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The 26S proteasome maintains cellular homeostasis by modulating the degradation of ubiquitinated proteins. Its 19S regulatory subcomplex topology had remained elusive for over three decades until recent in vitro cryo-electron microscopy studies in the yeast 26S proteasome. Though successful in determining in vitro tertiary structures in yeast, we must eventually elucidate peptide-level details in the homologous human 26S for physiologically relevant translational information. The development of alternative in vivo strategies is required. Over the past decade, protein cross-linking coupled with mass spectrometry (XL-MS) has quickly become recognized as a promising new technology for the characterization of protein topologies. Identification of residues that are covalently cross-linked together can determine sites of interaction interfaces. These interfaces can be used in subsequent modeling analyses akin to distance constraints generated in other structural biology techniques. Though powerful, this strategy is hindered by complicated analysis of cross-linked peptides, the lack of specialized and comprehensive computational analysis tools, and the need for efficient in vivo cross-linking methods to investigate physiological inter-actions. A practical XL-MS workflow must address these issues by simplifying the sequencing and/or the identification of cross-linked species during MS, providing streamlined tools for cross-linked peptide identification, and providing membrane permeable capabilities for in vivo study. My development of an integrated XL-MS methodology during my doctoral studies has overcome these three obstacles by providing a rapid and accurate workflow to identify cross-linked peptides in vivo. From proof-of-concept, our methods evolved to allow for the first successful application of probabilistic 19S topology characterization and the first human in vivo XL-MS data. Here, I present an integrated workflow to provide rapid MS raw file-to-result analysis of cross-linked peptides using our novel CID-cleavable reagents, our Thermo Scientific Orbitrap MS instrumentation, and my comprehensive analysis software.
This work presents a definitive interpretation of the current status of and future trends in natural products—a dynamic field at the intersection of chemistry and biology concerned with isolation, identification, structure elucidation, and chemical characteristics of naturally occurring compounds such as pheromones, carbohydrates, nucleic acids, and enzymes. With more than 1,800 color figures, Comprehensive Natural Products II features 100% new material and complements rather than replaces the original work (©1999). Reviews the accumulated efforts of chemical and biological research to understand living organisms and their distinctive effects on health and medicine Stimulates new ideas among the established natural products research community—which includes chemists, biochemists, biologists, botanists, and pharmacologists Informs and inspires students and newcomers to the field with accessible content in a range of delivery formats Includes 100% new content, with more than 6,000 figures (1/3 of these in color) and 40,000 references to the primary literature, for a thorough examination of the field Highlights new research and innovations concerning living organisms and their distinctive role in our understanding and improvement of human health, genomics, ecology/environment, and more Adds to the rich body of work that is the first edition, which will be available for the first time in a convenient online format giving researchers complete access to authoritative Natural Products content
Anthropic Awareness: The Human Aspects of Scientific Thinking in NMR Spectroscopy and Mass Spectrometry blends psychology, philosophy, physics, mathematics, and chemistry, describing a human-centered philosophy of the essence of scientific thinking in the natural sciences and in everyday life. It addresses the reasons why we are prone to make errors in our conclusions and how to avoid such mistakes, also exploring a number of the "mental traps" that can lead to both individual mistakes and mass misconceptions. The book advocates that by understanding the nature of these mental traps we can adopt tactics to safely evade them. It includes Illustrative examples of common scientific misunderstandings and mental traps in both the theory and real-life application of NMR spectroscopy and mass spectrometry. Provides strategies on how to deal with molecular challenges and instrument limitations Presents multiple applications of small molecule structure elucidation using NMR, MS, IR, and UV Explores critical topics, including anthropic awareness (AA), NMR Spectroscopy, mass spectrometry, scientific thinking, and more Includes tactics on how to Improve quality control and data interpretation skills while minimizing data analysis time and increasing confidence in results Presents coverage on tactics to optimize experimental NMR parameters and enhance NMR vocabulary
