Structural analysis of CACHE domain of the McpA chemoreceptor from Leptospira interrogans
Not Available
Santos, Jademilson C.↗
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Results for “DOMAIN STRUCTURE”
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Crystal structure of human IRAK1
Interleukin 1 (IL-1) receptor-associated kinases (IRAKs) are serine/threonine kinases that play critical roles in initiating innate immune responses against foreign pathogens and other types of dangers through their role in Toll-like receptor (TLR) and interleukin 1 receptor (IL-1R) mediated signaling pathways. Upon ligand binding, TLRs and IL-1Rs recruit adaptor proteins, such as myeloid differentiation primary response gene 88 (MyD88), to the membrane, which in turn recruit IRAKs via the death domains in these proteins to form the Myddosome complex, leading to IRAK kinase activation. Despite their biological and clinical significance, only the IRAK4 kinase domain structure has been determined among the four IRAK family members. Here, in this work, we report the crystal structure of the human IRAK1 kinase domain in complex with a small molecule inhibitor. The structure reveals both similarities and differences between IRAK1 and IRAK4 and is suggestive of approaches to develop IRAK1- or IRAK4-specific inhibitors for potential therapeutic applications. While the IRAK4 kinase domain is capable of homodimerization in the unphosphorylated state, we found that the IRAK1 kinase domain is constitutively monomeric regardless of its phosphorylation state. Additionally, the IRAK1 kinase domain forms heterodimers with the phosphorylated, but not unphosphorylated, IRAK4 kinase domain. Collectively, these data indicate a two-step kinase activation process in which the IRAK4 kinase domain first homodimerizes in the Myddosome, leading to its trans -autophosphorylation and activation. The phosphorylated IRAK4 kinase domain then forms heterodimers with the IRAK1 kinase domain within the Myddosome, leading to its subsequent phosphorylation and activation.
60 APPLIED LIFE SCIENCES↗
Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14
Abstract Substantial progresses in protein structure prediction have been made by utilizing deep‐learning and residue‐residue distance prediction since CASP13. Inspired by the advances, we improve our CASP14 MULTICOM protein structure prediction system by incorporating three new components: (a) a new deep learning‐based protein inter‐residue distance predictor to improve template‐free (ab initio) tertiary structure prediction, (b) an enhanced template‐based tertiary structure prediction method, and (c) distance‐based model quality assessment methods empowered by deep learning. In the 2020 CASP14 experiment, MULTICOM predictor was ranked seventh out of 146 predictors in tertiary structure prediction and ranked third out of 136 predictors in inter‐domain structure prediction. The results demonstrate that the template‐free modeling based on deep learning and residue‐residue distance prediction can predict the correct topology for almost all template‐based modeling targets and a majority of hard targets (template‐free targets or targets whose templates cannot be recognized), which is a significant improvement over the CASP13 MULTICOM predictor. Moreover, the template‐free modeling performs better than the template‐based modeling on not only hard targets but also the targets that have homologous templates. The performance of the template‐free modeling largely depends on the accuracy of distance prediction closely related to the quality of multiple sequence alignments. The structural model quality assessment works well on targets for which enough good models can be predicted, but it may perform poorly when only a few good models are predicted for a hard target and the distribution of model quality scores is highly skewed. MULTICOM is available at https://github.com/jianlin-cheng/MULTICOM_Human_CASP14/tree/CASP14_DeepRank3 and https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .
