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At least 181 records · Page 10

Assembly and Repair of the Photosystem II Reaction Center

This project investigated the biochemical and biophysical mechanisms governing assembly and repair of Photosystem II (PSII), the membrane protein complex responsible for solar-driven water oxidation in oxygenic photosynthesis. The work focused on three integrated areas: (1) protein–protein interactions that facilitate PSII assembly in cyanobacterial biogenesis centers, (2) the chemical mechanism of photo-assembly of the Mn 4 CaO 5 oxygen-evolving complex (OEC), and (3) mechanisms that target PSII reaction centers for degradation and repair in photosynthetic organisms. Using electron paramagnetic resonance spectroscopy, protein biochemistry, molecular genetics, quantitative mass spectrometry, and computational modeling, the project demonstrated that proton release events limit early steps of OEC assembly and that chloride and calcium ions facilitate Mn oxidation and intermediate stabilization. Complementary studies identified chaperone recruitment mechanisms in cyanobacterial PSII biogenesis centers and translation and protease factors involved in PSII turnover in Chlamydomonas. Together, these results establish proton management and coordinated protein quality control as central design principles in PSII assembly and repair and provide mechanistic insight relevant to biological and artificial photosynthetic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electrochemical approaches for chemical and biological analysis on Mars

Obtaining in situ chemical data from planetary bodies such as Mars or Europa can present significant challenges. The one analytical technique that has many of the requisite characteristics to meet such a challenge is electroanalysis. Described here are three electroanalytical devices designed for in situ geochemical and biological analysis on Mars. The Mars Environmental Compatibility Assessment (MECA) was built and flight qualified for the now cancelled NASA Mars 2001 Lander. Part of MECA consisted of four "cells" containing arrays of electrochemical based sensors for measuring the ionic species in soil samples. A next-generation MECA, the Robotic Chemical Analysis Laboratory (RCAL), uses a carousel-type system to allow for greater customization of analytical procedures. A second instrument, proposed as part of the 2007 CryoScout mission, consists of a flow-through inorganic chemical analyzer (MICA). CryoScout is a torpedo-like device designed for subsurface investigation of the stratigraphic climate record embedded in Mars' north polar cap. As the CryoScout melts its way through the ice cap, MICA will collect and analyze the meltwater for a variety of inorganics and chemical parameters. By analyzing the chemistry locked in the layers of dust, salt, and ice, geologists will be able to determine the recent history of climate, water, and atmosphere on Mars and link it to the past. Finally, electroanalysis shows its abilities in the detection of possible microorganism on Mars or elsewhere in the solar system. To identify an unknown microorganism, one that may not even use Earth-type biochemistry, requires a detection scheme which makes minimal assumptions and looks for the most general features. Recent work has demonstrated that the use of an array of electrochemical sensors which monitors the changes in a solution via electrical conductivity, pH, and ion selective electrodes, can be used to detect minute chemical perturbations caused by the growth of bacteria and with the correct methodology provide unamibiguous detection of such life forms.

Non-NASA Center↗

Robotic automation of droplet microfluidics

Droplet microfluidics enables powerful analytic capabilities but often requires workflows involving macro- and microfluidic processing steps that are cumbersome to perform manually. Here, we demonstrate the automation of droplet microfluidics with commercial fluid-handling robotics. The workflows incorporate common microfluidic devices including droplet generators, mergers, and sorters and utilize the robot's native capabilities for thermal control, incubation, and plate scanning. The ability to automate microfluidic devices using commercial fluid handling will speed up the integration of these methods into biological workflows.

