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  • Biochemistry
  • Chemical Engineering
  • Computational Chemistry and Molecular Modeling
  • Deutschland
  • American Association for the Advancement of Science (AAAS)  (162)
  • Springer  (28)
  • Springer Nature  (10)
  • Boston, MA : Springer  (5)
  • De Gruyter  (3)
  • Universität Göttingen,Abteilung Bodenphysik
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  • 1
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    Springer Nature | Springer Fachmedien Wiesbaden
    Publication Date: 2024-03-29
    Description: Dieser Open-Access-Sammelband hinterfragt, wie sich internationale Kulturzusammenarbeit zwischen Ländern unterschiedlicher Kultursysteme und -traditionen erreichen lässt. In Deutschland ist Auswärtige Kulturpolitik von dem Gedanken geleitet, dass globale Herausforderungen Multilateralismus erfordern. Im chinesischen Diskurs dagegen finden andere Kernbegriffe wie z.B. „Tianxia“ Verwendung, die im nicht-chinesischen Kontext einer Interpretation bedürfen. Um der Differenz – aber auch den Gemeinsamkeiten – auf den Grund zu gehen, untersuchen Wissenschaftler*innen und Praktiker*innen aus China und Deutschland Selbst- und Fremdwahrnehmungen sowie Kooperationen in kulturellen Begegnungen. Auf diese Weise sollen Grundlagen für ein besseres gegenseitiges Verständnis sowie für kulturelle Kooperation zwischen beiden Ländern ermöglicht werden.
    Keywords: Auswärtige Kulturpolitik ; Kulturaustausch ; Forschungszusammenarbeit ; Tianxia ; Deutschland ; Globale Herausforderung ; China ; bic Book Industry Communication::J Society & social sciences::JP Politics & government ; bic Book Industry Communication::J Society & social sciences::JF Society & culture: general::JFC Cultural studies ; bic Book Industry Communication::J Society & social sciences::JP Politics & government::JPS International relations ; bic Book Industry Communication::J Society & social sciences::JF Society & culture: general::JFF Social issues & processes::JFFS Globalization ; thema EDItEUR::J Society and Social Sciences::JP Politics and government ; thema EDItEUR::J Society and Social Sciences::JB Society and culture: general::JBC Cultural and media studies::JBCC Cultural studies ; thema EDItEUR::J Society and Social Sciences::JP Politics and government::JPS International relations ; thema EDItEUR::G Reference, Information and Interdisciplinary subjects::GT Interdisciplinary studies::GTQ Globalization
    Language: German
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  • 2
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    De Gruyter | De Gruyter
    Publication Date: 2022-11-22
    Description: This volume includes lectures and discussions from the Conference of the Association of German Constitutional Lawyers in Speyer from 7 to 10 October 2015.
    Keywords: Deutschland ; Verfassung ; Rechtsordnung ; bic Book Industry Communication::L Law::LN Laws of Specific jurisdictions::LND Constitutional & administrative law ; bic Book Industry Communication::L Law::LN Laws of Specific jurisdictions::LNU Taxation & duties law
    Language: German
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  • 3
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    Springer Nature | Springer Fachmedien Wiesbaden
    Publication Date: 2022-11-19
    Description: Die Open-Access-Publikation präsentiert umfangreiche empirische Analysen zu Halte- und Bleibeorientierung Geflüchteter und richtet den Blick dabei besonders auf die Situation der ländlichen Regionen Deutschlands. Migrations- und Integrationsforschung in Deutschland war bislang überwiegend auf Großstädte ausgerichtet. Durch den vermehrten Zuzug geflüchteter Menschen seit 2014 sehen sich jedoch auch Kleinstädte und Dörfer in ländlichen Regionen verstärkt mit Aufgaben der Aufnahme und Integration von Geflüchteten konfrontiert. Ziel dieses Buches ist es, empirisch fundiert zu beantworten, unter welchen Voraussetzungen und wie humanitäres Engagement und ländliche Entwicklung erfolgreich verbunden werden können und wie dies von Politik und Zivilgesellschaft positiv beeinflusst werden kann.
    Keywords: Geflüchtete ; Migration ; Migrationspolitik ; Migrationsforschung ; Integration ; Integrationsbereitschaft ; ländliche Räume ; Deutschland ; Mobilität ; lokale Integrations- und Migrationspolitik ; Aufnahmegesellschaft ; Bleibeorientierung ; soziales Wohlbefinden ; German Politics ; bic Book Industry Communication::J Society & social sciences::JP Politics & government::JPP Public administration ; bic Book Industry Communication::J Society & social sciences::JP Politics & government ; bic Book Industry Communication::J Society & social sciences::JP Politics & government::JPH Political structure & processes ; bic Book Industry Communication::J Society & social sciences::JH Sociology & anthropology::JHB Sociology
    Language: German
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  • 4
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    De Gruyter | De Gruyter
    Publication Date: 2024-04-05
    Description: The essential principles of green chemistry are the use of renewable raw materials, highly efficient catalysts and green solvents linked with energy efficiency and process optimization in real-time. Experts from different fields show, how to examine all levels from the molecular elementary steps up to the design and operation of an entire plant for developing novel and efficient production processes.
    Keywords: Process Engineering ; Chemical Engineering ; Technical Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry ; thema EDItEUR::R Earth Sciences, Geography, Environment, Planning::RN The environment ; thema EDItEUR::R Earth Sciences, Geography, Environment, Planning::RN The environment::RNU Sustainability ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TD Industrial chemistry and manufacturing technologies::TDC Industrial chemistry and chemical engineering ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TG Mechanical engineering and materials::TGM Materials science ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TQ Environmental science, engineering and technology
    Language: English
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  • 5
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    Springer Nature | Springer
    Publication Date: 2024-04-14
    Description: This open access book highlights concepts discussed at two international conferences that brought together world-renowned scientists to advance the science of potassium (K) recommendations for crops. There was general agreement that the potassium recommendations currently in general use are oversimplified, outdated, and jeopardize soil, plant, and human health. Accordingly, this book puts forward a significantly expanded K cycle that more accurately depicts K inputs, losses and transformations in soils. This new cycle serves as both the conceptual basis for the scientific discussions in this book and a framework upon which to build future improvements. Previously used approaches are critically reviewed and assessed, not only for their relevance to future enhancements, but also for their use as metrics of sustainability. An initial effort is made to link K nutrition in crops and K nutrition in humans. The book offers an invaluable asset for graduate students, educators, industry scientists, data scientists, and advanced agronomists.
