Structural and functional characterization of the dominant negative P-loop lysine mutation in the dy
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Tornabene, Bryan A.↗
SEARCH · Engineering Papers
Results for “structural characterization”
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In Crystallo Snapshots of Rh 2 -Catalyzed C–H Amination
While X-ray crystallography routinely provides structural characterization of kinetically stable pre-catalysts and intermediates, elucidation of the structures of transient reactive intermediates, which are intimately engaged in bond-breaking and -making during catalysis, is generally not possible. Here, we demonstrate in crystallo synthesis of Rh 2 nitrenoids that participate in catalytic C-H amination, and characterize these transient intermediates as triplet adducts of Rh 2 . Further, we observe the impact of coordinating substrate, which is present in excess during catalysis, on the structure of transient Rh 2 nitrenoids. By providing structural characterization of authentic C-H functionali-zation intermediates, and not kinetically stabilized model complexes, these experiments provide the opportunity to define critical structure-activity relationships.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural and functional characterization explains loss of dNTPase activity of the cancer-specific
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Bowen, Nicole E.↗
Installation protocol for charge transfer dissociation mass spectrometry on ion trapping mass spectrometers
Abstract Rationale Charge transfer dissociation (CTD) is a novel fragmentation technique that demonstrates enhanced structural characterization for a wide variety of molecules compared to standard fragmentation techniques like collision‐induced dissociation (CID). Alternative fragmentation techniques, such as electron transfer dissociation, electron capture dissociation, and ultraviolet photodissociation, also overcome many of the shortfalls of CID, but none of them are a silver bullet that can adequately characterize a wide variety of structures and charge states of target compounds. Given the diversity of structural classes and their occasional obstinance towards certain activation techniques, alternative fragmentation techniques are required that rely on novel or alternative modes of activation. Methods Herein, we present a step‐by‐step protocol for the installation of CTD on a quadrupole ion trap mass spectrometer and best practices for optimizing the signal‐to‐noise ratio and acquisition times for CTD mass spectra. Results In addition to two CTD installations in the Jackson laboratory, CTD has also been installed, and is currently in operation, on two 3D ion trap mass spectrometers in France: one in the laboratory of Dr. David Ropartz and Dr. Hélène Rogneaux at INRAE in Nantes, and the other in the laboratory of Dr. Jean‐Yves Salpin at Université d'Évry Val‐d'Essonne, part of the Paris‐Saclay University system. Conclusions Here, we provide a visual protocol to help others accomplish the instrument modification.
47 OTHER INSTRUMENTATION↗
Electrochemical Oxidation in Garnet-Type Solid Electrolyte by Formation of Point Defects
All-solid-state batteries hold greater promise for improving safety and energy density over conventional battery technology employing organic liquid electrolytes. One of the required features of a Li + conducting solid electrolyte is electrochemical stability, attained thermodynamically or kinetically, within the targeted operating voltage and temperature ranges. Therefore, understanding of the oxidative or reductive degradation mechanism is important to allow the design of stable solid electrolyte materials. This work contributes to building an understanding of the oxidative degradation mechanism in lithium solid electrolytes at cell operating conditions. Here, we have focused on resolving the oxidative decomposition mechanism of Al-doped lithium garnet Li 6.28 Al 0.24 La 3 Zr 2 O 12 (LLZO) as a state-of-the-art inorganic ceramic electrolyte. By combining experimental and computational analyses, we show that oxidation of LLZO occurs by simultaneous loss of oxygen and lithium from the structure, resulting in substoichiometric LLZO, at a moderate temperature (80 °C) and a high electrode potential (4.3 V vs Li/Li + ). Based on X-ray absorption and diffraction analyses, we find that the zirconium coordination shells in LLZO contract while the crystal structure experiences positive chemical strain upon electrochemical oxidation. The results from ex situ structural characterization of both the local structure and crystal symmetry are supported by a substoichiometric LLZO with lithium and oxygen vacancies, modeled by density functional theory (DFT) calculations. These chemical and structural changes in LLZO suppress effective lithium-ion conductivity by an order of magnitude. Formation of lithium and oxygen vacancies in LLZO upon electrochemical oxidation is different from prior thermodynamic predictions of phase decomposition of LLZO. The difference here is that the experiments were conducted at near-room temperature, which can hinder the kinetics of phase separation, and thus, the resultant LLZO solid electrolyte is still single-phase but substoichiometric in Li and O. In conclusion, these findings contribute an important degradation mechanism of the electrolyte, relevant for practical operational conditions of solid-state batteries.