59 BASIC BIOLOGICAL SCIENCES↗

The Search for Chiral Asymmetry as a Potential Biosignature in Samples from Mars

The search for evidence of extraterrestrial life in our solar system has been guided by our under-standing of terrestrial biology and its associated biosignatures. The observed homochirality in all life on Earth, that is, the predominance of “left-handed” or L-amino acids and “right-handed” or D-sugars, is a unique property of life that is crucial for molecular recognition, enzymatic function, information storage and structure, and is thought to be a prerequisite for the origin or early evolution of life. Therefore, the detection of L- or D-excesses of chiral amino acids or sugars could be a powerful indicator of extant or extinct life on Mars or other habitable environments in our solar system. However, studies of primitive meteorites have revealed that they contain extraterrestrial amino acids and sugar acids with large enantiomeric excesses (60% and higher) that resulted from non-biological processes [1], complicating the use of chiral asymmetry by itself as a definitive biosignature. The exploration of habitable environments on Mars, including an assessment of the preservation potential for complex organics of either abiotic or biological origin, is an objective of both current and future Mars missions. Now with the unambiguous detection of indigenous organic matter in sedimentary rocks by the Sample Analysis at Mars (SAM) instrument suite on Mars [2-5], NASA’s Curiosity rover has found evidence of the preservation of potential chemical biosignatures in the martian near surface. Although amino acids have not yet been identified by in situ measurements on Mars [5], indigenous achiral amino acids have been identified in one martian meteorite [6]. It is expected that amino acid racemization would be very slow and any chiral or isotopic signatures from an extinct martian biota could be preserved for billions of years, given the extremely cold and dry surface conditions [7]. The ESA/Roscosmos ExoMars mission scheduled for launch next year includes the Rosalind Franklin rover designed to acquire samples from a depth of ~2 m and deliver them to a suite of instruments, including the Mars Organic Molecule Analyzer (MOMA). The MOMA instrument contains a wet chemistry experiment designed specifically for the detection of amino acids and measurement of their enantiomeric compositions [8]. The complexity and limited duration of spaceflight operations, and the known analytical challenges associated with in situ extraction and characterization of trace reduced organic com-pounds in ancient rocks, make it challenging to determine the origins of martian organic matter found to date. Coordinated state-of-the-art laboratory measurements of returned samples from Mars that include spatially resolved chemical, mineralogical, bulk and molecule-specific isotopic, and enantiomeric measurements will be required to firmly establish whether the complex organic matter detected on Mars derives from bio-tic or abiotic processes. Ultimately, Mars Sample Return of rock cores collected by NASA’s Perseverance rover may be our best chance of identifying chemical biosignatures, including any chiral amino acid asymmetry resulting from a past or present martian biota, if one ever existed on Mars. Here we review our current knowledge of the distributions, and enantiomeric and isotopic com-positions of amino acids found in meteorites compared to terrestrial biochemistry. We also propose a set of measurement criteria that should be used to help establish the sources of any amino acids detected in samples returned from Mars using state-of-the-art gas and liquid chromatography mass spectrometry techniques [1].

D P Glavin↗

The Search for Chiral Asymmetry as a Potential Biosignature in Samples from Mars

The search for evidence of extraterrestrial life in our solar system is currently guided by our understanding of terrestrial biology and its associated biosignatures. The observed homochirality in all life on Earth, that is, the predominance of “left-handed” or L-amino acids and “right-handed” or D-sugars, is a unique property of life that is crucial for molecular recognition, enzymatic function, information storage and structure and is thought to be a prerequisite for the origin or early evolution of life. Therefore, the detection of L- or D-enantiomeric excesses of chiral amino acids and sugars could be a powerful indicator of extant or extinct life on Mars or other habitable environments in our solar system. The exploration of habitable environments on Mars, including an assessment of the preservation potential for complex organics of either abiotic or biological origin, remains a key goal of both current and future Mars missions. Now with the unambiguous detection of indigenous organic matter in sedimentary rocks on Mars [1-3], NASA’s Curiosity rover has significantly advanced our understanding of the preservation of potential chemical biosignatures in the martian near surface. Although amino acids have not yet been identified by in situ measurements on Mars, if they were present, it is expected that amino acid hydrolysis and racemization would be very slow and any chiral or isotopic signatures from an extinct martian biota could be preserved for billions of years, given the extremely cold and dry surface conditions [4]. One of ESA’s Rosalind Franklin rover payload instruments called the Mars Organic Molecule Analyzer (MOMA) includes a wet chemistry package capable of measuring the enantiomeric ratios of any chiral amino acids present at part-per-million concentrations or higher [5]. The complexity and limited duration of spaceflight operations and the known analytical challenges associated with in situ extraction and characterization of trace reduced organic compounds in ancient rocks make it challenging to determine the origins of martian organic matter found to date. Coordinated state-of-the-art laboratory measurements of returned samples from Mars that include spatially resolved chemical, mineralogical, and isotopic studies and molecule-specific isotopic and enantiomeric measurements will be required to firmly establish whether the complex organic matter detected on Mars comes from biotic or abiotic sources. Ultimately, sample return may be our best chance of identifying chemical biosignatures from a past or present martian biota, if one ever existed on Mars. NASA’s Perseverance rover will collect dozens of surface sample cores for possible future return to Earth by NASA and ESA. Here we review our current knowledge of the distributions and enantiomeric and isotopic compositions of non-biological amino acids found in meteorites compared to terrestrial biochemistry and propose a set of measurement criteria that should be used to help establish the origin of any chiral asymmetry detected in samples from Mars [6].