    Keywords: Agriculture ; Plant Biochemistry ; Soil Science & Conservation ; Applied Ecology ; Soil Science ; Bioavailable Potassium ; Fertilizer Management ; Plant Nutrition ; Potash ; Soil Chemistry ; Sustainability ; Open access ; Agricultural science ; Botany & plant sciences ; Biochemistry ; Sedimentology & pedology ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TV Agriculture and farming::TVB Agricultural science ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PST Botany and plant sciences ; thema EDItEUR::R Earth Sciences, Geography, Environment, Planning::RB Earth sciences::RBG Geology, geomorphology and the lithosphere::RBGB Sedimentology and pedology ; thema EDItEUR::R Earth Sciences, Geography, Environment, Planning::RN The environment::RNC Applied ecology
    Language: English
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  • 6
    Publication Date: 2024-04-05
    Description: Biochemistry laboratory manual for undergraduates – an inquiry based approach by Gerczei and Pattison is the first textbook on the market that uses a highly relevant model, antibiotic resistance, to teach seminal topics of biochemistry and molecular biology while incorporating the blossoming field of bioinformatics. The novelty of this manual is the incorporation of a student-driven real real-life research project into the undergraduate curriculum. Since students test their own mutant design, even the most experienced students remain engaged with the process, while the less experienced ones get their first taste of biochemistry research. Inclusion of a research project does not entail a limitation: this manual includes all classic biochemistry techniques such as HPLC or enzyme kinetics and is complete with numerous problem sets relating to each topic.
    Keywords: QD415-436 ; Molecular Biology ; Biochemistry ; Laboratory Manual ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSB Biochemistry
    Language: English
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  • 7
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    Springer Nature | Springer
    Publication Date: 2024-04-14
    Description: This book is open access under a CC BY 4.0 license. By 2050, human population is expected to reach 9.7 billion. The demand for increased food production needs to be met from ever reducing resources of land, water and other environmental constraints. Rice remains the staple food source for a majority of the global populations, but especially in Asia where ninety percent of rice is grown and consumed. Climate change continues to impose abiotic and biotic stresses that curtail rice quality and yields. Researchers have been challenged to provide innovative solutions to maintain, or even increase, rice production. Amongst them, the ‘green super rice’ breeding strategy has been successful for leading the development and release of multiple abiotic and biotic stress tolerant rice varieties. Recent advances in plant molecular biology and biotechnologies have led to the identification of stress responsive genes and signaling pathways, which open up new paradigms to augment rice productivity. Accordingly, transcription factors, protein kinases and enzymes for generating protective metabolites and proteins all contribute to an intricate network of events that guard and maintain cellular integrity. In addition, various quantitative trait loci associated with elevated stress tolerance have been cloned, resulting in the detection of novel genes for biotic and abiotic stress resistance. Mechanistic understanding of the genetic basis of traits, such as N and P use, is allowing rice researchers to engineer nutrient-efficient rice varieties, which would result in higher yields with lower inputs. Likewise, the research in micronutrients biosynthesis opens doors to genetic engineering of metabolic pathways to enhance micronutrients production. With third generation sequencing techniques on the horizon, exciting progress can be expected to vastly improve molecular markers for gene-trait associations forecast with increasing accuracy. This book emphasizes on the areas of rice science that attempt to overcome the foremost limitations in rice production. Our intention is to highlight research advances in the fields of physiology, molecular breeding and genetics, with a special focus on increasing productivity, improving biotic and abiotic stress tolerance and nutritional quality of rice. ; Up-to-date contributions by experts from international research centers and universities Provides practical knowledge and strong scientific foundation on rice biotechnology All-in-one resource for current advances in rice breeding Open Access
    Keywords: Agriculture ; Plant Breeding/Biotechnology ; Plant Genetics and Genomics ; Plant Physiology ; Nutrition ; Plant Biotechnology ; Plant Genetics ; Open Access ; Rice Biotechnologies ; Rice Breeding ; biotic stress tolerance ; abiotic stress tolerance ; Submergence tolerance ; Biofortification ; Marker Assisted and Forward Breeding ; disease resistance ; CRISPR/CAS ; Agricultural science ; Botany & plant sciences ; Biotechnology ; Genetics (non-medical) ; Biochemistry ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TV Agriculture and farming::TVB Agricultural science ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PST Botany and plant sciences ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSB Biochemistry
    Language: English
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  • 8
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    Springer Nature | Springer
    Publication Date: 2024-04-11
    Description: This open access book reports on a pilot project aiming at collecting information on the socio-ecological risks that could arise in the event of an uncontrolled spread of genetically engineered organisms into the environment. The researchers will, for instance, be taking a closer look at genetically engineered oilseed rape, genetically engineered olive flies as well as plants and animals with so-called gene drives. The book mainly adresses researchers.
    Keywords: Ecotoxicology ; Environmental Health ; Environmental Management ; Genetically modified organisms ; Socio-ecological risk ; Olive flies ; Environmental spread ; Open Access book ; Environmental science, engineering & technology ; Biochemistry ; Environmental medicine ; Environmental management, ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TQ Environmental science, engineering and technology ; thema EDItEUR::M Medicine and Nursing::MK Medical specialties, branches of medicine::MKV Environmental medicine ; thema EDItEUR::R Earth Sciences, Geography, Environment, Planning::RN The environment::RNF Environmental management
    Language: English
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  • 9
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    Springer Nature
    Publication Date: 2024-04-01
    Description: This open access book is the proceedings of the 14th International Symposium on Biomineralization (BIOMIN XIV) held in 2017 at Tsukuba. Over the past 45 years, biomineralization research has unveiled details of the characteristics of the nano-structure of various biominerals; the formation mechanism of this nano-structure, including the initial stage of crystallization; and the function of organic matrices in biominerals, and this knowledge has been applied to dental, medical, pharmaceutical, materials, agricultural and environmental sciences and paleontology. As such, biomineralization is an important interdisciplinary research area, and further advances are expected in both fundamental and applied research.