36 MATERIALS SCIENCE↗
Combinatorial Synthesis of Oxysulfides in the Lanthanum–Bismuth-Copper System
Establishing synthesis approaches for a target material constitutes a grand challenge in materials research, which is compounded with use-inspired specifications on the format of the material. Solar photochemistry using thin film materials is a promising technology for which many complex materials are being proposed, and the present work describes application of combinatorial methods to explore the synthesis of predicted La–Bi–Cu oxysulfide photocathodes, in particular alloys of LaCuOS and BiCuOS. The variation in concentration of three cations and two anions in thin film materials, and crystallization thereof, is achieved by a combination of reactive sputtering and thermal processes including reactive annealing and rapid thermal processing. Composition and structural characterization establish composition-processing-structure relationships that highlight the breadth of processing conditions required for synthesis of LaCuOS and BiCuOS. The relative irreducibility of La oxides and limited diffusion indicate the need for high temperature processing, which conflicts with the temperature limits for mitigating evaporation of Bi and S. Collectively the findings indicate that alloys of these phases will require reactive annealing protocols that are uniquely tailored to each composition, motivating advancement of dynamic processing capabilities to further automate discovery of synthesis routes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants
Microbial rhodopsins are versatile and ubiquitous retinal-binding proteins that function as light-driven ion pumps, light-gated ion channels, and photosensors, with potential utility as optogenetic tools for altering membrane potential in target cells. Insights from crystal structures have been central for understanding proton, sodium, and chloride transport mechanisms of microbial rhodopsins. Two of three known groups of anion pumps, the archaeal halorhodopsins (HRs) and bacterial chloride-pumping rhodopsins, have been structurally characterized. Here we report the structure of a representative of a recently discovered third group consisting of cyanobacterial chloride and sulfate ion-pumping rhodopsins, the Mastigocladopsis repens rhodopsin (MastR). Chloride-pumping MastR contains in its ion transport pathway a unique Thr-Ser-Asp (TSD) motif, which is involved in the binding of a chloride ion. The structure reveals that the chloride-binding mode is more similar to HRs than chloride-pumping rhodopsins, but the overall structure most closely resembles bacteriorhodopsin (BR), an archaeal proton pump. The MastR structure shows a trimer arrangement reminiscent of BR-like proton pumps and shows features at the extracellular side more similar to BR than the other chloride pumps. We further solved the structure of the MastR-T74D mutant, which contains a single amino acid replacement in the TSD motif. We provide insights into why this point mutation can convert the MastR chloride pump into a proton pump but cannot in HRs. Our study points at the importance of precise coordination and exact location of the water molecule in the active center of proton pumps, which serves as a bridge for the key proton transfer.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Synthesis, crystal structure and magnetic properties of K Ln Se 2 ( Ln = La, Ce, Pr, Nd) structures: A family of 2D triangular lattice frustrated magnets
Here, we report the detail synthesis, single crystal structure characterization and magnetic properties of KLnSe 2 series obtained via solid state molten flux growth method. The crystal structures were characterized using single crystal x-ray diffraction. The KLnSe 2 (Ln = La, Ce, Pr and Nd) series crystallizes in the trigonal crystal system with the space group of R-3m (No. 166). The overall structure contains two-dimensional (2D) layers made from edged shared LnSe 6 -octahedra. Ln 3+ ions form a perfect triangular magnetic lattice which propagates along ab-plane. These triangular lattices are separated by the K + ions. The magnetic properties confirm that, Ce, Pr and Nd do not show any long-range ordering down to 0.4 K indicating frustrated magnetism in the KLnSe 2 series.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural and spectroscopic characterization of photoactive yellow protein and photoswitchable fluorescent protein constructs containing heavy atoms
Photo-induced structural rearrangements of chromophore-containing proteins are essential for various light-dependent signaling pathways and optogenetic applications. Ultrafast structural and spectroscopic methods have offered insights into these structural rearrangements across many timescales. However, questions still remain about exact mechanistic details, especially regarding photoisomerization of the chromophore within these proteins femtoseconds to picoseconds after photoexcitation. Instrumentation advancements for time-resolved crystallography and ultrafast electron diffraction provide a promising opportunity to study these reactions, but achieving enough signal-to-noise is a constant challenge. In this work, we present four new photoactive yellow protein constructs and one new fluorescent protein construct that contain heavy atoms either within or around the chromophore and can be expressed with high yields. Structural characterization of these constructs, most at atomic resolution, show minimal perturbation caused by the heavy atoms compared to wild-type structures. Spectroscopic studies report the effects of the heavy atom identity and location on the chromophore’s photophysical properties. None of the substitutions prevent photoisomerization, although certain rates within the photocycle may be affected. Overall, these new proteins containing heavy atoms are ideal samples for state-of-the-art time-resolved crystallography and electron diffraction experiments to elucidate crucial mechanistic information of photoisomerization.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Multi-Scale Characterization of Porosity and Cracks in Silicon Carbide Cladding after Transient Reactor Test Facility Irradiation