59 BASIC BIOLOGICAL SCIENCES↗
Probing Metastable Domain Dynamics via Automated Experimentation in Piezoresponse Force Microscopy
The dynamics of complex topological defects in ferroelectric materials is explored using automated experimentation in piezoresponse force microscopy. Specifically, a complex trigger system (i.e., “FerroBot”) is employed to study metastable domain-wall dynamics in Pb 0.6 Sr 0.4 TiO 3 thin films. Several regimes of superdomain wall dynamics have been identified, including smooth domain-wall motion and significant reconfiguration of the domain structures. We have further demonstrated that microscopic mechanisms of the domain-wall dynamics can be identified; i.e., domain-wall bending can be separated from irreversible domain reconfiguration regimes. In conjunction, phase-field modeling was used to corroborate the observed mechanisms. As such, the observed superdomain dynamics can provide a model system for classical ferroelectric dynamics, much like how colloidal crystals provide a model system for atomic and molecular systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Unusual dynamic susceptibility arising from soft ferromagnetic domains in MnBi 8 Te 13 and Sb-doped MnBi 2n Te 3n+1 (n = 2, 3)
MnBi$_{2n}$Te$_{3n+1}$ (MBT) is the first intrinsic magnetic topological insulator and is promising to host emergent phenomena such as quantum anomalous Hall effect. They can be made ferromagnetic by having n ≥ 4 or with Sb doping. In this work, we studied the magnetic dynamics in a few selected ferromagnetic (FM) MBT compounds, including MnBi 8 Te 13 and Sb doped MnBi$_{2n}$Te$_{3n+1}$ ($n = 2, 3)$ using AC susceptibility and magneto-optical imaging. Slow relaxation behavior is observed in all three compounds, suggesting its universality among FM MBT. We attribute the origin of the relaxation behavior to the irreversible domain movements since they only appear below the saturation fields when ferromagnetic domains form. The very soft ferromagnetic domain nature is revealed by the low-field fine-structured domains and high-field sea-urchin-shaped remanent-state domains imaged via our magneto-optical measurements. Finally, we ascribe the rare 'double-peak' behavior observed in the AC susceptibility under small DC bias fields to the very soft ferromagnetic domain formations.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Phase-field-guided design of record-high piezoelectricity and discovery of simultaneous high light transparency and high piezoelectricity in relaxor ferroelectrics
Here, the phase-field method has been extensively applied to predicting the domain structures and their responses to external fields and understanding experimentally observed domain states under different electromechanical conditions in ferroelectric heterostructures. This article highlights the successful examples of phase-field applications in guiding the design of relaxor ferroelectric ceramics and crystals with record-high piezoelectricity and the discovery of simultaneous high light transparency and piezoelectricity of relaxor ferroelectric crystals for a wide range of biomedical, robotics, and optoelectronics applications.
36 MATERIALS SCIENCE↗
2.4 Å resolution crystal structure of human TRAP1 NM , the Hsp90 paralog in the mitochondrial matrix
TRAP1 is an organelle-specific Hsp90 paralog that is essential for neoplastic growth. As a member of the Hsp90 family, TRAP1 is presumed to be a general chaperone facilitating the late-stage folding of Hsp90 client proteins in the mitochondrial matrix. Interestingly, TRAP1 cannot replace cytosolic Hsp90 in protein folding, and none of the known Hsp90 co-chaperones are found in mitochondria. Thus, the three-dimensional structure of TRAP1 must feature regulatory elements that are essential to the ATPase activity and chaperone function of TRAP1. Here, the crystal structure of a human TRAP1 NM dimer is presented, featuring an intact N-domain and M-domain structure, bound to adenosine 5'-β,γ-imidotriphosphate (ADPNP). The crystal structure together with epitope-mapping results shows that the TRAP1 M-domain loop 1 contacts the neighboring subunit and forms a previously unobserved third dimer interface that mediates the specific interaction with mitochondrial Hsp70.
36 MATERIALS SCIENCE↗
Adaptive methods of generating complex light arrays
Structured light arrays of various shapes have been a cornerstone in optical science, driven by the complexities of precise and adaptable generation. This study introduces an approach using a spatial light modulator (SLM) as a generator for these arrays. By projecting a holographic mask onto the SLM, it functions simultaneously as an optical convolution device, focusing mechanism, and structured light beam mask. Our approach offers unmatched versatility, allowing for the experimental fabrication of traditional beam arrays like azimuthal Laguerre–Gaussian (LG), Bessel–Gaussian (BG), and Hermite–Gauss (HG) in the far-field. Notably, it has enabled a method of generating Ince–Gauss (IG) and LG radial mode beam arrays using a convolution solution. Our system provides exceptional control over array periodicity and intensity distribution, bypassing the Talbot self-imaging phenomenon seen in traditional setups. We provide an in-depth theoretical discussion, supported by empirical evidence, of our far-field results. This method has vast potential for applications in optical communication, data processing, and multi-particle manipulation. It paves the way for rapid generation of structured light with high spatial frequencies and complex shapes, promising transformative advances in these domains.
Optics↗
Effect of correlated oxide electrodes on disorder pinning and thermal roughening of ferroelectric domain walls in epitaxial PbZr 0.2 Ti 0.8 O 3 thin films
We report the competing effects of disorder pinning and thermal roughening on ferroelectric domain walls as a function of temperature in epitaxial PbZr 0.2 Ti 0.8 O 3 thin films deposited on (001) SrTiO 3 substrates buffered by three types of correlated oxide electrodes, La 0.67 Sr 0.33 MnO 3 , LaNiO 3 , and SrIrO 3 . Piezo-response force microscopy studies show that the 50 nm PbZr 0.2 Ti 0.8 O 3 films are uniformly polarized in the as-grown states, with the patterned domain structures persisting above 700 °C. For all three types of films, the domain wall roughness is dominated by 2D random bond disorder at room temperature, and transitions to 1D thermal roughening upon heating. The roughness exponent ζ increases progressively from 0.3 to 0.5 within a temperature window that depends on the bottom conducting oxide type, from which we extracted the distribution of disorder pinning energy. Lastly, we discuss the possible origins of the disorder pinning and the effect of the correlated oxide electrodes on the energy landscape of DW motion.