    Keywords: Life sciences ; Biochemistry ; Mineralogy ; Inorganic chemistry ; Cell biology ; Biomaterials ; Dentistry ; thema EDItEUR::M Medicine and Nursing::MK Medical specialties, branches of medicine::MKE Dentistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNK Inorganic chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNV Chemistry of minerals, crystals and gems ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSB Biochemistry ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSF Cellular biology (cytology) ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TG Mechanical engineering and materials::TGM Materials science
    Language: English
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  • 10
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    Springer Nature
    Publication Date: 2024-04-01
    Description: This open access book presents recent advances in the pure sciences that are of significance in the quest for alternatives to the use of animals in research and describes a variety of practical applications of the three key guiding principles for the more ethical use of animals in experiments – replacement, reduction, and refinement, collectively known as the 3Rs. Important examples from across the world of implementation of the 3Rs in the testing of cosmetics, chemicals, pesticides, and biologics, including vaccines, are described, with additional information on relevant regulations. The coverage also encompasses emerging approaches to alternative tests and the 3Rs. The book is based on the most informative contributions delivered at the Asian Congress 2016 on Alternatives and Animal Use in the Life Sciences. It will be of value for those working in R&D, for graduate students, and for educators in various fields, including the pharmaceutical and cosmetic sciences, pharmacology, toxicology, and animal welfare. The free, open access distribution of Alternatives to Animal Testing is enabled by the Creative Commons Attribution license in International version 4: CC BY 4.0.
    Keywords: Medicine ; Pharmacology ; Biochemistry ; Animal welfare ; thema EDItEUR::M Medicine and Nursing::MK Medical specialties, branches of medicine::MKG Pharmacology ; thema EDItEUR::M Medicine and Nursing::MZ Veterinary medicine ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSB Biochemistry
    Language: English
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  • 11
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    Springer Nature | Springer
    Publication Date: 2024-04-05
    Description: This open access book offers a comprehensive overview of the role and potential of microorganisms in the degradation and preservation of cultural materials (e.g. stone, metals, graphic documents, textiles, paintings, glass, etc.). Microorganisms are a major cause of deterioration in cultural artefacts, both in the case of outdoor monuments and archaeological finds. This book covers the microorganisms involved in biodeterioration and control methods used to reduce their impact on cultural artefacts. Additionally, the reader will learn more about how microorganisms can be used for the preservation and protection of cultural artefacts through bio-based and eco-friendly materials. New avenues for developing methods and materials for the conservation of cultural artefacts are discussed, together with concrete advances in terms of sustainability, effectiveness and toxicity, making the book essential reading for anyone interested in microbiology and the preservation of cultural heritage.
    Keywords: Microbiology ; Cultural Heritage ; Microbial Ecology ; Microbial Genetics and Genomics ; Enzymology ; Applied Microbiology ; Microbial Genetics ; Industrial Microbiology ; Open Access ; Restoration ; Conservation ; Biodeterioration ; Bioweathering ; Bioremediation ; Biocleaning ; Biotechnology ; Green Chemistry ; Fungi ; Bacteria ; Artwork ; Antimicrobial protection ; Biocides ; Microbiology (non-medical) ; Cultural studies ; Social & cultural history ; Ecological science, the Biosphere ; Genetics (non-medical) ; Biochemistry ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical) ; thema EDItEUR::J Society and Social Sciences::JB Society and culture: general::JBC Cultural and media studies::JBCC Cultural studies ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAF Ecological science, the Biosphere ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSB Biochemistry
    Language: English
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  • 12
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    Springer Nature | Springer Fachmedien Wiesbaden
    Publication Date: 2024-03-29
    Description: Dieses open access-Buch analysiert den Zusammenhang von Berufsorientierung und politischer Bildung von Jugendlichen. Der Anspruch der Mündigkeitsbildung stellt die Ausgangsposition für die Vorstellungsforschung subjektiver Sinnbilder über die Berufs- und Arbeitswelt von Jugendlichen in der Sekundarstufe I dar. Dabei zeichnen sich Unterschiede in den Vorstellungen entlang der Trennlinien von sozioökonomischem Hintergrund, Herkunft, Geschlecht und Schulform ab. Die empirische Studie liefert wichtige Erkenntnisse zu den Vorstellungen und Handlungsmöglichkeiten von Schüler*innen und hilft zu verstehen, wovon diese abhängen und welche didaktischen Ansätze sich für die Berufsorientierung ableiten lassen.
    Keywords: Berufsorientierung ; Arbeitswelt ; Berufsvorstellungen ; Bildungsvorstellungen ; Jugendliche ; Didaktik der politischen Bildung ; Politische Bildung ; Schule ; Unterricht ; Sekundarstufe I ; Empirische Sozialforschung ; Biografie ; Gesellschaft ; Migrationshintergrund ; Deutschland ; Österreich ; German Politics ; open access ; bic Book Industry Communication::J Society & social sciences::JP Politics & government::JPA Political science & theory ; bic Book Industry Communication::J Society & social sciences::JH Sociology & anthropology::JHB Sociology ; bic Book Industry Communication::J Society & social sciences::JP Politics & government::JPB Comparative politics ; bic Book Industry Communication::J Society & social sciences::JP Politics & government::JPQ Central government::JPQB Central government policies ; bic Book Industry Communication::J Society & social sciences::JN Education::JNF Educational strategies & policy ; bic Book Industry Communication::J Society & social sciences::JN Education ; thema EDItEUR::J Society and Social Sciences::JP Politics and government::JPA Political science and theory ; thema EDItEUR::J Society and Social Sciences::JH Sociology and anthropology::JHB Sociology ; thema EDItEUR::J Society and Social Sciences::JP Politics and government::JPB Comparative politics ; thema EDItEUR::J Society and Social Sciences::JP Politics and government::JPQ Central / national / federal government::JPQB Central / national / federal government policies ; thema EDItEUR::J Society and Social Sciences::JN Education::JNF Educational strategies and policy ; thema EDItEUR::J Society and Social Sciences::JN Education
    Language: German
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  • 13
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    Springer Nature | Springer Berlin Heidelberg
    Publication Date: 2024-04-01
    Description: This Open Access volume explains how major nuclear and radiological emergencies (NREs) can have implications at local, national and international level. The response to NREs requires a competent decision-making structure, clear communication and effective information exchange. National veterinary services have the responsibility to plan, design and manage animal production system in their countries. These activities cover animal health, animal movement control, production control and improvement, and control of the products of animal origin before their placement on the market. Release of radionuclides after NREs can cause substantial contamination in the animal production systems. Critical responsibility of veterinary authorities is therefore to prevent such contamination, establish early response mechanisms to mitigate the consequences and prevent placement of contaminated products of animal origin on the market for human consumption. This work summarizes the critical technical points for effective management of NREs for national veterinary services.
