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Orotate phosphoribosyltransferase (OPRT) catalyzes the reaction that adds the pyrimidine base to the ribose in the penultimate step of the de novo biosynthesis of pyrimidine nucleotides. The OPRT structure consists of an obligate dimer, conserved throughout the phosphoribosyltransferase family. Here, we describe the structural characterization of Burkholderia cenocepacia OPRT (BcOPRT), both by X-ray crystallography and Cryo electron microscopy (Cryo-EM). While the known dimer is present in the structure of BcOPRT, a putative hexameric form was also observed by multiple methods. Analyses by chromatography, Cryo-EM, and kinetics indicate that both dimeric and hexameric forms of this enzyme are present together in solution. Comparison of the kinetics of the native protein and two variants, which were specifically designed to prevent hexamerization, reveal that only the hexameric form is enzymatically active. Collectively, these data suggest that BcOPRT may use oligomerization to control overall enzymatic activity, thus contributing to the local regulation of pyrimidine biosynthesis in this organism. 

This release makes a new command line interface (CLI) available for CaltechDATA. It allows you to create and edit records in CaltechDATA using the API entirely from the command line. You can create metadata entirely on the command line, or utilize a README template https://github.com/caltechlibrary/caltechdata_api/blob/main/templates/README.md, or use the previously supported json file https://github.com/caltechlibrary/caltechdata_api/blob/main/example.json. As we bring online new storage options online for Caltech, the CLI will be updated and enhanced. 

Kinetoplast DNA is a complex nanoscale network, naturally assembled from thousands of interconnected DNA circles within the mitochondrion of certain parasites. Despite the relevance of this molecule to parasitology and... 

The plane-wave pseudopotential (PW-PP) formalism is widely used for the first-principles electronic structure calculation of extended periodic systems. The PW-PP approach has also been adapted for real-time time-dependent density functional theory (RT-TDDFT) to investigate time-dependent electronic dynamical phenomena. In this work, we detail recent advances in the PW-PP formalism for RT-TDDFT, particularly how maximally localized Wannier functions (MLWFs) are used to accelerate simulations using the exact exchange. We also discuss several related developments, including an anti-Hermitian correction for the time-dependent MLWFs (TD-MLWFs) when a time-dependent electric field is applied, the refinement procedure for TD-MLWFs, comparison of the velocity and length gauge approaches for applying an electric field, and elimination of long-range electrostatic interaction, as well as usage of a complex absorbing potential for modeling isolated systems when using the PW-PP formalism. 

Various technologies and strategies have been proposed to decarbonize the chemical industry. Assessing the decarbonization, environmental, and economic implications of these technologies and strategies is critical to identifying pathways to a more sustainable industrial future. This study reviews recent advancements and integration of systems analysis models, including process analysis, material flow analysis, life cycle assessment, techno-economic analysis, and machine learning. These models are categorized based on analytical methods and application scales (i.e., micro-, meso-, and macroscale) for promising decarbonization technologies (e.g., carbon capture, storage, and utilization, biomass feedstock, and electrification) and circular economy strategies. Incorporating forward-looking, data-driven approaches into existing models allows for optimizing complex industrial systems and assessing future impacts. Although advances in industrial ecology–, economic-, and planetary boundary–based modeling support a more holistic systems-level assessment, more effects are needed to consider impacts on ecosystems. Effective applications of these advanced, integrated models require cross-disciplinary collaborations across chemical engineering, industrial ecology, and economics. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering , Volume 15 is June 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates. 

The isothermal compressibility (i.e., related to the asymptotic number variance) of equilibrium liquid water as a function of temperature is minimal under near-ambient conditions. This anomalous non-monotonic temperature dependence is due to a balance between thermal fluctuations and the formation of tetrahedral hydrogen-bond networks. Since tetrahedrality is a many-body property, it will also influence the higher-order moments of density fluctuations, including the skewness and kurtosis. To gain a more complete picture, we examine these higher-order moments that encapsulate many-body correlations using a recently developed, advanced platform for local density fluctuations. We study an extensive set of simulated phases of water across a range of temperatures (80–1600 K) with various degrees of tetrahedrality, including ice phases, equilibrium liquid water, supercritical water, and disordered nonequilibrium quenches. We find clear signatures of tetrahedrality in the higher-order moments, including the skewness and excess kurtosis, which scale for all cases with the degree of tetrahedrality. More importantly, this scaling behavior leads to non-monotonic temperature dependencies in the higher-order moments for both equilibrium and non-equilibrium phases. Specifically, under near-ambient conditions, the higher-order moments vanish most rapidly for large length scales, and the distribution quickly converges to a Gaussian in our metric. However, under non-ambient conditions, higher-order moments vanish more slowly and hence become more relevant, especially for improving information-theoretic approximations of hydrophobic solubility. The temperature non-monotonicity that we observe in the full distribution across length scales could shed light on water’s nested anomalies, i.e., reveal new links between structural, dynamic, and thermodynamic anomalies. 

Programmable self-assembly has seen an explosion in the diversity of synthetic crystalline materials, but developing strategies that target “self-limiting” assemblies has remained a challenge. Among these, self-closing structures, in which the local curvature defines the finite global size, are prone to polymorphism due to thermal bending fluctuations, a problem that worsens with increasing target size. Here, we show that assembly complexity can be used to eliminate this source of polymorphism in the assembly of tubules. Using many distinct components, we prune the local density of off-target geometries, increasing the selectivity of the tubule width and helicity to nearly 100%. We further show that by reducing the design constraints to target either the pitch or the width alone, fewer components are needed to reach complete selectivity. Combining experiments with theory, we reveal an economical limit, which determines the minimum number of components required to create arbitrary assembly sizes with full selectivity.