Daniel P Glavin↗

Parallels between enzyme catalysis, electrocatalysis, and photoelectrosynthesis

Catalysts are central to accelerating chemistry in biology and technology. In biochemistry, the relationship between the velocity of an enzymatic reaction and the concentration of chemical substrates is described via the Michaelis-Menten model. Additionally, the modeling and benchmarking of synthetic molecular electrocatalysts are also well developed. However, such efforts have not been as rigorously extended to photoelectrosynthetic reactions, where, in addition to chemical substrates and charge carriers, light is a required reagent. In this perspective, we draw parallels between concepts involving enzyme catalytic efficiency, the benchmarking of molecular electrocatalysts, and the performance of photoelectrosynthetic assemblies, while highlighting key differences, assumptions, and limitations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Biosynthesis of Haloterpenoids in Red Algae via Microbial-like Type I Terpene Synthases

Red algae or seaweeds produce highly distinctive halogenated terpenoid compounds, including the pentabromochlorinated monoterpene halomon that was once heralded as a promising anticancer agent. The first dedicated step in the biosynthesis of these natural product molecules is expected to be catalyzed by terpene synthase (TS) enzymes. Recent work has demonstrated an emerging class of type I TSs in red algal terpene biosynthesis. However, only one such enzyme from a notoriously haloterpenoid-producing red alga (Laurencia pacifica) has been functionally characterized and the product structure is not related to halogenated terpenoids. Herein, we report 10 new type I TSs from the red algae Portieria hornemannii, Plocamium pacificum, L. pacifica, and Laurencia subopposita that produce a diversity of halogenated mono- and sesquiterpenes. Here we used a combination of genome sequencing, terpenoid metabolomics, in vitro biochemistry, and bioinformatics to establish red algal TSs in all four species, including those associated with the selective production of key halogenated terpene precursors myrcene, trans-β-ocimene, and germacrene D-4-ol. These results expand on a small but growing number of characterized red algal TSs and offer insight into the biosynthesis of iconic halogenated algal compounds that are not without precedence elsewhere in biology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The promising role of proteomes and metabolomes in defining the single-cell landscapes of plants

The plant community has a strong track-record of RNA sequencing technology deployment, which combined with the recent advent of spatial platforms (e.g., 10x genomics), has resulted in an explosion of outstanding single cell and nuclei datasets that can be put in an in situ context within tissues (e.g., a cell atlas)1. In the genomics era, application of proteomics technologies in the plant sciences has always trailed behind that of RNA sequencing technologies, largely due to accessibility, ease-of-use and access to expertise along with depth of analysis benefits. On the other hand, the use of early analytical tools for characterizing small molecules (metabolites) from plant systems predates nucleic acid sequencing and proteomics analysis2, as the search for plant-based natural products has played a significant role in improving human health throughout history. However, the employment of proteomics and metabolomics assays for characterizing plant cell processes now remains significantly behind transcriptional approaches, even though both provide a direct functional readout of cell states and phenotypes.