    Keywords: Veterinary Medicine/Veterinary Science ; Public Health ; Emergency Services ; Animal Ecology ; Nutrition ; Veterinary Science ; Ecology ; Nuclear and Radiological Emergencies ; Radiological Contamination ; Animal Production Systems ; Disaster Management ; Open Access ; Veterinary medicine ; Public health & preventive medicine ; Accident & emergency medicine ; Zoology & animal sciences ; Biochemistry ; thema EDItEUR::M Medicine and Nursing::MZ Veterinary medicine ; thema EDItEUR::M Medicine and Nursing::MB Medicine: general issues::MBN Public health and preventive medicine ; thema EDItEUR::M Medicine and Nursing::MK Medical specialties, branches of medicine::MKP Accident and emergency medicine ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSV Zoology and animal sciences ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSB Biochemistry
    Language: English
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  • 14
    Publication Date: 2018-12-14
    Description: Primordial sequence signatures in modern proteins imply ancestral origins tracing back to simple peptides. Although short peptides seldom adopt unique folds, metal ions might have templated their assembly into higher-order structures in early evolution and imparted useful chemical reactivity. Recapitulating such a biogenetic scenario, we have combined design and laboratory evolution to transform a zinc-binding peptide into a globular enzyme capable of accelerating ester cleavage with exacting enantiospecificity and high catalytic efficiency ( k cat / K M ~ 10 6 M –1 s –1 ). The simultaneous optimization of structure and function in a naïve peptide scaffold not only illustrates a plausible enzyme evolutionary pathway from the distant past to the present but also proffers exciting future opportunities for enzyme design and engineering.
    Keywords: Biochemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 15
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-31
    Description: Cryo–electron microscopy, or simply cryo-EM, refers mainly to three very different yet closely related techniques: electron crystallography, single-particle cryo-EM, and electron cryotomography. In the past few years, single-particle cryo-EM in particular has triggered a revolution in structural biology and has become a newly dominant discipline. This Review examines the fascinating story of its start and evolution over the past 40-plus years, delves into how and why the recent technological advances have been so groundbreaking, and briefly considers where the technique may be headed in the future.
    Keywords: Biochemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 16
    Publication Date: 2018-08-31
    Description: Riback et al . (Reports, 13 October 2017, p. 238) used small-angle x-ray scattering (SAXS) experiments to infer a degree of compaction for unfolded proteins in water versus chemical denaturant that is highly consistent with the results from Förster resonance energy transfer (FRET) experiments. There is thus no "contradiction" between the two methods, nor evidence to support their claim that commonly used FRET fluorophores cause protein compaction.
    Keywords: Biochemistry
    Print ISSN: 0036-8075
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  • 17
    Publication Date: 2018-08-31
    Description: Best et al . claim that we provide no convincing basis to assert that a discrepancy remains between FRET and SAXS results on the dimensions of disordered proteins under physiological conditions. We maintain that a clear discrepancy is apparent in our and other recent publications, including results shown in the Best et al . comment. A plausible origin is fluorophore interactions in FRET experiments.
    Keywords: Biochemistry
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  • 18
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-28
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-05
    Keywords: Biochemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 20
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-12
    Keywords: Biochemistry
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  • 21
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-12-21
    Keywords: Biochemistry
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  • 22
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-12-21
    Keywords: Biochemistry
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 23
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-02
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 24
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-12-14
    Keywords: Biochemistry
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  • 25
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-19
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 26
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-16
    Keywords: Biochemistry
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-30
    Keywords: Biochemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 28
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-30
    Keywords: Biochemistry
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  • 29
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-10
    Keywords: Biochemistry
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  • 30
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-10
    Description: The Hedgehog (Hh) pathway involved in development and regeneration is activated by the extracellular binding of Hh to the membrane receptor Patched (Ptch). We report the structures of human Ptch1 alone and in complex with the N-terminal domain of human Sonic hedgehog (ShhN) at resolutions of 3.9 and 3.6 angstroms, respectively, as determined by cryo–electron microscopy. Ptch1 comprises two interacting extracellular domains, ECD1 and ECD2, and 12 transmembrane segments (TMs), with TMs 2 to 6 constituting the sterol-sensing domain (SSD). Two steroid-shaped densities are resolved in both structures, one enclosed by ECD1/2 and the other in the membrane-facing cavity of the SSD. Structure-guided mutational analysis shows that interaction between ShhN and Ptch1 is steroid-dependent. The structure of a steroid binding–deficient Ptch1 mutant displays pronounced conformational rearrangements.
    Keywords: Biochemistry
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  • 31
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-31
    Description: Super-resolution microscopy has overcome a long-held resolution barrier—the diffraction limit—in light microscopy and enabled visualization of previously invisible molecular details in biological systems. Since their conception, super-resolution imaging methods have continually evolved and can now be used to image cellular structures in three dimensions, multiple colors, and living systems with nanometer-scale resolution. These methods have been applied to answer questions involving the organization, interaction, stoichiometry, and dynamics of individual molecular building blocks and their integration into functional machineries in cells and tissues. In this Review, we provide an overview of super-resolution methods, their state-of-the-art capabilities, and their constantly expanding applications to biology, with a focus on the latter. We will also describe the current technical challenges and future advances anticipated in super-resolution imaging.
    Keywords: Biochemistry
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  • 32
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-05-11
    Keywords: Biochemistry
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  • 33
    Publication Date: 2018-11-02
    Description: Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo–electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(–6), SHL(–5), SHL(–2), and SHL(–1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(–1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation.
    Keywords: Biochemistry
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  • 34
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-09
    Keywords: Biochemistry
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  • 35
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-09
    Keywords: Biochemistry
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  • 36
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-09
    Keywords: Biochemistry
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  • 37
    Publication Date: 2018-11-09
    Description: We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. Cryo–electron microscopy structures of six designs are close to the computational design models. The filament building blocks are idealized repeat proteins, and thus the diameter of the filaments can be systematically tuned by varying the number of repeat units. The assembly and disassembly of the filaments can be controlled by engineered anchor and capping units built from monomers lacking one of the interaction surfaces. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials.
