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Abstract 2193 A Rieske Catalytic Journey

Journal of Biological Chemistry 2024年第3期300卷 106228-106228页

作者： Jennifer Bridwell-Rabb Jiayi Tian Alejandro Garcia University of Michigan

Rieske oxygenases are characterized by the presence of two metallocenters, a [2Fe-2S] cluster and a mononuclear iron site. This set of metallocenters, in coordination with molecular oxygen, create a high valent Fe-based oxidant that can be used to facilitate monooxygenation, dioxygenation, and other types of chemical reactions. Remarkably, despite this extensive catalytic repertoire, Rieske oxygenases demonstrate exquisite control in differentiating between these reaction types to ensure that only the intended transformation is catalyzed. This precision is demonstrated in a number of biosynthetic pathways that produce medically and industrially relevant natural products, as well as in pathways that degrade xenobiotic compounds. However, the molecular details that enable these enzymes to catalyze site-specific reactions with diverse outcomes remain largely enigmatic. Therefore, in this presentation, I will highlight our progress toward identifying the structural trends that Rieske oxygenases employ to dictate selective reaction outcomes.

关键词： Rieske oxygenases Metalloproteins structure-function relationships Structural Biology Enzymology

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Probing Surface Oxide Formation and Dissolution on/of Ir Single Crystals via X-ray Photoelectron Spectroscopy and Inductively Coupled Plasma Mass Spectrometry

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ACS CATALYSIS 2019年第11期9卷 9859-9869页

作者： Scohy, Marion Abbou, Sofyane Martin, Vincent Gilles, Bruno Sibert, Eric Dubau, Laetitia Maillard, Frederic Univ Savoie Mt Blanc Univ Grenoble Alpes CNRS Grenoble INPLEPMI F-38000 Grenoble France Univ Grenoble Alpes CNRS Grenoble INP SIMAP F-38000 Grenoble France

Gaining fundamental insights into the formation and the stability of surface oxides on iridium (Ir) surfaces is pivotal to oxygen evolution reaction (OER) electrocatalysis. Herein, we examined the potential-dependent structural and chemical changes occurring on planar Ir(111), Ir(210), and nanofaceted Ir(210) single-crystal surfaces using electrochemistry, scanning probe microscopy, X-ray photoelectron spectroscopy, and inductively coupled plasma mass spectrometry. We show that, after polarization in OER conditions, Ir surface atoms feature mixed oxidation states-(0), (+III), and (+IV)-and then enrich into Ir(+IV) due to the dissolution of Ir(+III) species. The rate of surface and near-surface layer enrichment in Ir(+IV) species depends on the modulation mode of the potential (linear potential sweeps vs. potential steps) and is faster on opened surfaces. By combining fits derived from the XPS spectra and OER activity measurements, we found that the OER specific activity varies with the Ir oxidation state and is closely related to the fraction of Ir(+III) species.

关键词： proton-exchange membrane water electrolyzers oxygen evolution reaction iridium single crystal structure-function relationships

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Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase structure and function

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CHEMICAL REVIEWS 2018年第22期118卷 10840-11022页

作者： Adam, Suzanne M. Wijeratne, Gayan B. Rogler, Patrick J. Diaz, Daniel E. Quist, David A. Liu, Jeffrey J. Karlin, Kenneth D. Johns Hopkins Univ Dept Chem Baltimore MD 21218 USA

Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H(+)/4e(-) reduction of dioxygen to water. This process involves a proton coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O-2 and copper-O-2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological 0, reduction.

关键词： inorganic chemistry ATP12A gene Complexes Oxidase Dioxygen hydrogen ions Mitochondria structure-function relationships ATP Synthesis Pathway oxygen SYNTHETICS ATP4A gene Attitude Redox processes proton pump

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Investigation of the role of central metal ion of Cyathus bulleri laccase 1 using guanidinium chloride-induced denaturation

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INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES 2019年第0期132卷 994-1000页

作者： Afreen, Sumbul Idrees, Danish Khera, Radhika Amir, Mohd Hassan, Md Imtaiyaz Mishra, Saroj Indian Inst Technol Delhi Dept Biochem Engn & Biotechnol New Delhi 110016 India Jamia Millia Islamia Ctr Interdisciplinary Res Basic Sci New Delhi 110025 India Jawaharlal Nehru Univ Sch Life Sci New Delhi 110065 India

