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At least 91 records · Page 5

Crystal structures of the complex of a kallikrein inhibitor from Bauhinia bauhinioides with trypsin and modeling of kallikrein complexes

Structures of a recombinant Kunitz-type serine protease inhibitor from Bauhinia bauhinioides (BbKI) complexed with bovine trypsin were determined in two crystal forms. The crystal structure with the L55R mutant of BbKI was determined in space group P 6 4 at 1.94 Å resolution and that with native BbKI in the monoclinic space group P 2 1 at 3.95 Å resolution. The asymmetric unit of the latter crystals contained 44 independent complexes, thus representing one of the largest numbers of independent objects deposited in the Protein Data Bank. Additionally, the structure of the complex with native BbKI was determined at 2.0 Å resolution from P 6 4 crystals isomorphous to those of the mutant. Since BbKI has previously been found to be a potent inhibitor of the trypsin-like plasma kallikrein, it was also tested against several tissue kallikreins. It was found that BbKI is a potent inhibitor of human tissue kallikrein 4 (KLK4) and the chymotrypsin-like human tissue kallikrein 7 (KLK7). Structures of BbKI complexed with the catalytic domain of human plasma kallikrein were modeled, as well as those with KLK4 and KLK7, and the structures were analyzed in order to identify the interactions that are responsible for inhibitory potency.

Li, Mi↗

Structural Diversity of Ultralong CDRH3s in Seven Bovine Antibody Heavy Chains

Antigen recognition by mammalian antibodies represents the most diverse setting for protein-protein interactions, because antibody variable regions contain exceptionally diverse variable gene repertoires of DNA sequences containing combinatorial, non-templated junctional mutational diversity. Some animals use additional strategies to achieve structural complexity in the antibody combining site, and one of the most interesting of these is the formation of ultralong heavy chain complementarity determining region 3 loops in cattle. Repertoire sequencing studies of bovine antibody heavy chain variable sequences revealed that bovine antibodies can contain heavy chain complementarity determining region 3 (CDRH3) loops with 60 or more amino acids, with complex structures stabilized by multiple disulfide bonds. It is clear that bovine antibodies can achieve long, peculiarly structured CDR3s, but the range of diversity and complexity of those structures is poorly understood. We determined the atomic resolution structure of seven ultralong bovine CDRH3 loops. The studies, combined with five previous structures, reveal a large diversity of cysteine pairing variations, and highly diverse globular domains.

59 BASIC BIOLOGICAL SCIENCES↗

A Micelle Electrolyte Enabled by Fluorinated Ether Additives for Polysulfide Suppression and Li Metal Stabilization in Li-S Battery

The Li-S battery is a promising next-generation technology due to its high theoretical energy density (2600 Wh kg -1 ) and low active material cost. However, poor cycling stability and coulombic efficiency caused by polysulfide dissolution have proven to be major obstacles for a practical Li-S battery implementation. In this work, we develop a novel strategy to suppress polysulfide dissolution using hydrofluoroethers (HFEs) with bi-functional, amphiphlic surfactant-like design: a polar lithiophilic "head" attached to a fluorinated lithiophobic "tail." A unique solvation mechanism is proposed for these solvents whereby dissociated lithium ions are readily coordinated with lithiophilic "head" to induce self-assembly into micelle-like complex structures. Complex formation is verified experimentally by changing the additive structure and concentration using small angle X-ray scattering (SAXS). These HFE-based electrolytes are found to prevent polysulfide dissolution and to have excellent chemical compatibility with lithium metal: Li||Cu stripping/plating tests reveal high coulombic efficiency (>99.5%), modest polarization, and smooth surface morphology of the uniformly deposited lithium. Li-S cells are demonstrated with 1395 mAh g-1 initial capacity and 71.9% retention over 100 cycles at >99.5% efficiency-evidence that the micelle structure of the amphiphilic additives in HFEs can prohibit polysulfide dissolution while enabling facile Li + transport and anode passivation.

