrate and Perhydrate of Dabrafenib by Magic-Angle Spinning Solid-State NMR.

Dabrafenib (DBF), an anticancer drug, exhibits isostructural properties in its hydrate (DBF⊃H2O) and perhydrate (DBF⊃H2O2) forms, as revealed by single-crystal X-ray diffraction. Despite the H2O and H2O2 solvent molecules occupying identical locations, the two polymorphs have different thermal behaviors. In general, determination of stoichiometry of H2O in the perhydrate crystals is difficult due to the presence of both H2O and H2O2 in the same crystal voids. This study utilizes magic-angle spinning (MAS) solid-state NMR (SSNMR) combined with gauge-included projector augmented wave calculations to characterize the influence of solvent molecules on the local environment in pseudopolymorphs. SSNMR experiments were employed to assign 1H, 13C, and 15N peaks and identify spectral differences in the isostructural pseudopolymorphs. Proton spectroscopy at fast MAS was used to identify and quantify H2O2/H2O in DBF⊃H2O2 (mixed hydrate/perhydrate). 1H-1H dipolar-coupling-based experiments were recruited to confirm the 3D molecular packing of solvent molecules in DBF⊃H2O and DBF⊃H2O2. Homonuclear (1H-1H) and heteronuclear (1H-14N) distance measurements, in conjunction with diffraction structures and optimized hydrogen atom positions by density functional theory, helped decipher local interactions of H2O2 with DBF and their geometry in DBF⊃H2O2. This integrated X-ray structure, quantum chemical calculations, and NMR study of pseudopolymorphs offer a practical approach to scrutinizing crystallized solvent interactions in the crystal lattice even without high-resolution crystal structures or artificial sample enrichment.

Resolving DJ-1 Glyoxalase Catalysis Using Mix-and-Inject Serial Crystallography at a Synchrotron.

DJ-1 (PARK7) is an intensively studied protein whose cytoprotective activities are dysregulated in multiple diseases. DJ-1 has been reported as having two distinct enzymatic activities in defense against reactive carbonyl species that are difficult to distinguish in conventional biochemical experiments. Here, we establish the mechanism of DJ-1 using a synchrotron-compatible version of mix-and-inject-serial crystallography (MISC), which was previously performed only at XFELs, to directly observe DJ-1 catalysis. We designed and used new diffusive mixers to collect time-resolved Laue diffraction data of DJ-1 catalysis at a pink beam synchrotron beamline. Analysis of structurally similar methylglyoxal-derived intermediates formed through the DJ-1 catalytic cycle shows that the enzyme catalyzes nearly two turnovers in the crystal and defines key aspects of its glyoxalase mechanism. In addition, DJ-1 shows allosteric communication between a distal site at the dimer interface and the active site that changes during catalysis. Our results rule out the widely cited deglycase mechanism for DJ-1 action and provide an explanation for how DJ-1 produces L-lactate with high chiral purity.

Structural Characterization of Disulfide-Linked p53-Derived Peptide Dimers.

Disulfide bonds provide a convenient method for chemoselective alteration of peptide and protein structure and function. We previously reported that mild oxidation of a p53-derived bisthiol peptide (CTFANLWRLLAQNC) under dilute non-denaturing conditions led to unexpected disulfide-linked dimers as the exclusive product. The dimers were antiparallel, significantly α-helical, resistant to protease degradation, and easily reduced back to the original bisthiol peptide. Here we examine the intrinsic factors influencing peptide dimerization using a combination of amino acid substitution, circular dichroism (CD) spectroscopy, and X-ray crystallography. CD analysis of peptide variants suggests critical roles for Leu6 and Leu10 in the formation of stable disulfide-linked dimers. The 1.0 Å resolution crystal structure of the peptide dimer supports these data, revealing a leucine-rich LxxLL dimer interface with canonical knobs-into-holes packing. Two levels of higher-order oligomerization are also observed in the crystal: an antiparallel "dimer of dimers" mediated by Phe3 and Trp7 residues in the asymmetric unit and a tetramer of dimers mediated by Trp7 and Leu10. In CD spectra of Trp-containing peptide variants, minima at 227 nm provide evidence for the dimer of dimers in dilute aqueous solution. Importantly, and in contrast to the original dimer model, the canonical leucine-rich core and robust dimerization of most peptide variants suggests a tunable molecular architecture to target various proteins and evaluate how folding and oligomerization impact various properties, such as cell permeability.