Anderton, Christopher R. [BATTELLE (PACIFIC NW LAB↗

A Radiation Chemistry Code Based on the Greens Functions of the Diffusion Equation

Ionizing radiation produces several radiolytic species such as.OH, e-aq, and H. when interacting with biological matter. Following their creation, radiolytic species diffuse and chemically react with biological molecules such as DNA. Despite years of research, many questions on the DNA damage by ionizing radiation remains, notably on the indirect effect, i.e. the damage resulting from the reactions of the radiolytic species with DNA. To simulate DNA damage by ionizing radiation, we are developing a step-by-step radiation chemistry code that is based on the Green's functions of the diffusion equation (GFDE), which is able to follow the trajectories of all particles and their reactions with time. In the recent years, simulations based on the GFDE have been used extensively in biochemistry, notably to simulate biochemical networks in time and space and are often used as the "gold standard" to validate diffusion-reaction theories. The exact GFDE for partially diffusion-controlled reactions is difficult to use because of its complex form. Therefore, the radial Green's function, which is much simpler, is often used. Hence, much effort has been devoted to the sampling of the radial Green's functions, for which we have developed a sampling algorithm This algorithm only yields the inter-particle distance vector length after a time step; the sampling of the deviation angle of the inter-particle vector is not taken into consideration. In this work, we show that the radial distribution is predicted by the exact radial Green's function. We also use a technique developed by Clifford et al. to generate the inter-particle vector deviation angles, knowing the inter-particle vector length before and after a time step. The results are compared with those predicted by the exact GFDE and by the analytical angular functions for free diffusion. This first step in the creation of the radiation chemistry code should help the understanding of the contribution of the indirect effect in the formation of DNA damage and double-strand breaks.

Plante, Ianik↗

Biochemistry of aerobic biological methane oxidation

Methanotrophic bacteria represent a potential route to methane utilization and mitigation of methane emissions. In the first step of their metabolic pathway, aerobic methanotrophs use methane monooxygenases (MMOs) to activate methane, oxidizing it to methanol. There are two types of MMOs: a particulate, membrane-bound enzyme (pMMO) and a soluble, cytoplasmic enzyme (sMMO). The two MMOs are completely unrelated, with different architectures, metal cofactors, and mechanisms. The more prevalent of the two, pMMO, is copper-dependent, but the identity of its copper active site remains unclear. By contrast, sMMO uses a diiron active site, the catalytic cycle of which is well understood. Here we review the current state of knowledge for both MMOs, with an emphasis on recent developments and emerging hypotheses. In addition, we discuss obstacles to developing expression systems, which are needed to address outstanding questions and to facilitate future protein engineering efforts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Engineering advancements in microfluidic systems for enhanced mixing at low Reynolds numbers

Mixing within micro- and millichannels is a pivotal element across various applications, ranging from chemical synthesis to biomedical diagnostics and environmental monitoring. The inherent low Reynolds number flow in these channels often results in a parabolic velocity profile, leading to a broad residence time distribution. Achieving efficient mixing at such small scales presents unique challenges and opportunities. This review encompasses various techniques and strategies to evaluate and enhance mixing efficiency in these confined environments. It explores the significance of mixing in micro- and millichannels, highlighting its relevance for enhanced reaction kinetics, homogeneity in mixed fluids, and analytical accuracy. We discuss various mixing methodologies that have been employed to get a narrower residence time distribution. The role of channel geometry, flow conditions, and mixing mechanisms in influencing the mixing performance are also discussed. Various emerging technologies and advancements in microfluidic devices and tools specifically designed to enhance mixing efficiency are highlighted. We emphasize the potential applications of micro- and millichannels in fields of nanoparticle synthesis, which can be utilized for biological applications. Additionally, the prospects of machine learning and artificial intelligence are offered toward incorporating better mixing to achieve precise control over nanoparticle synthesis, ultimately enhancing the potential for applications in these miniature fluidic systems.