25 ENERGY STORAGE↗

Accurate Thermochemistry of Complex Lignin Structures via Density Functional Theory, Group Additivity, and Machine Learning

A molecular-level understanding of lignin structures and bond dissociation energies could facilitate depolymerization technologies. Still, this information is currently limited due to the lack of databases and the simplification of surrogate models. Here, substitution effects on seven common linkages in lignin polymers are systematically investigated. An automated reaction network generator is employed to create a database of structures. A new group additivity (GA) model based on principal component analysis (PCA) descriptors is introduced and trained on gas-phase density functional theory data of 4100 species at the M06-2X/6-311++G(d,p) level. Hydrogen bonds, local steric, and nonaromatic ring contributions are also incorporated. Lastly, we improve the accuracy of the group additivity model to reach the G4 theory by computing a data set of 770 species at this level and using a data fusion approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Uncertainty-Aware, Structure-Preserving Machine Learning Approach for Domain Shift Detection From Nonlinear Dynamic Responses of Structural Systems

Complex structural systems deployed for aerospace, civil, or mechanical applications must operate reliably under varying operational conditions. Structural health monitoring (SHM) systems help ensure the reliability of these systems by providing continuous monitoring of the state of the structure. SHM relies on synthesizing measured data with a predictive model to make informed decisions about structural states. However, these models—which may be thought of as a form of a digital twin—need to be updated continuously as structural changes (e.g., due to damage) arise. We propose an uncertainty-aware machine learning model that enforces distance preservation of the original input state space and then encodes a distance-aware mechanism via a Gaussian process (GP) kernel. The proposed approach leverages the spectral-normalized neural GP algorithm to combine the flexibility of neural networks with the advantages of GP, subjected to structure-preserving constraints, to produce an uncertainty-aware model. This model is used to detect domain shift due to structural changes that cannot be observed directly because they may be spatially isolated (e.g., inside a joint or localized damage). This work leverages detection theory to detect domain shift systematically given statistical features of the prediction variance produced by the model. The proposed approach is demonstrated on a nonlinear structure being subjected to damage conditions. In conclusion, it is shown that the proposed approach is able to rely on distances of the transformed input state space to predict increased variance in shifted domains while being robust to normative changes.

Algorithms↗

Imaging Complex Subsurface Structures for Geothermal Exploration at Pirouette Mountain and Eleven-Mile Canyon in Nevada

Accurate imaging of subsurface complex structures with faults is crucial for geothermal exploration because faults are generally the primary conduit of hydrothermal flow. It is very challenging to image geothermal exploration areas because of complex geologic structures with various faults and noisy surface seismic data with strong and coherent ground-roll noise. In addition, fracture zones and most geologic formations behave as anisotropic media for seismic-wave propagation. Properly suppressing ground-roll noise and accounting for subsurface anisotropic properties are essential for high-resolution imaging of subsurface structures and faults for geothermal exploration. We develop a novel wavenumber-adaptive bandpass filter to suppress the ground-roll noise without affecting useful seismic signals. This filter adaptively exploits both characteristics of the lower frequency and the smaller velocity of the ground-roll noise than those of the signals. Consequently, this filter can effectively differentiate the ground-roll noise from the signal. We use our novel filter to attenuate the ground-roll noise in seismic data along five survey lines acquired by the U.S. Navy Geothermal Program Office at Pirouette Mountain and Eleven-Mile Canyon in Nevada, United States. We then apply our novel anisotropic least-squares reverse-time migration algorithm to the resulting data for imaging subsurface structures at the Pirouette Mountain and Eleven-Mile Canyon geothermal exploration areas. The migration method employs an efficient implicit wavefield-separation scheme to reduce image artifacts and improve the image quality. Our results demonstrate that our wavenumber-adaptive bandpass filtering method successfully suppresses the strong and coherent ground-roll noise in the land seismic data, and our anisotropic least-squares reverse-time migration produces high-resolution subsurface images of Pirouette Mountain and Eleven-Mile Canyon, facilitating accurate fault interpretation for geothermal exploration.

15 GEOTHERMAL ENERGY↗

Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering

The structures of RNA:RNA complexes regulate many biological processes. Despite their importance, protein-free RNA:RNA complexes represent a tiny fraction of experimentally determined structures. Here, we describe a joint small-angle X-ray and neutron scattering (SAXS/SANS) approach to structurally interrogate conformational changes in a model RNA:RNA complex. Using SAXS, we measured the solution structures of the individual RNAs and of the overall RNA:RNA complex. With SANS, we demonstrate, as a proof of principle, that isotope labeling and contrast matching (CM) can be combined to probe the bound state structure of an RNA within a selectively deuterated RNA:RNA complex. Furthermore, we show that experimental scattering data can validate and improve predicted AlphaFold 3 RNA:RNA complex structures to reflect its solution structure. In conclusion, our work demonstrates that in silico modeling, SAXS, and CM-SANS can be used in concert to directly analyze conformational changes within RNAs when in complex, enhancing our understanding of RNA structure in functional assemblies.