Exploring the complexity of amyloid-beta fibrils: structural polymorphisms and molecular interactions.

The aggregation of amyloid-beta (Aβ) peptides into cross-β structures forms a variety of distinct fibril conformations, potentially correlating with variations in neurodegenerative disease progression. Recent advances in techniques such as X-ray crystallography, solid-state NMR, and cryo-electron microscopy have enabled the development of high-resolution molecular structures of these polymorphic amyloid fibrils, which are either grown in vitro or isolated from human and transgenic mouse brain tissues. This article reviews our current understanding of the structural polymorphisms in amyloid fibrils formed by Aβ40 and Aβ42, as well as disease-associated mutants of Aβ peptides. The aim is to enhance our understanding of various molecular interactions, including hydrophobic and ionic interactions, within and among cross-β structures.

Accurate Structure Prediction for Cyclic Peptides Containing Proline Residues with High-Temperature Molecular Dynamics.

Cyclic peptides (CPs) are emerging as promising drug candidates. Numerous natural CPs and their analogs are effective therapeutics against various diseases. Notably, many of them contain peptidyl cis-prolyl bonds. Due to the high rotational barrier of peptide bonds, conventional molecular dynamics simulations struggle to effectively sample the cis/trans-isomerization of peptide bonds. Previous studies have highlighted the high accuracy of the residue-specific force field (RSFF) and the high sampling efficiency of high-temperature molecular dynamics (high-T MD). Herein, we propose a protocol that combines high-T MD with RSFF2C and a recently developed reweighting method based on probability densities for accurate structure prediction of proline-containing CPs. Our method successfully predicted 19 out of 23 CPs with the backbone rmsd < 1.0 Å compared to X-ray structures. Furthermore, we performed high-T MD and density reweighting on the sunflower trypsin inhibitor (SFTI-1)/trypsin complex to demonstrate its applicability in studying CP-complexes containing cis-prolines. Our results show that the conformation of SFTI-1 in aqueous solution is consistent with its bound conformation, potentially facilitating its binding.

N,C,N-Pincers in Platinum Bimetallic Complexes: Influence of the Pincer and Bridging Ligands on the Metal-Metal Bond and the Photophysical Properties.

Precursors PtCl{κ3-N,C,N-[py-C6HMe2-py]} (1), PtCl{κ3-N,C,N-[py-O-C6H3-O-py]} (2), Pt(OH){κ3-N,C,N-[py-C6HMe2-py]} (3), and Pt(OH){κ3-N,C,N-[py-O-C6H3-O-py]} (4) were used to prepare d8-platinum bimetallic complexes. Precursors 1 and 2 react with AgBF4 and 7-azaindole (Haz) to give [Pt{κ3-N,C,N-[py-C6HMe2-py]}{κ1-N-[Haz]}]BF4 (5) and [Pt{κ3-N,C,N-[py-O-C6H3-O-py]}{κ1-N-[Haz]}]BF4 (6) and 3 and 4 with indolo[2,3-b]indole (H2ii) to generate Pt{κ1-N-[Hii]}{κ3-N,C,N-[py-C6HMe2-py]} (7) and Pt{κ1-N-[Hii]}{κ3-N,C,N-[py-O-C6H3-O-py]} (8). Subsequent addition of 3 and 4 to 5-7 affords bimetallic derivatives [{Pt[κ3-N,C,N-(py-C6HMe2-py)]}2{μ-N,N-[az]}]BF4 (9), [{Pt[κ3-N,C,N-(py-O-C6H3-O-py)]}2{μ-N,N-[az]}]BF4 (10), and {Pt[κ3-N,C,N-(py-C6HMe2-py)]}2{μ-N,N-[ii]} (11). X-ray structures of 9-11 reveal separations between the metals in sequence 9 (3.0515(4) Å) < 10 (3.2689(9) Å) < 11 (3.2949(2) Å). DFT calculations support σ overlap of the dz2 orbitals of platinum atoms, for 9 and 10. Accordingly, their absorption spectra show a MMLCT transition. Complex 9 is a red emitter. The excited state has 3MMLCT characteristics and a Pt-Pt separation of 2.763 Å. Complex 11 is a dual emitter in the red and NIR regions, in solid. Both excited states have a 3LC/LMCT characteristic and platinum-platinum separations of 3.290 and 3.202 Å. Intermediate 5 is a green emitter that achieves quantum yields close to unity, when diluted in PMMA and 1,2-dichloroethane at low concentrations.