    Keywords: Biochemistry
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  • 38
    Publication Date: 2018-11-16
    Description: Membrane proteins reside in lipid bilayers and are typically extracted from this environment for study, which often compromises their integrity. In this work, we ejected intact assemblies from membranes, without chemical disruption, and used mass spectrometry to define their composition. From Escherichia coli outer membranes, we identified a chaperone-porin association and lipid interactions in the β-barrel assembly machinery. We observed efflux pumps bridging inner and outer membranes, and from inner membranes we identified a pentameric pore of TonB, as well as the protein-conducting channel SecYEG in association with F 1 F O adenosine triphosphate (ATP) synthase. Intact mitochondrial membranes from Bos taurus yielded respiratory complexes and fatty acid–bound dimers of the ADP (adenosine diphosphate)/ATP translocase (ANT-1). These results highlight the importance of native membrane environments for retaining small-molecule binding, subunit interactions, and associated chaperones of the membrane proteome.
    Keywords: Biochemistry
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  • 39
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-29
    Description: The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo–electron microscopy structures of the Saccharomyces cerevisiae pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, respectively. In the pre-B complex, the duplex between the 5' splice site (5'SS) and U1 small nuclear RNA (snRNA) is recognized by Yhc1, Luc7, and the Sm ring. In the B complex, U1 small nuclear ribonucleoprotein is dissociated, the 5'-exon–5'SS sequences are translocated near U6 snRNA, and three B-specific proteins may orient the precursor messenger RNA. In both complexes, U6 snRNA is anchored to loop I of U5 snRNA, and the duplex between the branch point sequence and U2 snRNA is recognized by the SF3b complex. Structural analysis reveals the mechanism of assembly and activation for the yeast spliceosome.
    Keywords: Biochemistry
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  • 40
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-30
    Keywords: Biochemistry
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  • 41
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-06
    Keywords: Biochemistry
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  • 42
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-06
    Keywords: Biochemistry
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  • 43
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-06
    Description: Small carbocycles are structurally rigid and possess high intrinsic energy due to their ring strain. These features lead to broad applications but also create challenges for their construction. We report the engineering of hemeproteins that catalyze the formation of chiral bicyclobutanes, one of the most strained four-membered systems, via successive carbene addition to unsaturated carbon-carbon bonds. Enzymes that produce cyclopropenes, putative intermediates to the bicyclobutanes, were also identified. These genetically encoded proteins are readily optimized by directed evolution, function in Escherichia coli , and act on structurally diverse substrates with high efficiency and selectivity, providing an effective route to many chiral strained structures. This biotransformation is easily performed at preparative scale, and the resulting strained carbocycles can be derivatized, opening myriad potential applications.
    Keywords: Biochemistry
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  • 44
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-13
    Keywords: Biochemistry
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  • 45
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-23
    Keywords: Biochemistry
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  • 46
    Publication Date: 2018-03-23
    Description: Metal homeostasis poses a major challenge to microbes, which must acquire scarce elements for core metabolic processes. Methanobactin, an extensively modified copper-chelating peptide, was one of the earliest natural products shown to enable microbial acquisition of a metal other than iron. We describe the core biosynthetic machinery responsible for the characteristic posttranslational modifications that grant methanobactin its specificity and affinity for copper. A heterodimer comprising MbnB, a DUF692 family iron enzyme, and MbnC, a protein from a previously unknown family, performs a dioxygen-dependent four-electron oxidation of the precursor peptide (MbnA) to install an oxazolone and an adjacent thioamide, the characteristic methanobactin bidentate copper ligands. MbnB and MbnC homologs are encoded together and separately in many bacterial genomes, suggesting functions beyond their roles in methanobactin biosynthesis.
    Keywords: Biochemistry
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  • 47
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-06
    Keywords: Biochemistry
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  • 48
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-30
    Keywords: Biochemistry
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  • 49
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-30
    Description: High resilience to mechanical stress is key when pathogens adhere to their target and initiate infection. Using atomic force microscopy–based single-molecule force spectroscopy, we explored the mechanical stability of the prototypical staphylococcal adhesin SdrG, which targets a short peptide from human fibrinogen β. Steered molecular dynamics simulations revealed, and single-molecule force spectroscopy experiments confirmed, the mechanism by which this complex withstands forces of over 2 nanonewtons, a regime previously associated with the strength of a covalent bond. The target peptide, confined in a screwlike manner in the binding pocket of SdrG, distributes forces mainly toward the peptide backbone through an intricate hydrogen bond network. Thus, these adhesins can attach to their target with exceptionally resilient mechanostability, virtually independent of peptide side chains.
    Keywords: Biochemistry
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  • 50
    Publication Date: 2018-04-06
    Description: It has been hypothesized that SMC protein complexes such as condensin and cohesin spatially organize chromosomes by extruding DNA into large loops. We directly visualized the formation and processive extension of DNA loops by yeast condensin in real time. Our findings constitute unambiguous evidence for loop extrusion. We observed that a single condensin complex is able to extrude tens of kilobase pairs of DNA at a force-dependent speed of up to 1500 base pairs per second, using the energy of adenosine triphosphate hydrolysis. Condensin-induced loop extrusion was strictly asymmetric, which demonstrates that condensin anchors onto DNA and reels it in from only one side. Active DNA loop extrusion by SMC complexes may provide the universal unifying principle for genome organization.
    Keywords: Biochemistry
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  • 51
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-13
    Description: The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo–electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60 S ) during 7 S -to-5.8 S rRNA processing. The cofactors of the nuclear exosome are sandwiched between the ribonuclease core complex (Exo-10) and the remodeled "foot" structure of the pre-60 S particle, which harbors the 5.8 S rRNA precursor. The exosome-associated helicase Mtr4 recognizes the preribosomal substrate by docking to specific sites on the 25 S rRNA, captures the 3' extension of the 5.8 S rRNA, and channels it toward Exo-10. The structure elucidates how the exosome forms a structural and functional unit together with its massive pre-60 S substrate to process rRNA during ribosome maturation.