Silicon carbide (SiC) ceramic matrix composite (CMC) cladding is currently being pursued as one of the leading candidates for accident-tolerant fuel (ATF) cladding for light water reactor applications. The morphology of fabrication defects, including the size and shape of voids, is one of the key challenges that impacts cladding performance and guarantees reactor safety. Therefore, quantification of defects’ size, location, distribution, and leak paths is critical to determining SiC CMC in-core performance. This research aims to provide quantitative insight into the defect’s distribution under multi-scale characterization at different length scales before and after different Transient Reactor Test Facility (TREAT) irradiation tests. A non-destructive multi-scale evaluation of irradiated SiC will help to assess critical microstructural defects from production and/or experimental testing to better understand and predict overall cladding performance. X-ray computed tomography (XCT), a non-destructive, data-rich characterization technique, is combined with lower length scale electronic microscopic characterization, which provides microscale morphology and structural characterization. This paper discusses a fully automatic workflow to detect and analyze SiC-SiC defects using image processing techniques on 3D X-ray images. Following the XCT data analysis, advanced characterizations from focused ion beam (FIB) and transmission electron microscopy (TEM) were conducted to verify the findings from the XCT data, especially quantitative results from local nano-scale TEM 3D tomography data, which were utilized to complement the 3D XCT results. In this work, three SiC samples (two irradiated and one unirradiated) provided by General Atomics are investigated. The irradiated samples were irradiated in a way that was expected to induce cracking, and indeed, the automated workflow developed in this work was able to successfully identify and characterize the defects formation in the irradiated samples while detecting no observed cracking in the unirradiated sample. These results demonstrate the value of automated XCT tools to better understand the damage and damage propagation in SiC-SiC structures for nuclear applications.
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
Two Polymorphs of BaZn 2 P 2 : Crystal Structures, Phase Transition, and Transport Properties
Here, the novel α-BaZn 2 P 2 structural polymorph has been synthesized and structurally characterized for the first time. Its structure, elu-cidated from single crystal X-ray diffraction, indicates that the compound crystallizes in the orthorhombic α-BaCu 2 S 2 structure type, with unit cell parameters a = 9.7567(14) Å, b = 4.1266(6) Å, and c = 10.6000(15) Å. With β-BaZn 2 P 2 being previously iden-tified as belonging to the ThCr 2 Si 2 family, and with the precedent of structural phase transitions between the α-BaCu 2 S 2 type and the ThCr 2 Si 2 type, the potential for the pattern to be extended to the two different structural forms of BaZn 2 P 2 was explored. Thermal analysis suggest that a first order phase transition occurs at ~1123 K, whereby the low-temperature orthorhombic α-phase transforms to a high-temperature tetragonal β-BaZn 2 P 2 ; the structure of which was also studied and confirmed by single-crystal X-ray diffraction. Preliminary transport properties and band structure calculations indicate that α-BaZn 2 P 2 is a p-type, narrow-gap semiconductor with a direct bandgap (Eg) of 0.5 eV. The Seebeck coefficient, S(T), for the material increases steadily from the room temperature value of 119 µV/K to 184 µV/K at 600 K. The electrical resistivity of α-BaZn 2 P 2 is relatively high, on the order of 40 mΩ·cm, and the ρ(T) dependence shows gradual decrease upon heating. Such behavior is comparable to those of the typical semimetals or degenerate semiconductors. Although the observed values of the as-synthesized samples are not optimal, the carrier concentration can apparently be tuned to fall between the values of metals and semiconductors, thus providing an open window for optimizing this phase towards achieving an enhanced thermoelectric figure of merit zT. The calculated indirect band gap for the β-BaZn 2 P 2 phase is Eg = 0.03 eV which is about an order of magnitude lower than that of α-BaZn 2 P 2 . It is expected that the cage-like structural motif and layered structure possessed by α-BaZn 2 P 2 and β-BaZn 2 P 2 phases, respectively, would promote the realiza-tion of a low thermal conductivity in both compounds.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Amidinate- and Dithiolene-Based Silicon Complexes