The isolation and structural characterization of substances present at very low concentrations, as is necessary to satisfy regulatory requirements for pharmaceutical drug degradants and impurities, can present scientific challenges. The coupling of HPLC with NMR spectroscopy has been at the forefront of cutting-edge technologies to address these issues. LC-NMR: Expanding the Limits of Structure Elucidation presents a comprehensive overview of key concepts in HPLC and NMR that are required to achieve definitive structure elucidation with very low levels of analytes. Because skill sets from both of these highly established disciplines are involved in LC-NMR, the author provides introductory background to facilitate readers’ proficiency in both areas, including an entire chapter on NMR theory. The much-anticipated second edition provides guidance in setting up LC-NMR systems, discussion of LC methods that are compatible with NMR, and an update on recent hardware and software advances for system performance, such as improvements in magnet design, probe technology, and solvent suppression techniques that enable unprecedented mass sensitivity in NMR. This edition features methods to quantify concentration and assess purity of isolated metabolites on the micro scale and incorporates computational approaches to accelerate the structure elucidation process. The author also includes implementation and application of qNMR and automated and practical use of computational chemistry combined with QM and DFT to predict highly accurate NMR chemical shifts. The text focuses on current developments in chromatographic-NMR integration, with particular emphasis on utility in the pharmaceutical industry. Applications include trace analysis, analysis of mixtures, and structural characterization of degradation products, impurities, metabolites, peptides, and more. The text discusses novel uses and emerging technologies that challenge detection limits as well future directions for this important technique. This book is a practical primary resource for NMR structure determination—including theory and application—that guides the reader through the steps required for isolation and NMR structure elucidation on the micro scale.
During the last few decades, research into natural products has advanced tremendously thanks to contributions from the fields of chemistry, life sciences, food science and material sciences. Comparisons of natural products from microorganisms, lower eukaryotes, animals, higher plants and marine organisms are now well documented. This book provides an easy-to-read overview of natural products. It includes twelve chapters covering most of the aspects of natural products chemistry. Each chapter covers general introduction, nomenclature, occurrence, isolation, detection, structure elucidation both by degradation and spectroscopic techniques, biosynthesis, synthesis, biological activity and commercial applications, if any, of the compounds mentioned in each topic. Therefore it will be useful for students, other researchers and industry. The introduction to each chapter is brief and attempts only to supply general knowledge in the particular field. Furthermore, at the end of each chapter there is a list of recommended books for additional study and a list of relevant questions for practice.
While there has always been a large public interest in ancient pictures painted or carved on stone, the archaeological study of rock art is in its infancy. But intensive amounts of research has revolutionized this field in the past decade. New methods of dating and analysis help to pinpoint the makers of these beautiful images, new interpretive models help us understand this art in relation to culture. Identification, conservation and management of rock art sites have become major issues in historical preservation worldwide. And the number of archaeologically attested sites has mushroomed. In this handbook, the leading researchers in the rock art area provide cogent, state-of-the-art summaries of the technical, interpretive, and regional advances in rock art research. The book offers a comprehensive, basic reference of current information on key topics over six continents for archaeologists, anthropologists, art historians, and rock art enthusiasts.
A comprehensive review of advances in one of today's most technologically important research fields. Spurred on by society's increasingly urgent demand for an inexpensive, environment-friendly alternative to the internal combustion engine, research into electrocatalytic fuel cells has yielded many exciting advances in the past few years. This rapid rate of progress, however, has created a daunting challenge for anyone attempting to track the important new trends in electrocatalysis by sorting through the huge and rapidly growing body of world literature in the field. Electrocatalysis was designed to save scientists hours of arduous legwork by providing an authoritative review of the most important recent advances in all technologically relevant aspects of electrocatalysis. Leading researchers from North America, Europe, and the Far East share what they know about an array of related topics, including: * Electrocatalysis of hydrogen and oxygen electrode reactions * Electrooxidation of small organic molecules * Design and synthesis of new electrocatalytic materials * The distribution and storage of hydrogen in metal hydrides * Hydrogenation of organic compounds as a means of hydrogen storage * Electron, ion, and atom transfer reactions * Influence of the double-layer structure on the rate of charge transfer * A unified theory of electron and ion transfer reactions at metal electrodes. Electrocatalysis is an indispensable working resource for electrochemists, chemical engineers, surface scientists, and materials scientists.