Biochemistry & Molecular Biology↗

Detection of non‐native species formed during fibrillization of the myocilin olfactomedin domain

Abstract Glaucoma is a group of neurodegenerative diseases that together are the leading cause of irreversible blindness worldwide. Myocilin‐associated glaucoma is an inherited form of this disease, caused by intracellular aggregation of misfolded mutant myocilin. In vitro, the myocilin C‐terminal olfactomedin domain (OLF), the relevant domain for glaucoma pathogenesis, can be driven to form amyloid‐like fibrils under mild conditions. Here we characterize a species present during in vitro fibrillization. Purified OLF was subjected to fibrillization at concentrations required for downstream electron microscopy imaging and NMR spectroscopy. Additional biophysical techniques, including analytical ultracentrifugation and X‐ray crystallography, were employed to further characterize the multicomponent mixture. Negative stain transmission electron microscopy (TEM) shows a non‐native species reminiscent of known prefibrillar oligomers from other amyloid systems, NMR indicates a minor population of partially misfolded species is present in solution, and cryo‐EM imaging shows two‐dimensional protein arrays. The predominant soluble species remaining in solution after the fibril reaction is natively folded, as evidenced by X‐ray crystallography. In summary, after incubating OLF under fibrillization‐promoting conditions, there is a heterogeneous mixture consisting of soluble folded protein, mature amyloid‐like fibrils, and partially misfolded intermediate species that at present belie additional molecular detail. The characterization of OLF fibrillar species illustrates the challenges associated with developing a comprehensive understanding of the fibrillization process for large, non‐model amyloidogenic proteins.

Scelsi, Hailee F. [School of Chemistry and Biochem↗

Cell-free synthetic biology for natural product biosynthesis and discovery

Natural products have applications as biopharmaceuticals, agrochemicals, and other high-value chemicals. However, there are challenges in isolating natural products from their native producers (e.g. bacteria, fungi, plants). In many cases, synthetic chemistry or heterologous expression must be used to access these important molecules. The biosynthetic machinery to generate these compounds is found within biosynthetic gene clusters, primarily consisting of the enzymes that biosynthesise a range of natural product classes (including, but not limited to ribosomal and nonribosomal peptides, polyketides, and terpenoids). Cell-free synthetic biology has emerged in recent years as a bottom-up technology applied towards both prototyping pathways and producing molecules. Recently, it has been applied to natural products, both to characterise biosynthetic pathways and produce new metabolites. This review discusses the core biochemistry of cell-free synthetic biology applied to metabolite production and critiques its advantages and disadvantages compared to whole cell and/or chemical production routes. Specifically, we review the advances in cell-free biosynthesis of ribosomal peptides, analyse the rapid prototyping of natural product biosynthetic enzymes and pathways, highlight advances in novel antimicrobial discovery, and discuss the rising use of cell-free technologies in industrial biotechnology and synthetic biology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Support for the 2024 American Conference on Theoretical Chemistry (ACTC) (Final Report)

Funds are requested in support of the 2024 American Conference on Theoretical Chemistry. Funds are being requested from the Department of Energy in support of conference registration fees for graduate student and post-doctoral researcher registration fees. This conference will be held in North Carolina, and between 200 and 250 participants are expected. This is the major North American meeting of theoretical chemists, showcasing diverse developments in all aspects of modern theory, including methods development and applications. Applications span all aspects of chemistry, biochemistry, and materials science, including important applications to energy science. The conference will include four days of seminars and poster sessions. As well as serving as a meeting ground for sharing scientific developments and discoveries, the meeting also serves as a locus for mentoring and career development involving younger scientists. The meeting will be chaired by Prof. David Beratan of Duke University, and he will be assisted by other faculty from the region: Profs. Weitao Yang (Duke), Patrick Charbonneau (Duke), Yosuke Kanai (University of North Carolina - Chapel Hill), Zhiyue Lu (University of North Carolina - Chapel Hill), and Elena Jakubikova (North Carolina State University). This group will form a conference commitee that will define thematic topics for the conference, will invite speakers, and will assist with running the conference.