Reactions of the amidinato-silylene chloride PhC( t BuN) 2 SiCl (1) with imidazole-based dithione dimer 2, lithium dithiolene radical 3, and dithiolate dimer 4 result in the synthesis of a series of silicon complexes 5-7, respectively, containing both amidinato and dithiolene ligands. 7 is the first structurally characterized silicon(II) dithiolene complex. The structural and bonding characteristics of 5-7 have been probed by both experimental and theoretical methods.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural basis for divergent C–H hydroxylation selectivity in two Rieske oxygenases
Biocatalysts that perform C–H hydroxylation exhibit exceptional substrate specificity and site-selectivity, often through the use of high valent oxidants to activate these inert bonds. Rieske oxygenases are examples of enzymes with the ability to perform precise mono- or dioxygenation reactions on a variety of substrates. Understanding the structural features of Rieske oxygenases responsible for control over selectivity is essential to enable the development of this class of enzymes for biocatalytic applications. Decades of research has illuminated the critical features common to Rieske oxygenases, however, structural information for enzymes that functionalize diverse scaffolds is limited. Here, we report the structures of two Rieske monooxygenases involved in the biosynthesis of paralytic shellfish toxins (PSTs), SxtT and GxtA, adding to the short list of structurally characterized Rieske oxygenases. Based on these structures, substrate-bound structures, and mutagenesis experiments, we implicate specific residues in substrate positioning and the divergent reaction selectivity observed in these two enzymes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
SPARC: Structural properties associated with residue constraints
SPARC facilitates the generation of plausible hypotheses regarding underlying biochemical mechanisms by structurally characterizing protein sequence constraints. Such constraints appear as residues co-conserved in functionally related subgroups, as subtle pairwise correlations (i.e., direct couplings), and as correlations among these sequence features or with structural features. SPARC performs three types of analyses. First, based on pairwise sequence correlations, it estimates the biological relevance of alternative conformations and of homomeric contacts, as illustrated here for death domains. Second, it estimates the statistical significance of the correspondence between directly coupled residue pairs and interactions at heterodimeric interfaces. Third, given molecular dynamics simulated structures, it characterizes interactions among constrained residues or between such residues and ligands that: (a) are stably maintained during the simulation; (b) undergo correlated formation and/or disruption of interactions with other constrained residues; or (c) switch between alternative interactions. We illustrate this for two homohexameric complexes: the bacterial enhancer binding protein (bEBP) NtrC1, which activates transcription by remodeling RNA polymerase (RNAP) containing σ 54 , and for DnaB helicase, which opens DNA at the bacterial replication fork. Based on the NtrC1 analysis, we hypothesize possible mechanisms for inhibiting ATP hydrolysis until ADP is released from an adjacent subunit and for coupling ATP hydrolysis to restructuring of σ 54 binding loops. Based on the DnaB analysis, we hypothesize that DnaB ‘grabs’ ssDNA by flipping every fourth base and inserting it into cavities between subunits and that flipping of a DnaB-specific glutamine residue triggers ATP hydrolysis.
97 MATHEMATICS AND COMPUTING↗
Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA
Abstract In selected Campylobacter species, the biosynthesis of N‐linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane‐associated GT‐B fold glycosyltransferases responsible for diversifying glycans in this pathway have not been structurally characterized which hinders the understanding of the structural factors that govern substrate specificity and prediction of resulting glycan composition. Herein, we report the 1.8 Å resolution structure of Campylobacter concisus PglA, the glycosyltransferase responsible for the transfer of N ‐acetylgalatosamine (GalNAc) from uridine 5′‐diphospho‐ N ‐acetylgalactosamine (UDP‐GalNAc) to undecaprenyl‐diphospho‐ N , N ′‐diacetylbacillosamine (UndPP‐diNAcBac) in complex with the sugar donor GalNAc. This study identifies distinguishing characteristics that set PglA apart within the GT4 enzyme family. Computational docking of the structure in the membrane in comparison to homologs points to differences in interactions with the membrane‐embedded acceptor and the structural analysis of the complex together with bioinformatics and site‐directed mutagenesis identifies donor sugar binding motifs. Notably, E113, conserved solely among PglA enzymes, forms a hydrogen bond with the GalNAc C6″‐OH. Mutagenesis of E113 reveals activity consistent with this role in substrate binding, rather than stabilization of the oxocarbenium ion transition state, a function sometimes ascribed to the corresponding residue in GT4 homologs. The bioinformatic analyses reveal a substrate‐specificity motif, showing that Pro281 in a substrate binding loop of PglA directs configurational preference for GalNAc over GlcNAc. This proline is replaced by a conformationally flexible glycine, even in distant homologs, which favor substrates with the same stereochemistry at C4, such as glucose. The signature loop is conserved across all Campylobacter PglA enzymes, emphasizing its importance in substrate specificity.