    Keywords: Biochemistry
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  • 52
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-15
    Keywords: Biochemistry
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  • 53
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-29
    Keywords: Biochemistry
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  • 54
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-07-13
    Keywords: Biochemistry
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  • 55
    Publication Date: 2018-06-15
    Description: Photosystems I and II convert solar energy into the chemical energy that powers life. Chlorophyll a photochemistry, using red light (680 to 700 nm), is near universal and is considered to define the energy "red limit" of oxygenic photosynthesis. We present biophysical studies on the photosystems from a cyanobacterium grown in far-red light (750 nm). The few long-wavelength chlorophylls present are well resolved from each other and from the majority pigment, chlorophyll a. Charge separation in photosystem I and II uses chlorophyll f at 745 nm and chlorophyll f (or d) at 727 nm, respectively. Each photosystem has a few even longer-wavelength chlorophylls f that collect light and pass excitation energy uphill to the photochemically active pigments. These photosystems function beyond the red limit using far-red pigments in only a few key positions.
    Keywords: Biochemistry
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  • 56
    Publication Date: 2018-02-23
    Description: Oligomeric proteins assemble with exceptional selectivity, even in the presence of closely related proteins, to perform their cellular roles. We show that most proteins related by gene duplication of an oligomeric ancestor have evolved to avoid hetero-oligomerization and that this correlates with their acquisition of distinct functions. We report how coassembly is avoided by two oligomeric small heat-shock protein paralogs. A hierarchy of assembly, involving intermediates that are populated only fleetingly at equilibrium, ensures selective oligomerization. Conformational flexibility at noninterfacial regions in the monomers prevents coassembly, allowing interfaces to remain largely conserved. Homomeric oligomers must overcome the entropic benefit of coassembly and, accordingly, homomeric paralogs comprise fewer subunits than homomers that have no paralogs.
    Keywords: Biochemistry
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  • 57
    Publication Date: 2018-02-23
    Description: Transcriptionally repressive histone H3 lysine 27 methylation by Polycomb repressive complex 2 (PRC2) is essential for cellular differentiation and development. Here we report cryo–electron microscopy structures of human PRC2 in a basal state and two distinct active states while in complex with its cofactors JARID2 and AEBP2. Both cofactors mimic the binding of histone H3 tails. JARID2, methylated by PRC2, mimics a methylated H3 tail to stimulate PRC2 activity, whereas AEBP2 interacts with the RBAP48 subunit, mimicking an unmodified H3 tail. SUZ12 interacts with all other subunits within the assembly and thus contributes to the stability of the complex. Our analysis defines the complete architecture of a functionally relevant PRC2 and provides a structural framework to understand its regulation by cofactors, histone tails, and RNA.
    Keywords: Biochemistry
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  • 58
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-01-12
    Description: Transient receptor potential melastatin (TRPM) cation channels are polymodal sensors that are involved in a variety of physiological processes. Within the TRPM family, member 8 (TRPM8) is the primary cold and menthol sensor in humans. We determined the cryo–electron microscopy structure of the full-length TRPM8 from the collared flycatcher at an overall resolution of ~4.1 ångstroms. Our TRPM8 structure reveals a three-layered architecture. The amino-terminal domain with a fold distinct among known TRP structures, together with the carboxyl-terminal region, forms a large two-layered cytosolic ring that extensively interacts with the transmembrane channel layer. The structure suggests that the menthol-binding site is located within the voltage-sensor–like domain and thus provides a structural glimpse of the design principle of the molecular transducer for cold and menthol sensation.
    Keywords: Biochemistry
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  • 59
    Publication Date: 2018-01-12
    Description: Transient receptor potential (TRP) melastatin 4 (TRPM4) is a widely expressed cation channel associated with a variety of cardiovascular disorders. TRPM4 is activated by increased intracellular calcium in a voltage-dependent manner but, unlike many other TRP channels, is permeable to monovalent cations only. Here we present two structures of full-length human TRPM4 embedded in lipid nanodiscs at ~3-angstrom resolution, as determined by single-particle cryo–electron microscopy. These structures, with and without calcium bound, reveal a general architecture for this major subfamily of TRP channels and a well-defined calcium-binding site within the intracellular side of the S1-S4 domain. The structures correspond to two distinct closed states. Calcium binding induces conformational changes that likely prime the channel for voltage-dependent opening.
    Keywords: Biochemistry
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  • 60
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-01-19
    Keywords: Biochemistry
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  • 61
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-01-19
    Description: Invertebrates rely on Dicer to cleave viral double-stranded RNA (dsRNA), and Drosophila Dicer-2 distinguishes dsRNA substrates by their termini. Blunt termini promote processive cleavage, while 3' overhanging termini are cleaved distributively. To understand this discrimination, we used cryo–electron microscopy to solve structures of Drosophila Dicer-2 alone and in complex with blunt dsRNA. Whereas the Platform-PAZ domains have been considered the only Dicer domains that bind dsRNA termini, unexpectedly, we found that the helicase domain is required for binding blunt, but not 3' overhanging, termini. We further showed that blunt dsRNA is locally unwound and threaded through the helicase domain in an adenosine triphosphate–dependent manner. Our studies reveal a previously unrecognized mechanism for optimizing antiviral defense and set the stage for the discovery of helicase-dependent functions in other Dicers.
    Keywords: Biochemistry
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  • 62
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-02-03
    Keywords: Biochemistry
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  • 63
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-02-03
    Keywords: Biochemistry
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  • 64
    Publication Date: 2018-02-03
    Description: Oligosaccharyltransferase (OST) is an essential membrane protein complex in the endoplasmic reticulum, where it transfers an oligosaccharide from a dolichol-pyrophosphate–activated donor to glycosylation sites of secretory proteins. Here we describe the atomic structure of yeast OST determined by cryo–electron microscopy, revealing a conserved subunit arrangement. The active site of the catalytic STT3 subunit points away from the center of the complex, allowing unhindered access to substrates. The dolichol-pyrophosphate moiety binds to a lipid-exposed groove of STT3, whereas two noncatalytic subunits and an ordered N-glycan form a membrane-proximal pocket for the oligosaccharide. The acceptor polypeptide site faces an oxidoreductase domain in stand-alone OST complexes or is immediately adjacent to the translocon, suggesting how eukaryotic OSTs efficiently glycosylate a large number of polypeptides before their folding.