36 MATERIALS SCIENCE↗
Domain fluctuations in a ferroelectric low-strain BaTiO 3 thin film
In this work, a ferroelectric BaTiO 3 thin film grown on a NdScO 3 substrate was studied using x-ray photon correlation spectroscopy (XPCS) to characterize thermal fluctuations near the a/b to a/c domain structure transformation present in this low-strain material, which is absent in the bulk. XPCS studies provide a direct comparison of the role of domain fluctuations in first- and second-order phase transformations. The a/b to a/c domain transformation is accompanied by a decrease in fluctuation timescales, and an increase in intensity and correlation length. Surprisingly, domain fluctuations are observed up to 25 °C above the transformation, concomitant with the growth of a/c domains and coexistence of both domain types. After a small window of stability, as the Curie temperature is approached, a/c domain fluctuations are observed, albeit slower, potentially due to the structural transformation associated with the ferroelectric to paraelectric transformation. The observed time evolution and reconfiguration of domain patterns highlight the role played by phase coexistence and elastic boundary conditions in altering fluctuation timescales in ferroelectric thin films.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Structural Determinants of the Stereoinverting Activity of Pseudomonas stutzeri d -Phenylglycine Aminotransferase
Aromatic d-amino acids are key precursors for the production of many small molecule therapeutics. Therefore, the development of biocatalytic methods for their synthesis is of great interest. An enzyme that has great potential as a biocatalyst for the synthesis of d-amino acids is the stereoinverting d-phenylglycine aminotransferase (DPAT) from Pseudomonas stutzeri ST-201. This enzyme catalyzes a unique l to d transamination reaction that produces d-phenylglycine and α-ketoglutarate from benzoylformate and l-glutamate, via a mechanism that is poorly understood. Here, we present the crystal structure of DPAT, which shows that the enzyme folds into a two-domain structure representative of class III aminotransferases. Guided by the crystal structure, we performed saturation mutagenesis to probe the substrate binding pockets of the enzyme. Here, these experiments helped us identify two arginine residues (R34 and R407), one in each binding pocket, that are essential to catalysis. Together with kinetic analyses using a library of amino acid substrates, our mutagenesis and structural studies allow us to propose a binding model that explains the dual l/d specificity of DPAT. Our kinetic analyses also demonstrate that DPAT can catalyze the transamination of β- and γ-amino acids, reclassifying this enzyme as an ω-aminotransferase. Collectively, our studies highlight that the DPAT active site is amenable to protein engineering for expansion of its substrate scope, which offers the opportunity to generate new biocatalysts for the synthesis of a variety of valuable optically pure d-amino acids from inexpensive and abundant l-amino acids.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Long-range stripe nanodomains in epitaxial (110) BiFeO 3 thin films on (100) NdGaO 3 substrate
Here, we report the observation of ferroelectric and ferroelastic nanodomains in (110)-oriented BiFeO 3 (BFO) thin films epitaxially grown on low symmetric (100) NdGaO 3 (NGO) substrate. We observed long range ordering of ferroelectric 109° stripe nanodomains separated by periodic vertical domain walls in as-grown 130 nm thick BFO films. The effect of La 0.67 Sr 0.33 CoO 3 (LSCO) conducting interlayer on domain configurations in BFO/NGO film was also observed with relatively short range-ordering of stripe domains due to the modified electrostatic boundary conditions in BFO/LSCO/NGO film. Additional studies on B-site doping of Nb ions in BFO films showed change in the domain structures due to doping induced change in lattice anisotropy while maintaining the stripe domain morphology with 109° domain wall. Finally, this long-range array of ferroelectric and ferroelastic domains can be useful for optoelectronic devices and ferroelastic templates for strain coupled artificial magnetoelectric heterostructures.
36 MATERIALS SCIENCE↗
Controlling quantum phases of electrons and excitons in moiré superlattices
Moiré lattices formed in twisted and lattice-mismatched van der Waals heterostructures have emerged as a platform to engineer the novel electronic and excitonic states at the nanoscale. This Perspective reviews the materials science of moiré heterostructures with a focus on the structural properties of the interface and its structural–property relationships. We first review the studies of the atomic relaxation and domain structures in moiré superlattices and how these structural studies provide critical insights into understanding the behaviors of quantum-confined electrons and excitons. We discuss the general frameworks to manipulate moiré structures and how such control can be harnessed for engineering new phases of matter and simulating various quantum phenomena. Lastly, we discuss routes toward large-scale moiré heterostructures and give an outlook on their applications in quantum electronics and optoelectronics. Special emphasis will be placed on the challenges and opportunities of the reliable fabrication and dynamical manipulation of moiré heterostructures.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Structure of the ordered compound V sub 6 C sub 5.