14 SOLAR ENERGY↗

Structural and functional insights into the interaction between the bacteriophage T4 DNA processing proteins gp32 and Dda

Abstract Bacteriophage T4 is a classic model system for studying the mechanisms of DNA processing. A key protein in T4 DNA processing is the gp32 single-stranded DNA-binding protein. gp32 has two key functions: it binds cooperatively to single-stranded DNA (ssDNA) to protect it from nucleases and remove regions of secondary structure, and it recruits proteins to initiate DNA processes including replication and repair. Dda is a T4 helicase recruited by gp32, and we purified and crystallized a gp32–Dda–ssDNA complex. The low-resolution structure revealed how the C-terminus of gp32 engages Dda. Analytical ultracentrifugation analyses were consistent with the crystal structure. An optimal Dda binding peptide from the gp32 C-terminus was identified using surface plasmon resonance. The crystal structure of the Dda–peptide complex was consistent with the corresponding interaction in the gp32–Dda–ssDNA structure. A Dda-dependent DNA unwinding assay supported the structural conclusions and confirmed that the bound gp32 sequesters the ssDNA generated by Dda. The structure of the gp32–Dda–ssDNA complex, together with the known structure of the gp32 body, reveals the entire ssDNA binding surface of gp32. gp32–Dda–ssDNA complexes in the crystal are connected by the N-terminal region of one gp32 binding to an adjacent gp32, and this provides key insights into this interaction.

Biochemistry & Molecular Biology↗

Isobutanol production freed from biological limits using synthetic biochemistry

Cost competitive conversion of biomass-derived sugars into biofuel will require high yields, high volumetric productivities and high titers. Suitable production parameters are hard to achieve in cell-based systems because of the need to maintain life processes. As a result, next-generation biofuel production in engineered microbes has yet to match the stringent cost targets set by petroleum fuels. Removing the constraints imposed by having to maintain cell viability might facilitate improved production metrics. Here, we report a cell-free system in a bioreactor with continuous product removal that produces isobutanol from glucose at a maximum productivity of 4 g L –1 h –1 , a titer of 275 g L –1 and 95% yield over the course of nearly 5 days. These production metrics exceed even the highly developed ethanol fermentation process. Our results suggest that moving beyond cells has the potential to expand what is possible for bio-based chemical production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of native four-repeat satellite III sequence with non-canonical base interactions

Abstract Tandem-repetitive DNA (where two or more DNA bases are repeated numerous times) can adopt non-canonical secondary structures. Many of these structures are implicated in important biological processes. Human Satellite III (HSat3) is enriched for tandem repeats of the sequence ATGGA and is located in pericentromeric heterochromatin in many human chromosomes. Here, we investigate the secondary structure of the four-repeat HSat3 sequence 5′-ATGGA ATGGA ATGGA ATGGA-3′ using X-ray crystallography, NMR, and biophysical methods. Circular dichroism spectroscopy, thermal stability, native PAGE, and analytical ultracentrifugation indicate that this sequence folds into a monomolecular hairpin with non-canonical base pairing and B-DNA characteristics at concentrations below 0.9 mM. NMR studies at 0.05–0.5 mM indicate that the hairpin is likely folded-over into a compact structure with high dynamics. Crystallographic studies at 2.5 mM reveal an antiparallel self-complementary duplex with the same base pairing as in the hairpin, extended into an infinite polymer. The non-canonical base pairing includes a G–G intercalation sandwiched by sheared A–G base pairs, leading to a cross-strand four guanine stack, so called guanine zipper. The guanine zippers are spaced throughout the structure by A–T/T–A base pairs. Our findings lend further insight into recurring structural motifs associated with the HSat3 and their potential biological functions.

59 BASIC BIOLOGICAL SCIENCES↗

Quantum Simulation of Polarized Light-Induced Electron Transfer with a Trapped-Ion Qutrit System

Electron transfer within and between molecules is crucial in chemistry, biochemistry, and energy science. Here this study describes a quantum simulation method that explores the influence of light polarization on electron transfer between two molecules. By implementing precise and coherent control among the quantum states of trapped atomic ions, we can induce quantum dynamics that mimic the electron-transfer dynamics in molecules. We use three-level systems (qutrits), rather than traditional two-level systems (qubits), to enhance the simulation efficiency and realize high-fidelity simulations of electron-transfer dynamics. We treat the quantum interference between the electron coupling pathways from a donor with two degenerate excited states to an acceptor and analyze the transfer efficiency. We also examine the potential error sources that enter the quantum simulations. The trapped-ion systems have favorable scalings with system size compared to those of classical computers, promising access to richer electron-transfer simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