    Keywords: Biochemistry
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  • 65
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-02-03
    Description: Splicing by the spliceosome involves branching and exon ligation. The branching reaction leads to the formation of the catalytic step I spliceosome (C complex). Here we report the cryo–electron microscopy structure of the human C complex at an average resolution of 4.1 angstroms. Compared with the Saccharomyces cerevisiae C complex, the human complex contains 11 additional proteins. The step I splicing factors CCDC49 and CCDC94 (Cwc25 and Yju2 in S. cerevisiae , respectively) closely interact with the DEAH-family adenosine triphosphatase/helicase Prp16 and bridge the gap between Prp16 and the active-site RNA elements. These features, together with structural comparison of the human C and C* complexes, provide mechanistic insights into ribonucleoprotein remodeling and allow the proposition of a working mechanism for the C-to-C* transition.
    Keywords: Biochemistry
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  • 66
    Publication Date: 2018-08-31
    Description: Editors at Science requested our input on the above discussion (comment by Best et al . and response by Riback et al .) because both sets of authors use our data from Fuertes et al . (2017) to support their arguments. The topic of discussion pertains to the discrepant inferences drawn from SAXS versus FRET measurements regarding the dimensions of intrinsically disordered proteins (IDPs) in aqueous solvents. Using SAXS measurements on labeled and unlabeled proteins, we ruled out the labels used for FRET measurements as the cause of discrepant inferences between the two methods. Instead, we propose that FRET and SAXS provide complementary readouts because of a decoupling of size and shape fluctuations that is intrinsic to finite-sized, heteropolymeric IDPs. Accounting for this decoupling resolves the discrepant inferences between the two methods, thus making a case for the utility of both methods.
    Keywords: Biochemistry
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  • 67
    Publication Date: 2018-03-06
    Description: The computational design of transmembrane proteins with more than one membrane-spanning region remains a major challenge. We report the design of transmembrane monomers, homodimers, trimers, and tetramers with 76 to 215 residue subunits containing two to four membrane-spanning regions and up to 860 total residues that adopt the target oligomerization state in detergent solution. The designed proteins localize to the plasma membrane in bacteria and in mammalian cells, and magnetic tweezer unfolding experiments in the membrane indicate that they are very stable. Crystal structures of the designed dimer and tetramer—a rocket-shaped structure with a wide cytoplasmic base that funnels into eight transmembrane helices—are very close to the design models. Our results pave the way for the design of multispan membrane proteins with new functions.
    Keywords: Biochemistry
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  • 68
    Publication Date: 2018-03-16
    Description: Diphthamide biosynthesis involves a carbon-carbon bond-forming reaction catalyzed by a radical S-adenosylmethionine (SAM) enzyme that cleaves a carbon-sulfur (C–S) bond in SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. Using rapid freezing, we have captured an organometallic intermediate with an iron-carbon (Fe–C) bond between ACP and the enzyme’s [4Fe-4S] cluster. In the presence of the substrate protein, elongation factor 2, this intermediate converts to an organic radical, formed by addition of the ACP radical to a histidine side chain. Crystal structures of archaeal diphthamide biosynthetic radical SAM enzymes reveal that the carbon of the SAM C–S bond being cleaved is positioned near the unique cluster Fe, able to react with the cluster. Our results explain how selective C–S bond cleavage is achieved in this radical SAM enzyme.
    Keywords: Biochemistry
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  • 69
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-02-23
    Keywords: Biochemistry
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  • 70
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-02-23
    Keywords: Biochemistry
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  • 71
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-06
    Keywords: Biochemistry
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  • 72
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-01-12
    Keywords: Biochemistry
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  • 73
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-01-12
    Keywords: Biochemistry
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  • 74
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-11
    Description: A parabolic relationship between lens radius and refractive index allows spherical lenses to avoid spherical aberration. We show that in squid, patchy colloidal physics resulted from an evolutionary radiation of globular S-crystallin proteins. Small-angle x-ray scattering experiments on lens tissue show colloidal gels of S-crystallins at all radial positions. Sparse lens materials form via low-valence linkages between disordered loops protruding from the protein surface. The loops are polydisperse and bind via a set of hydrogen bonds between disordered side chains. Peripheral lens regions with low particle valence form stable, volume-spanning gels at low density, whereas central regions with higher average valence gel at higher densities. The proteins demonstrate an evolved set of linkers for self-assembly of nanoparticles into volumetric materials.
    Keywords: Biochemistry
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  • 75
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-18
    Keywords: Biochemistry
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  • 76
    Publication Date: 2017-09-01
    Description: In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we report the structure of the Pol II elongation complex bound with the basal elongation factors Spt4/5, Elf1, and TFIIS. Spt4/5 (the Spt4/Spt5 complex) and Elf1 modify a wide area of the Pol II surface. Elf1 bridges the Pol II central cleft, completing a "DNA entry tunnel" for downstream DNA. Spt4 and the Spt5 NGN and KOW1 domains encircle the upstream DNA, constituting a "DNA exit tunnel." The Spt5 KOW4 and KOW5 domains augment the "RNA exit tunnel," directing the exiting nascent RNA. Thus, the elongation complex establishes a completely different transcription and regulation platform from that of the initiation complexes.
    Keywords: Biochemistry
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  • 77
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-01
    Keywords: Biochemistry
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  • 78
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-01
    Keywords: Biochemistry
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  • 79
    Publication Date: 2017-09-01
    Description: NAD + (oxidized form of NAD:nicotinamide adenine dinucleotide)–reducing soluble [NiFe]-hydrogenase (SH) is phylogenetically related to NADH (reduced form of NAD + ):quinone oxidoreductase (complex I), but the geometrical arrangements of the subunits and Fe–S clusters are unclear. Here, we describe the crystal structures of SH in the oxidized and reduced states. The cluster arrangement is similar to that of complex I, but the subunits orientation is not, which supports the hypothesis that subunits evolved as prebuilt modules. The oxidized active site includes a six-coordinate Ni, which is unprecedented for hydrogenases, whose coordination geometry would prevent O 2 from approaching. In the reduced state showing the normal active site structure without a physiological electron acceptor, the flavin mononucleotide cofactor is dissociated, which may be caused by the oxidation state change of nearby Fe–S clusters and may suppress production of reactive oxygen species.