HIV-1 dimerization initiation site↗

Synthesis, structure, electronic characterization, and halogenation of gold(III) phlorin complexes

The metalation chemistry of the phlorin, which is a non-aromatic tetrapyrrole macrocycle containing a single sp 3 -hybridized meso-carbon has remained underdeveloped, as compared to that of more traditional tetrapyrroles such as porphyrins, corroles and phthalocyanines. There have been few prior efforts to prepare metallophlorins, and those that have been reported have relied on either reduction or nucleophilic attack of parent metalloporphyrins, rather than direct metalation of freebase phlorin constructs. In this work, an alternate synthetic approach for preparation of gold(III) phlorin complexes that involves the first direct metalation of two different freebase phlorin derivatives (3H(Phl tBu ) and 3H(Phl F )) with AuBr 3 to produce the stable and fully isolable gold(III) phlorin complexes Au(Phl tBu ) and Au(Phl F ) is reported. The first structural characterization of a metallophlorin bearing geminal dimethyl substituents at the sp 3 -hybridized meso-carbon via X-ray crystallography is also reported. In addition to the preparation of Au(Phl tBu ) and Au(Phl F ), the UV-vis absorption and redox properties of these two gold(III) phlorins in comparison to those of their freebase homologues is also detailed. Notably, the metallophlorins are characterized by panchromatic absorbance profiles and intense and broad bands that span the long-visible and into the near-IR regions, as well as two fully reversible oxidation and reduction waves as probed by cyclic voltammetry. Lastly, the chlorination of Au(Phl tBu ) using PhI(Cl 2 ) was probed and it was found that this regioslective reaction generates monochlorinated (Au(Phl tBu Cl)) and dichlorinated (Au(Phl tBu Cl 2 )) products, which were both structurally characterized by X-ray crystallography.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exceptionally Complex Electronic Structures of Lanthanide Oxides and Small Molecules

Lanthanide (Ln) oxide clusters and molecular systems provide a bottom-up look at the electronic structures of the bulk materials because of close parallels in the patterns of Ln 4fN subshell occupancy between the molecular and bulk Ln 2 O 3 size limits. At the same time, these clusters and molecules offer a challenge to the theory community to find appropriate and robust treatments for the 4f N patterns across the Ln series. Anion photoelectron (PE) spectroscopy provides a powerful experimental tool for studying these systems, mapping the energies of the ground and low-lying excited states of the neutral relative to the initial anion state, providing spectroscopic patterns that reflect the Ln 4f N occupancy. In this Account, we review our anion PE spectroscopic and computational studies on a range of small lanthanide molecules and cluster species. The PE spectra of LnO – (Ln = Ce, Pr, Sm, Eu) diatomic molecules show spectroscopic signatures associated with detachment of an electron from what can be described as a diffuse Ln 6s-like orbital. While the spectra of all four diatomics share this common transition, the fine structure in the transition becomes more complex with increasing 4f occupancy. This effect reflects increased coupling between the electrons occupying the corelike 4f and diffuse 6s orbitals with increasing N. Understanding the PE spectra of these diatomics sets the stage for interpreting the spectra of polyatomic molecular and cluster species. In general, the results confirm that the partial 4f N subshell occupancy is largely preserved between molecular and bulk oxides and borides. However, they also suggest that surfaces and edges of bulk materials may support a low-energy, diffuse Ln 6s band, in contrast to bulk interiors, in which the 6s band is destabilized relative to the 5d band. We also identify cases in which the molecular Ln centers have 4f N+1 occupancy rather than bulklike 4f N , which results in weaker Ln–O bonding. Specifically, Sm centers in mixed Ce–Sm oxides or in Sm x O y – (y ≤ x) clusters have this higher 4f N+1 occupancy. The PE spectra of these particular species exhibit a striking increase in the relative intensities of excited-state transitions with decreasing photon energy (resulting in lower photoelectron kinetic energy). Furthermore, this is opposite of what is expected on the basis of the threshold laws that govern photodetachment. We relate this phenomenon to strong electron–neutral interactions unique to these complex electronic structures. The time scale of the interaction, which shakes up the electronic configuration of the neutral, increases with decreasing electron momentum. From a computational standpoint, we point out that special care must be taken when considering Ln cluster and molecular systems toward the center of the Ln series (e.g., Sm, Eu), where treatment of electrons explicitly or using an effective core potential can yield conflicting results on competing subshell occupancies. However, despite the complex electronic structures associated with partially filled 4f N subshells, we demonstrate that inexpensive and tractable calculations yield useful qualitative insight into the general electronic structural features.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A chiral alkali metal capped Ni 4 cubane complex: Synthesis, structure, magnetic and catalytic bromination studies