Action and cooperation in alginate degradation by three enzymes from the human gut bacterium Bacteroides eggerthii DSM 20697

Alginate is a polysaccharide consumed by humans in edible seaweed and different foods where it is applied as a texturizing hydrocolloid or in encapsulations of drugs and probiotics. While gut bacteria are found to utilize and ferment alginate to health beneficial short chain fatty acids, knowledge on details of the molecular reactions is sparse. Alginates are composed of mannuronic acid (M) and its C-5 epimer guluronic acid (G). An alginate related polysaccharide utilization locus (PUL) has been identified in the gut bacterium Bacteroides eggerthii DSM 20697. The PUL encodes two polysaccharide lyases (PLs) from the PL6 (BePL6) and PL17 (BePL17) families as well as a KdgF-like metalloprotein (BeKdgF) known to catalyze ring-opening of 4,5-unsaturated monouronates yielding 4-deoxy-l-erythro-5-hexoseulose uronate (DEH). B. eggerthii DSM 20697 does not grow on alginate, but readily proliferates with a lag phase of a few hours in the presence of an endo-acting alginate lyase A1-I from the marine bacterium Sphingomonas sp. A1. The B. eggerthii lyases are both exo-acting and while BePL6 is strictly G-block specific, BePL17 prefers M-blocks. BeKdgF retained 10−27% activity in the presence of 0.1−1 mM EDTA. X-ray crystallography was used to investigate the three-dimensional structure of BeKdgF, based on which a catalytic mechanism was proposed to involve Asp102, acting as acid/base having pKa of 5.9 as determined by NMR pH titration. BePL6 and BePL17 cooperate in alginate degradation with BeKdgF linearizing produced 4,5-unsaturated monouronates. Their efficiency of alginate degradation was much enhanced by addition of the A1-I alginate lyase.

Capturing Mercury-197m/g for Auger Electron Therapy and Cancer Theranostic with Sulfur-Containing Cyclen-Based Macrocycles.