    Keywords: Biochemistry
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  • 80
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-15
    Keywords: Biochemistry
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  • 81
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-23
    Keywords: Biochemistry
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  • 82
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-23
    Keywords: Biochemistry
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  • 83
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-11
    Keywords: Biochemistry
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  • 84
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-11
    Keywords: Biochemistry
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  • 85
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-11
    Keywords: Biochemistry
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  • 86
    Publication Date: 2017-08-11
    Description: Small basic proteins present in most Archaea share a common ancestor with the eukaryotic core histones. We report the crystal structure of an archaeal histone-DNA complex. DNA wraps around an extended polymer, formed by archaeal histone homodimers, in a quasi-continuous superhelix with the same geometry as DNA in the eukaryotic nucleosome. Substitutions of a conserved glycine at the interface of adjacent protein layers destabilize archaeal chromatin, reduce growth rate, and impair transcription regulation, confirming the biological importance of the polymeric structure. Our data establish that the histone-based mechanism of DNA compaction predates the nucleosome, illuminating the origin of the nucleosome.
    Keywords: Biochemistry
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  • 87
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-18
    Description: Vinculin is an actin-binding protein thought to reinforce cell-cell and cell-matrix adhesions. However, how mechanical load affects the vinculin–F-actin bond is unclear. Using a single-molecule optical trap assay, we found that vinculin forms a force-dependent catch bond with F-actin through its tail domain, but with lifetimes that depend strongly on the direction of the applied force. Force toward the pointed (–) end of the actin filament resulted in a bond that was maximally stable at 8 piconewtons, with a mean lifetime (12 seconds) 10 times as long as the mean lifetime when force was applied toward the barbed (+) end. A computational model of lamellipodial actin dynamics suggests that the directionality of the vinculin–F-actin bond could establish long-range order in the actin cytoskeleton. The directional and force-stabilized binding of vinculin to F-actin may be a mechanism by which adhesion complexes maintain front-rear asymmetry in migrating cells.
    Keywords: Biochemistry
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  • 88
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-01
    Keywords: Biochemistry
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  • 89
    Publication Date: 2017-06-02
    Description: The arenavirus Lassa causes severe hemorrhagic fever and a significant disease burden in West Africa every year. The glycoprotein, GPC, is the sole antigen expressed on the viral surface and the critical target for antibody-mediated neutralization. Here we present the crystal structure of the trimeric, prefusion ectodomain of Lassa GP bound to a neutralizing antibody from a human survivor at 3.2-angstrom resolution. The antibody extensively anchors two monomers together at the base of the trimer, and biochemical analysis suggests that it neutralizes by inhibiting conformational changes required for entry. This work illuminates pH-driven conformational changes in both receptor-binding and fusion subunits of Lassa virus, illustrates the unique assembly of the arenavirus glycoprotein spike, and provides a much-needed template for vaccine design against these threats to global health.
    Keywords: Biochemistry
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  • 90
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-02
    Keywords: Biochemistry
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  • 91
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-23
    Keywords: Biochemistry
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  • 92
    Publication Date: 2017-06-23
    Description: Hormones can transmit signals through adenosine 3',5'-monophosphate (cAMP) to precise intracellular locations. The fidelity of these responses relies on the activation of localized protein kinase A (PKA) holoenzymes. Association of PKA regulatory type II (RII) subunits with A-kinase–anchoring proteins (AKAPs) confers location, and catalytic (C) subunits phosphorylate substrates. Single-particle electron microscopy demonstrated that AKAP79 constrains RII-C subassemblies within 150 to 250 angstroms of its targets. Native mass spectrometry established that these macromolecular assemblies incorporated stoichiometric amounts of cAMP. Chemical-biology– and live cell–imaging techniques revealed that catalytically active PKA holoenzymes remained intact within the cytoplasm. These findings indicate that the parameters of anchored PKA holoenzyme action are much more restricted than originally anticipated.
    Keywords: Biochemistry
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  • 93
    Publication Date: 2017-06-23
    Description: The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe–S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe–S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. The 4 kcal/mol is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.
    Keywords: Biochemistry
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  • 94
    Publication Date: 2017-07-21
    Description: Hsp100 polypeptide translocases are conserved members of the AAA+ family (adenosine triphosphatases associated with diverse cellular activities) that maintain proteostasis by unfolding aberrant and toxic proteins for refolding or proteolytic degradation. The Hsp104 disaggregase from Saccharomyces cerevisiae solubilizes stress-induced amorphous aggregates and amyloids. The structural basis for substrate recognition and translocation is unknown. Using a model substrate (casein), we report cryo–electron microscopy structures at near-atomic resolution of Hsp104 in different translocation states. Substrate interactions are mediated by conserved, pore-loop tyrosines that contact an 80-angstrom-long unfolded polypeptide along the axial channel. Two protomers undergo a ratchet-like conformational change that advances pore loop–substrate interactions by two amino acids. These changes are coupled to activation of specific nucleotide hydrolysis sites and, when transmitted around the hexamer, reveal a processive rotary translocation mechanism and substrate-responsive flexibility during Hsp104-catalyzed disaggregation.
    Keywords: Biochemistry
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  • 95
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-28
    Keywords: Biochemistry
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  • 96
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-28
    Keywords: Biochemistry
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  • 97
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-28
    Keywords: Biochemistry
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  • 98
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-28
    Keywords: Biochemistry
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  • 99
    Publication Date: 2017-07-28
    Description: Ribosome stalling leads to recruitment of the ribosome quality control complex (RQC), which targets the partially synthesized polypeptide for proteasomal degradation through the action of the ubiquitin ligase Ltn1p. A second core RQC component, Rqc2p, modifies the nascent polypeptide by adding a carboxyl-terminal alanine and threonine (CAT) tail through a noncanonical elongation reaction. Here we examined the role of CAT-tailing in nascent-chain degradation in budding yeast. We found that Ltn1p efficiently accessed only nascent-chain lysines immediately proximal to the ribosome exit tunnel. For substrates without Ltn1p-accessible lysines, CAT-tailing enabled degradation by exposing lysines sequestered in the ribosome exit tunnel. Thus, CAT-tails do not serve as a degron, but rather provide a fail-safe mechanism that expands the range of RQC-degradable substrates.
    Keywords: Biochemistry
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  • 100
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-28
    Keywords: Biochemistry
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