The structure and folding/unfolding kinetics of Cyathus bulleri laccase 1 (Lcc1), expressed in Pichia pastoris, were analyzed by spectroscopic methods to understand the role of central metal ion. Far UV CD structure analysis revealed major beta-sheet and minor a helical segments present in the Lcc1. A significant change in the spectrum of Lcc1, indicative of unfolding of secondary structures, was observed with increasing concentrations of guanidinium chloride (GdnHCl) during Trp fluorescence, absorption and CD measurements. A similar trend was also noticed for enzyme activity with respect to GdnHCl concentrations. To establish the role of copper ion in the catalytic activity of laccase, a complete removal of copper was carried out and addition of copper was found to restore the structure and activity during the refolding process. The apo form was also reconstituted by addition of zinc ion which restored nearly 84% of enzyme activity, indicating non-essential role of copper in maintaining conformation and activity. Structural studies and inductively coupled plasma mass spectrometry data supported these observations. (C) 2019 Elsevier B.V. All rights reserved.

关键词： Lactase Unfolding/refolding Apoenzyme formation Metal replacement structure-function relationships GdnHCl-induced denaturation

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On the form and bio-mechanics of venom-injection elements

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ACTA BIOMATERIALIA 2019年 85卷 263-271页

作者： Bar-On, Benny Ben Gurion Univ Negev Dept Mech Engn IL-84105 Beer Sheva Israel

A wide variety of animals-from insects to snakes-crucially depend on their ability to inject venom into their target, be it their prey or their predator. To effectively deliver their venom, venomous animals use a specialized biomechanical element whose tip must penetrate through the integument of the target. During this process, the tip of the venom-injection element (VIE) is subject to local forces, which may deform it and cause considerable structural damage to the VIE, with devastating consequences for the survival of the animal or, in the case of eusocial insects, to the colony. Hence, it is plausible that millions of years of evolution have carefully 'shaped' the architecture of VIEs across different taxa toward a similar mechanical function, namely, to effectively resist the mechanical forces exerted on the tip. The present study aims to identify such a common architecture by analyzing the form-function relationships in various biological VIEs. A universal structural modeling, which quantifies the fundamental geometrical characteristics of a wide range of VIEs is constituted, and a theoretical mechanical framework that analytically correlates these characteristics with the material stress fields is introduced. This investigation reveals that the architecture of biological VIEs reduces the magnitude of applied stresses and confines the maximal stress to the near-tip region of the element. The presented analytical approach and modeling can be straightforwardly applied to various other types of bio-mechanical elements and can potentially be employed for developing a new class of microscopic injection elements for bio-medical and engineering applications. Statement of Significance Venomous animals-both vertebrate and invertebrate-use an extremely wide variety of venom-injection elements to incapacitate their prey or predator. Despite the clear differences in their typical dimensions, shapes, and evolutionary paths, all venom-injection elements have evolved to perf

关键词： Bio-mechanics Venom-injection element Mechanics of biomaterials structure-function relationships Analytical modeling

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structure-function relationship during CO₂ methanation over Rh/Al₂O₃ and Rh/SiO₂ catalysts under atmospheric pressure conditions

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CATALYSIS SCIENCE & TECHNOLOGY 2018年第10期8卷 2686-2696页

作者： Martin, Natalia M. Hemmingsson, Felix Wang, Xueting Merte, Lindsay R. Hejral, Uta Gustafson, Johan Skoglundh, Magnus Meira, Debora Motta Dippel, Ann-Christin Gutowski, Olof Bauer, Matthias Carlsson, Per-Anders Chalmers Univ Technol Competence Ctr Catalysis Dept Chem & Chem Engn S-41296 Gothenburg Sweden Chalmers Univ Technol Dept Phys Div Chem Phys S-41296 Gothenburg Sweden Lund Univ Div Synchrotron Radiat Res S-22100 Lund Sweden ESRF F-38043 Grenoble France DESY D-22607 Hamburg Germany Paderborn Univ Dept Chem D-33098 Paderborn Germany