A new chiral NaO 2 Ni 4 O 2 N 2 cluster has been developed with a distorted capped cubane-type structure. The structure was determined by single crystal X-ray diffraction. The tetradentate Schiff-base ligand was synthesized by the condensation of o-vanillin and $\textit{D}$-(-)–threo-2-amino-1-(4-nitrophenyl)-1,3-propanediol. X-ray structure reveals that the complex possesses a Ni 4 cubane cluster where sodium ion is anchored on the face of the cubane structure. Continuous shape measurement studies revealed that all the Ni centres are in distorted octahedral geometry and sodium ion adopts the spherical square pyramidal geometry. Further structural exploration reveals that the complex shows local distortions of the coordination geometries at each metal site, and these distortions govern the magnetic anisotropy associated with each Ni II ion. For the present case, an elongation ($d_{str}$ > 0) of the octahedral coordination sphere results in a local easy-plane anisotropy, with a positive $D_{Ni(II)}$ parameter. Temperature dependant magnetization measurements showed a predominant ferromagnetic interaction amongst the four Ni centres. This complex is also catalytically active towards bromination of aromatic phenolic compounds. Initial catalytic activity was verified with the conversion of phenol red to bromophenol blue. Different phenolic substances show good conversion to their corresponding bromo derivatives. The complex showed good catalytic activity towards bromination of aromatic phenolic compounds, offering up to 99% conversion with 100% selectively to their corresponding bromo derivatives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Symmetry in Seeded Metal Nanocrystal Growth

Symmetry underpins the structure and function of the world around us and is also captured in modern nanomaterials, where changing the symmetry of a nanocrystal or the interparticle spacing and orientation of nanocrystal building blocks in a superlattice can give new function. However, the synthesis and assembly of nanocrystals have been limited largely to simple compositions and structures. It remains a grand challenge to achieve nanocrystals with compositional and structural complexity while maintaining the monodispersity required for their use. This Account will illustrate through recent examples that seeded methods enable the synthesis of compositionally and structurally complex multimetallic crystals with defined and predictable symmetries for applications in plasmonics and catalysis. This outcome arises because the barrier for heterogeneous nucleation (i.e., seeded) is lower than that of homogeneous nucleation, where seeds can serve as preferential sites for the growth of complex structures and crystal phases. Our analysis begins by considering metal overgrowth from single-crystalline seeds of different shapes and symmetries, where the kinetics of adatom addition to seeds relative to their diffusion across seeds accounts for the expressed nanocrystal shapes. These results are then compared to overgrowth from seeds with different internal structures (i.e., planar defects), where the relationships between nanocrystal size and volumetric strain energy and surface energy are discussed. A major finding from this analysis is that often the underlying symmetry of seeds can be predictably transferred to the final crystals during overgrowth processes. Consequences of this finding are the predictable syntheses of crystals with different hierarchies akin to snowcrystals as well as nanocrystals with complex compositions (e.g., quaternary nanoparticles). Yet, there are subtle aspects to seeded growth that pave a path toward examples where nanocrystal symmetry has been reduced compared to the original seeds in a controlled manner. As we found, both the concentrations of metal precursors and capping agents can impact whether symmetry is transferred or reduced during overgrowth. Examples from our laboratory will be placed in context to other reported strategies for symmetry breaking. As will be argued, understanding what conditions favor symmetry preservation versus symmetry reduction during seeded crystal growth is central to accessing next-generation crystal forms. The Account concludes by outlining synthetic challenges associated with forming nanoscale heterostructures with precise 3-D placement of different materials within a given nanocrystal as well as facet control within different material domain and interface engineering. Furthermore, we envision meeting these challenges through regioselective and chemoselective seeded syntheses for which a foundation is outlined herein.