Structure of ordered compound vanadium carbide, discussing carbon vacancy in hexagonal superlattice and domain structure
Kahn, D.↗
Origin of enhanced performance when Mn-rich rocksalt cathodes transform to δ -DRX
Most Mn-rich cathodes are known to undergo phase transformation into structures resembling spinel-like ordering upon electrochemical cycling. Recently, the irreversible transformation of Ti-containing Mn-rich disordered rock-salt cathodes into a phase — named δ — with nanoscale spinel-like domains has been shown to increase energy density, capacity retention, and rate capability. However, the nature of the boundaries between domains and their relationship with composition and electrochemistry are not well understood. In this work, we discuss how the transformation into the multi-domain structure results in eight variants of Spinel domains, which is crucial for explaining the nanoscale domain formation in the δ -phase. We study the energetics of crystallographically unique boundaries and the possibility of Li-percolation across them with a fine-tuned CHGNet machine learning interatomic potential. Energetics of 16 d vacancies reveal a strong affinity to segregate to the boundaries, thereby opening Li-pathways at the boundary to enhance long-range Li-percolation in the δ structure. Defect calculations of the relatively low-mobility Ti show how it can influence the extent of Spinel ordering, domain morphology and size significantly; leading to guidelines for engineering electrochemical performance through changes in composition.
Anand, Shashwat↗
Tunable electroresistance and electro-optic effects of transparent molecular ferroelectrics
Recent progress in molecular ferroelectrics (MOFEs) has been overshadowed by the lack of high-quality thin films for device integration. We report a water-based air-processable technique to prepare large-area MOFE thin films, controlled by supersaturation growth at the liquid-air interface under a temperature gradient and external water partial pressure. We used this technique to fabricate ImClO4 thin films and found a large, tunable room temperature electroresistance: a 20-fold resistance variation upon polarization switching. The as-grown films are transparent and consist of a bamboo-like structure of ($2,\overline{1},0$) and ($1,0,\overline{2}$) structural variants of R3m symmetry with a reversible polarization of 6.7 μC/cm 2 . The resulting ferroelectric domain structure leads to a reversible electromechanical response of d 33 = 38.8 pm/V. Polarization switching results in a change of the refractive index, n, of single domains, $\frac{Δn}{n}$ = 0.3. The remarkable combination of these characteristics renders MOFEs a prime candidate material for new nanoelectronic devices. The information that we present in this work will open a new area of MOFE thin-film technologies.
36 MATERIALS SCIENCE↗
Mesoscopic structure of mixed type domain walls in multiaxial ferroelectrics
The structure of a 180° uncharged rotational domain wall in a multiaxial ferroelectric film is studied in the framework of an analytical Landau-Ginzburg-Devonshire (LGD) approach. Finite element modeling (FEM) is used to solve numerically the system of the coupled nonlinear Euler-Lagrange (EL) second-order differential equations for two components of polarization. We show that the structure of the domain wall and corresponding metastable or stable phase of the film are controlled by a single parameter—the dimensionless ferroelectric anisotropy factor μ. We fitted the static profile of a solitary domain wall, calculated by FEM, with kinklike functions for polarization components, and extracted the five μ-dependent parameters from the fitting to FEM curves. The surprisingly high accuracy of the fitting results for two polarization components in the entire μ range allows us to conclude that the analytical functions, which are trial functions in the direct variational method, can be treated as a high-accuracy variational solution of the static EL equations. We further derive exact two-component analytical solutions of the static EL equations for a polydomain 180° domain structure in a multiaxial ferroelectric film. Using these, we derive analytical expressions for the system free energy and analyze its dependence on the film thickness and boundary conditions at the film surfaces. The single-domain state is ground for zero polarization derivative at the surfaces, while the polydomain states minimize the system energy for zero polarization at the surfaces. Counterintuitively, the energy of the polydomain states split into two levels, “0” and “1,” for zero polarization at the surfaces, and each of the levels contains a large number of close-energy sublevels, whose structure is characterized by a different number and type of domain walls. The analytical solutions can become a useful tool for Bayesian analysis of high-resolution scanning transmission electron microscopy images in ferroelectric films.
36 MATERIALS SCIENCE↗
Characterization of the structure and catalytic activity of Legionella pneumophila VipF: L. pneumophila VipF Modifies Chloramphenicol
Abstract not provided
Young, Byron H.↗