The effect of the support material and chemical state of Rh in Rh/A(2)O(3) and Rh/SiO2 model catalysts during CO2 hydrogenation were studied by a combined array of in situ characterisation techniques including diffuse reflectance infrared Fourier transform spectroscopy, energy-dispersive X-ray absorption spectroscopy and high-energy X-ray diffraction at 250-350 degrees C and atmospheric pressure. CO2 methanation proceeds via intermediate formation of adsorbed CO species on metallic Rh, likely followed by their hydrogenation to methane. The linearly-bonded CO species is suggested to be a more active precursor in the hydrogenation compared to the bridge-bonded species, which seems to be related to particle size effects: for larger particles mainly the formation of inactive bridge-bonded CO species takes place. Further, analysis of the chemical state of Rh under the reaction conditions reveal a minor formation of RhOx from dissociation of CO2, which is a consequence of the increased activity observed over the Rh/Al2O3 catalyst.

关键词： Atmospheric Pressure SUPPORT MATERIALS methanation Carbon Dioxide structure-function relationships Catalysts Hydrogenation

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Subnanometer structure and function from ion beams through complex fluidics to fluorescent particles

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LAB ON A CHIP 2018年第1期18卷 139-152页

作者： Liao, Kuo-Tang Schumacher, Joshua Lezec, Henri J. Stavis, Samuel M. NIST Ctr Nanoscale Sci & Technol Gaithersburg MD 20899 USA Univ Maryland Maryland Nanoctr College Pk MD 20742 USA

The vertical dimensions of complex nanostructures determine the functions of diverse nanotechnologies. In this paper, we investigate the unknown limits of such structure-function relationships at subnanometer scales. We begin with a quantitative evaluation of measurement uncertainty from atomic force microscopy, which propagates through our investigation from ion beam fabrication to fluorescent particle characterization. We use a focused beam of gallium ions to subtractively pattern silicon surfaces, and silicon nitride and silicon dioxide films. Our study of material responses quantifies the atomic limits of forming complex topographies with subnanometer resolution of vertical features over a wide range of vertical and lateral dimensions. Our results demonstrate the underutilized capability of this standard system for rapid prototyping of subnanometer structures in hard materials. We directly apply this unprecedented dimensional control to fabricate nanofluidic devices for the analytical separation of colloidal nanoparticles by size exclusion. Optical microscopy of single nanoparticles within such reference materials establishes a subnanometer limit of the fluidic manipulation of particulate matter and enables critical-dimension particle tracking with subnanometer accuracy. After calibrating for optical interference within our multifunctional devices, which also enables device metrology and integrated spectroscopy, we reveal an unexpected relationship between nanoparticle size and emission intensity for common fluorescent probes. Emission intensity increases supervolumetrically with nanoparticle diameter and then decreases as nanoparticles with different diameters photobleach to similar values of terminal intensity. We propose a simple model to empirically interpret these surprising results. Our investigation enables new control and study of structure-function relationships at subnanometer scales.

关键词： structure-function relationships silicon dioxide Quantitative Evaluation measurement uncertainty Hard materials vertical Ions Nanoparticles Fluidics Vertical separation Light interference focused beam rapid prototyping Ion beams

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Automated Glycan Assembly: A Perspective

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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2019年第14期141卷 5581-5592页

作者： Guberman, Monica Seeberger, Peter H. Max Planck Inst Colloids & Interfaces Dept Biomol Syst Muhlenberg 1 D-14476 Potsdam Germany Free Univ Berlin Dept Chem & Biochem Arnimalle 22 D-14195 Berlin Germany

The intrinsic complexity of carbohydrate structures has hampered access to pure glycans and hence impeded progress in the glycosciences. Automated Glycan Assembly (AGA) has facilitated the procurement of synthetic glycans, to be used in diagnostics, vaccine development, enzyme characterization and structure function relationship studies. A general approach for obtaining complex glycans from mammalian, bacterial, fungal and plant classes provides molecular tools for glycobiology research. Recent advances in AGA technology pave the way for the production of novel carbohydrate materials. This perspective describes the state-of-the art of AGA and aspects of the technology where additional improvements are needed.