The interest in mercury radioisotopes, 197mHg (t1/2 = 23.8 h) and 197gHg (t1/2 = 64.14 h), has recently been reignited by the dual diagnostic and therapeutic nature of their nuclear decays. These isotopes emit γ-rays suitable for single photon emission computed tomography imaging and Auger electrons which can be exploited for treating small and metastatic tumors. However, the clinical utilization of 197m/gHg radionuclides is obstructed by the lack of chelators capable of securely binding them to tumor-seeking vectors. This work aims to address this challenge by investigating a series of chemically tailored macrocyclic platforms with sulfur-containing side arms, namely, 1,4,7,10-tetrakis[2-(methylsulfanyl)ethyl]-1,4,7,10-tetraazacyclododecane (DO4S), 1,4,7-tris[2-(methylsulfanyl)ethyl]-1,4,7,10-tetraazacyclododecane (DO3S), and 1,7-bis[2-(methylsulfanyl)ethyl]-1,4,7,10-tetraazacyclododecane-4,10-diacetic acid (DO2A2S). 1,4,7,10-Tetrazacyclododecane-1,4,7,10-tetracetic acid (DOTA), the widest explored chelator in nuclear medicine, and the nonfunctionalized backbone 1,4,7,10-tetrazacyclododecane (cyclen) were considered as well to shed light on the role of the sulfanyl arms in the metal coordination. To this purpose, a comprehensive experimental and theoretical study encompassing aqueous coordination chemistry investigations through potentiometry, nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography, and density functional theory (DFT) calculations, as well as concentration- and temperature-dependent [197m/gHg]Hg2+ radiolabeling and in vitro stability assays in human serum was conducted. The obtained results reveal that the investigated chelators rapidly complex Hg2+ in aqueous media, forming extremely thermodynamically stable 1:1 metal-to-ligand complexes with superior stabilities compared to those of DOTA or cyclen. These complexes exhibited 6- to 8-fold coordination environments, with donors statically bound to the metal center, as evidenced by the presence of 1H-199Hg spin-spin coupling via NMR. A similar octacoordinated environment was also found for DOTA in both solution and solid state, but in this case, multiple slowly exchanging conformers were detected at ambient temperature. The sulfur-rich ligands quantitatively incorporate cyclotron-produced [197m/gHg]Hg2+ under relatively mild reaction conditions (pH = 7 and T = 50 °C), with the resulting radioactive complexes exhibiting decent stability in human serum (up to 75% after 24 h). By developing viable chelators and understanding the impact of structural modifications, our research addresses the scarcity of suitable chelating agents for 197m/gHg, offering promise for its future in vivo application as a theranostic Auger-emitter radiometal.

Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination

Guanine-rich nucleic acids can form intramolecularly folded four-stranded structures known as G-quadruplexes (G4s). Traditionally, G4 research has focused on short, highly modified DNA or RNA sequences that form well-defined homogeneous compact structures. However, the existence of longer sequences with multiple G4 repeats, from proto-oncogene promoters to telomeres, suggests the potential for more complex higher-order structures with multiple G4 units that might offer selective drug-targeting sites for therapeutic development. These larger structures present significant challenges for structural characterization by traditional high-resolution methods like multi-dimensional NMR and X-ray crystallography due to their molecular complexity. To address this current challenge, we have developed an integrated structural biology (ISB) platform, combining experimental and computational methods to determine self-consistent molecular models of higher-order G4s (xG4s). Here we outline our ISB method using two recent examples from our lab, an extended c-Myc promoter and long human telomere G4 repeats, that highlights the utility and generality of our approach to characterizing biologically relevant xG4s.

Synthesis of triphyrin(2.1.1)-triphyrin(2.1.1) homo dimers and bis-Re(I) triphyrin dimer complex.

First examples of covalently linked triphyrin(2.1.1)-triphyrin(2.1.1) homo dimers connected via flexible alkoxy linkers at β-pyrrole positions were synthesized in 28-30% yields by reacting 2-bromo triphyrin(2.1.1) with three different alkane diols such as 1,2-ethanediol, 1,4-butanediol and 1,6-hexanediol in toluene under Pd2(dba)3/DPEphos catalyzed conditions by refluxing for 12-20 h. One of the free base triphyrin-triphyrin homo dimers was metallated by treating the homo dimer with Re(CO)5Cl in toluene under reflux and afforded bis-Re(I) homo dimer complex in 53% yield. Three free base homo dimers and one bis-Re(I) homo dimer complex were thoroughly characterized and studied using HR-MS, 1D and 2D NMR, absorption spectroscopy, cyclic voltammetry and DFT calculations. Our attempts to obtain the X-ray structure of homo dimers were not successful. However, DFT studies revealed that homo dimers prefer to exist in anti-conformation rather than syn-conformation and both triphyrin macrocycles in homo dimers were similar in terms of the deviation of pyrrole rings from the mean plane defined by the four meso carbons of the respective triphyrin unit. Absorption spectra of homo dimers showed similar absorption features such as in triphyrin(2.1.1) with slight changes in their absorption peak maxima. Electrochemical studies revealed that the homo dimers were electron rich, whereas the bis-Re(I) complex was electron deficient in nature.