Vuksanovic, Nemanja↗
Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning
Microbiome assembly, structure, and dynamics significantly influence plant health. Secreted microbial signaling molecules initiate and mediate symbiosis by binding to structurally compatible plant receptors. For example, lipo-chitooligosaccharides (LCOs), produced by nitrogen-fixing rhizobial bacteria and various fungi, are recognized by plant lysin motif receptor-like kinases (LysM-RLKs), which activate the common symbiotic pathway. Accurately predicting these molecular interactions could reveal complementary signatures underlying the initial stages of endosymbiosis. Despite the breakthrough in protein-ligand structure prediction with deep learning-based tools, such as AlphaFold3, the large size and highly flexible nature of signaling compounds like LCOs present major challenges for detailed structural characterization and binding-affinity prediction. Typical structure-/physics-based methods of ligand virtual screening are designed for small, drug-like molecules, often rely on high-resolution, experimentally determined structures of the protein receptors, and rarely achieve sufficient sampling to obtain converged thermodynamic quantities with large ligands. In this study, we developed a hybrid molecular dynamics/machine learning (MD/ML) approach capable of predicting binding affinity rankings with high accuracy in systems involving large, flexible ligands, despite limited experimental structural information. Using coarse initial structural models, the predictions using the MD/ML workflow achieved strong alignment with experimental trends, particularly in the top-affinity tier for four legume LysM-RLKs (LYR3) binding to LCOs and a chitooligosaccharide. Furthermore, the MD-based conformation selection protocol provided critical structural insights into substrate specificity and binding mechanisms. This study demonstrates a powerful method to screen for challenging cognate ligand-receptors and advance our understanding of the molecular basis of microbial colonization in plants.
Lipo-chitooligosaccharides↗
Americium Oxalate: An Experimental and Computational Investigation of Metal–Ligand Bonding
A novel actinide-containing coordination polymer, [Am(C 2 O 4 )(H 2 O) 3 Cl] (Am-1), has been synthesized and structurally characterized. The crystallographic analysis reveals that the structure is two-dimensional and comprised of pseudo-dimeric Am 3+ nodes that are bridged by oxalate ligands to form sheets. Each metal center is nine-coordinate, forming a distorted capped square antiprism geometry with a C 1 symmetry, and features bound oxalate, aqua, and chloro ligands. The Am 3+ –ligand bonds were probed computationally using the quantum theory of atoms in molecules nd natural localized molecular orbital approaches to investigate the underlying mechanisms and hybrid atomic orbital contributions therein. The analyses indicate that the bonds within Am-1 are predominantly ionic and the 5f shell of the Am 3+ metal centers does not add a significant covalent contribution to the bonds. Further, our bonding assessment is supported by measurements on the optical properties of Am-1 using diffuse reflectance and photoluminescence spectroscopies. The position of the principal absorption band at 507 nm ( 5 L 6' ← 7 F 0' ) is notable because it is consistent with previously reported americium oxalate complexes in solution, indicating similarities in the electronic structure and ionic bonding. Compound Am-1 is an active phosphor, featuring strong bright-blue oxalate-based luminescence with no evidence of metal-centered emission.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Effective Local Geometry Descriptor for 29Si NMR Q4 Anisotropy
The nuclear shielding anisotropy, ζ, is a useful nuclear magnetic resonance (NMR) shielding tensor parameter in describing the extent of electron cloud distortion about an atom. Despite the advantages afforded by NMR in structural characterization, the relationship between ζ and local structure of an atom in high-symmetry environments, such as Si-Q 4 sites, is poorly understood. Here, we use a data-driven approach combining random forest feature ranking and the Sure Independence Screening and Sparsifying Operator (SISSO) approach to derive a simple and accurate geometric descriptor for ζ with a root-mean-squared prediction error of 6.77 ppm and an R 2 of 0.761. We then apply this descriptor to describe the local geometric distortion of zeolites Sigma-2 and silica-ZSM-5 whose chemical shift anisotropy tensor has been reported. We envision that this geometric descriptor will allow for structural description and refinement in previously difficult-to-describe materials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