关键词： AGA gene Technology glycobiology structure-function relationships Polysaccharides Arts Automation carbohydrate structure Perspective Procurement

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Environmental and spatial variables determine the taxonomic but not functional structure patterns of microbial communities in alpine grasslands

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SCIENCE OF THE TOTAL ENVIRONMENT 2019年 654卷 960-968页

作者： Wang, Xiao-Bo Yao, Jing Zhang, Hai-Yang Wang, Xiao-Guang Li, Kai-Hui Lu, Xiao-Tao Wang, Zheng-Wen Zhou, Ji-Zhong Han, Xing-Guo Chinese Acad Sci Inst Appl Ecol Key Lab Forest Ecol & Management Erguna Forest Steppe Ecotone Res Stn Shenyang 110016 Liaoning Peoples R China Northeast Normal Univ Key Lab Vegetat Ecol Changchun Jilin Peoples R China Chinese Acad Sci Inst Bot Beijing 100093 Peoples R China Dalian Minzu Univ Coll Environm & Resources Dalian 116600 Peoples R China Chinese Acad Sci Xinjiang Inst Ecol & Geog Key Lab Biogeog & Bioresource Arid Land Urumqi 830011 Peoples R China Univ Oklahoma Inst Environm Genom Dept Microbiol & Plant Biol Norman OK 73019 USA

There is considerable debate regarding how the taxonomic diversity of microbial communities relates to the functional diversity across space while similar questions have been explored in macro-organism communities. Here, we investigated the taxonomic and functional diversity patterns of soil microbial communities by coupling the data obtained from marker genes sequencing and functional gene surveys. Meanwhile, we evaluated the relative effects of environment and geographic distance on shaping these patterns in alpine grasslands of northern China. Although the taxonomic diversity and composition of microbial communities varied across sites, we found no consistent changes in the functional structure. Both the environmental factors and geographic distance concurrently affected the taxonomic diversity patterns but they had no effects on the spatial variations in functional genes. The functional alpha diversity was weakly correlated to the taxonomic alpha diversity across sites. Moreover, we found no significant relationship between the taxonomic and functional composition similarity among microbial communities. Together, our results provide evidence that spatial variation in microbial functions could be independent of their variations in taxonomic diversity. Even the drivers of spatial variations in the functional structure could be totally different from those of taxonomic variations such as environmental differences and dispersal limitation. Our findings suggest that spatial variations of microbial function structure within a community would not follow the variations of taxonomic structures due to different drivers between both of them over space. (C) 2018 Elsevier B.V. All rights reserved.

关键词： Spatial distribution Soil microorganisms Microbial diversity functional genes structure-function relationships Drylands

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structure and function of high Arctic pelagic, particle-associated and benthic bacterial communities

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ENVIRONMENTAL MICROBIOLOGY 2018年第8期20卷 2941-2954页

作者： Balmonte, John Paul Teske, Andreas Arnosti, Carol Univ N Carolina Dept Marine Sci 3202 Venable Hall Chapel Hill NC 27599 USA

Arctic marine microbes are affected by environmental changes that may ultimately influence their functions in carbon cycling. Here, we investigated in concert the structure and enzymatic activities of pelagic, particle-associated and benthic bacterial communities in the central Arctic Ocean, and used these data to evaluate microbial structure-function relationships. Our findings showed influences of hydrographic conditions and particle association on community composition, and sharp pelagic-benthic contrasts. In addition to community compositional differences, regional and depth-related patterns in enzymatic activities were observed. Peptide hydrolysis rates were highest in surface waters, especially at ice-free and first year ice-covered regions, and decreased with depth. While the range of hydrolysed polysaccharides showed varying geographic patterns, particles often showed a wider spectrum of polysaccharide hydrolase activities. Summed benthic peptidase rates differed across stations but showed similar proportions of individual enzyme activities. Analysing for potential linkages between structure and function after subtracting the effect of environmental conditions revealed no direct link, indicating functional redundancy to carry out peptide hydrolysis among pelagic microbes. Thus, while community composition and activities are influenced by environmental conditions, bacterial functional redundancy suggests that compositional shifts - in response to the changing Arctic - may have complex and less predictable functional consequences than previously anticipated. (c) 2018 Society for Applied Microbiology and John Wiley & Sons Ltd

关键词： Community composition Microbes functional redundancy structure-function relationships Arctic Ocean Environmental conditions Environmental changes Enzymatic activity surface water Arctic Polysaccharides

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