36 MATERIALS SCIENCE↗

Artificial intelligence methods for protein structure and interaction prediction: Recent advances and challenges

Recent advances in artificial intelligence have introduced novel methods for high-accuracy prediction of protein tertiary structures, protein complex structures, and interactions between proteins and other biomolecules, such as small molecules and nucleic acids. Such advancements are accelerating biomedical research and the development of new protein design and bioengineering methods among many other important biotechnology applications. Here, in this review, we outline the recent advances in protein-centric biomolecular structure and interaction prediction, highlight some major challenges in the field, and discuss potential directions to address them.

Morehead, Alex [Lawrence Berkeley National Laborat↗

Structure of Complex Liquid–Liquid Extraction Organic Phases for Rare Earth Separations

Complex, multicomponent liquids with hierarchical structure and phase transitions are encountered in many natural and industrial processes, including in chemical separations. One notable example is aggregation and organic phase splitting in liquid–liquid extraction (LLE) of metal ions. While these two phenomena that have long been closely associated, a mechanistic link between mesoscale structure and the capacity-limiting organic phase splitting remains elusive due to complexity of these systems. Here, in this study, we combine small-angle X-ray scattering (SAXS), X-ray photon correlation spectroscopy (XPCS), and molecular dynamics simulation to reveal a comprehensive picture of structure at the nano- and mesoscale in these complex solutions. For the representative case of rare earth extraction from an acidic aqueous phase by a malonamide extractant in dodecane, we investigate a wide range of process-relevant extractant and acid concentrations to provide a complete picture of how aggregation depends on composition. We decompose organic phase structure from SAXS into two contributions, which together can capture the scattering at all compositions: composition fluctuations described by the Ornstein–Zernike equation at low wavenumber Q, and nanostructure modeled by a “pre-peak” at intermediate Q. The former contains information about the thermodynamics of demixing, while the latter reflects nanoscopic self-assembly of the extractant and extracted solutes. While fluctuations have typically not been considered in the literature, we find they in fact dominate the total structure for nearly all practical conditions. As only the fluctuations have a strong temperature response, we confirm this attribution with temperature-dependent SAXS measurements, including for extracted europium nitrate complexes. SAXS and XPCS measurements near the critical point find static and dynamic scaling consistent with theory. Overall, this new paradigm for understanding LLE organic phases connects composition, nanoscale, and mesoscale structuring to phase behavior, providing both a comprehensive picture of solution structure and a quantitative link between aggregation and third phase formation.

Peroutka, Allison A. [Argonne National Laboratory ↗

Crystal structure of SSB complexed with inhibitor myricetin

Highlights: • The first inhibitor-complexed crystal structure of SSB was determined. • Two SSB-myricetin interaction modes were found. • Lys7, Arg62, Glu80, and Gly107 in PaSSB were found crucial for forming hydrogen bond to myricetin. Single-stranded DNA-binding protein (SSB) is essential for all DNA-dependent cellular processes. SSB inhibitors have been recently suggested as broad-spectrum antibacterial agents in antibiotic development. In this paper, we report the first inhibitor-complexed crystal structure of SSB from Pseudomonas aeruginosa PAO1 (PaSSB) at 2.68 Å resolution (PDB entry 5YUN). The inhibitor, myricetin, is a flavonol that possesses many pharmacological activities, such as anticancer, anti-inflammatory, and antibacterial properties, and is beneficial for humans. Four monomers of PaSSB and two of myricetins were found per asymmetric unit. Various interactions between myricetin and PaSSB were examined. Among these, four residues in PaSSB, Lys7, Arg62, Glu80, and Gly107 were found crucial for forming hydrogen bond to myricetin. These two myricetins occupy the grooves for ssDNA-binding of SSB that may prevent ssDNA-wrapping and ssDNA-binding stably from SSB. In addition to explaining how SSB can be inhibited, the myricetin–SSB interaction modes in this paper may also provide insights into how myricetin can bind and inhibit proteins on cancer-signaling pathways.

60 APPLIED LIFE SCIENCES↗