Tubulin code eraser CCP5 binds branch glutamates by substrate deformation.

Microtubule function is modulated by the tubulin code, diverse posttranslational modifications that are altered dynamically by writer and eraser enzymes1. Glutamylation-the addition of branched (isopeptide-linked) glutamate chains-is the most evolutionarily widespread tubulin modification2. It is introduced by tubulin tyrosine ligase-like enzymes and erased by carboxypeptidases of the cytosolic carboxypeptidase (CCP) family1. Glutamylation homeostasis, achieved through the balance of writers and erasers, is critical for normal cell function3-9, and mutations in CCPs lead to human disease10-13. Here we report cryo-electron microscopy structures of the glutamylation eraser CCP5 in complex with the microtubule, and X-ray structures in complex with transition-state analogues. Combined with NMR analysis, these analyses show that CCP5 deforms the tubulin main chain into a unique turn that enables lock-and-key recognition of the branch glutamate in a cationic pocket that is unique to CCP family proteins. CCP5 binding of the sequences flanking the branch point primarily through peptide backbone atoms enables processing of diverse tubulin isotypes and non-tubulin substrates. Unexpectedly, CCP5 exhibits inefficient processing of an abundant β-tubulin isotype in the brain. This work provides an atomistic view into glutamate branch recognition and resolution, and sheds light on homeostasis of the tubulin glutamylation syntax.

Structural Complexities in Sodium Ion Conductive Antiperovskite Revealed by Cryogenic Transmission Electron Microscopy.

We use low-dose cryogenic transmission electron microscopy (cryo-TEM) to investigate the atomic-scale structure of antiperovskite Na2NH2BH4 crystals by preserving the room-temperature cubic phase and carefully monitoring the electron dose. Via quantitative analysis of electron beam damage using selected area electron diffraction, we find cryogenic imaging provides 6-fold improvement in beam stability for this solid electrolyte. Cryo-TEM images obtained from flat crystals revealed the presence of a new, long-range-ordered supercell with a cubic phase. The supercell exhibits doubled unit cell dimensions of 9.4 Å × 9.4 Å as compared to the cubic lattice structure revealed by X-ray crystallography of 4.7 Å × 4.7 Å. The comparison between the experimental image and simulated potential map indicates the origin of the supercell is a vacancy ordering of sodium atoms. This work demonstrates the potential of using cryo-TEM imaging to study the atomic-scale structure of air- and electron-beam-sensitive antiperovskite-type solid electrolytes.

Development of a first-in-class antibody and a specific assay for α-1,6-fucosylated prostate-specific antigen

Prostate-specific antigen (PSA) levels are widely used to screen for prostate cancer, yet the test has poor sensitivity, specificity and predictive value, which leads to overdiagnosis and overtreatment. Alterations in the glycosylation status of PSA, including fucosylation, may offer scope for an improved biomarker. We sought to generate a monoclonal antibody (mAb) targeting α-1,6-fucosylated PSA (fuc-PSA) and to develop a tissue-based immunological assay for fuc-PSA detection. Immunogens representing fuc-PSA were used for immunisation and resultant mAbs were extensively characterised. The mAbs reacted specifically with fuc-PSA-specific glycopeptide, but not with aglycosylated PSA or glycan without the PSA peptide. Reactivity was confirmed using high-throughput surface plasmon resonance spectroscopy. X-ray crystallography investigations showed that the mAbs bound to an α-helical form of the peptide, whereas the native PSA epitope is linear. Protein unfolding was required for detection of fuc-PSA in patient samples. Peptide inhibition of fuc-PSA mAbs was observed with positive screening reagents, and target epitope specificity was observed in formalin-fixed, paraffin-embedded tissue samples. This research introduces a well-characterised, first-in-class antibody targeting fuc-PSA and presents the first crystal structure of an antibody demonstrating glycosylation-specific binding to a peptide.