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Uv And Chemical Crosslinking Mass Spectrometry For The Analysis Of Protein Nucleic Acid Interactions
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Book Synopsis UV and Chemical Crosslinking Mass Spectrometry for the Analysis of Protein-nucleic Acid Interactions by : Luisa Welp
Download or read book UV and Chemical Crosslinking Mass Spectrometry for the Analysis of Protein-nucleic Acid Interactions written by Luisa Welp and published by . This book was released on 2024 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein-nucleic acid interactions are a key part of essential cellular processes and their disturbance often results in the development of diseases. Crosslinking mass spectrometry (XL-MS)-based approaches have become increasingly popular for the proteome-wide discovery of nucleic acid-binding proteins. The basic principle of the methodology relies on covalent attachment of proteins and binding nucleic acids by crosslinking, which makes the heteroconjugates amenable to MS analysis. Building up on comprehensive nucleic acid-binding protein inventories, there is an increasing demand for higher...
Book Synopsis Implementation of Chemical Protein-nucleic Acid Cross-linking Into Mass Spectrometric Workflows and Mass Spectrometric Database Searches by : Fanni Laura Bazsó
Download or read book Implementation of Chemical Protein-nucleic Acid Cross-linking Into Mass Spectrometric Workflows and Mass Spectrometric Database Searches written by Fanni Laura Bazsó and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein nucleic acid interactions play a pivotal role in cells, from transcription to translation. Functions of proteins in protein nucleic acid interactions are diverse: histones are responsible for the packaging of the genomic DNA; ribosomal proteins are part of the ribosome, which is responsible for protein synthesis. Crosslinking mass spectrometry proved to be a useful tool to identify protein-nucleic acid interactions and their dynamics in the cell. A vast amount of effort has been spent to elucidate protein-nucleic acid interactions with UV crosslinking mass spectrometry, whereas chem...
Book Synopsis Characterization of Photochemically Cross-linked Protein-nucleic Acid Complexes by Mass Spectrometry by : Ole Nørregaard Jensen
Download or read book Characterization of Photochemically Cross-linked Protein-nucleic Acid Complexes by Mass Spectrometry written by Ole Nørregaard Jensen and published by . This book was released on 1994 with total page 318 pages. Available in PDF, EPUB and Kindle. Book excerpt: A novel protocol for the study of protein-nucleic acid interactions is presented and demonstrated to be feasible. The protocol combines photochemical crosslinking techniques and mass spectrometric methods into a new strategy for identifying protein domains or amino acid residues that are in close contact with nucleic acid in protein-nucleic acid complexes. Identifying nucleic acid binding domains in proteins provides a starting point for understanding structure-function relationships in protein-nucleic acid complexes. The protocol can be divided into three parts: 1) Cross linking of the protein-nucleic acid complex by irradiation with ultraviolet light and subsequently verifying the crosslinking by mass spectrometry; 2) Mass spectrometric peptide mapping of crosslinked protein-nucleic acid complexes to identify crosslinked peptide-nucleic acid hybrids; 3) Tandem mass spectrometric sequencing of peptide-nucleic acid hybrids to localize the crosslinked amino acid residue(s). The experimental data described in this dissertation documents our efforts to establish and implement this analytical protocol. Using several different protein-nucleic acid systems and different crosslinking techniques, we have demonstrated the feasibility of a mass spectrometric based approach to structurally characterize UV-crosslinked protein-nucleic acid complexes. Matrix-assisted laser desorption/ionization mass spectrometry was for the first time demonstrated to be highly effective for detection and molecular weight determination of intact, UV-crosslinked protein-nucleic acid complexes and for molecular weight determination of synthetic and UV-crosslinked peptide-nucleic acid hybrids. Electrospray ionization mass spectrometry and tandem mass spectrometry was demonstrated to be effective for analysis of synthetic peptide-nucleic acid hybrids and, in conjunction with HPLC, for peptide mapping of a protein. The first application of MALDI mass spectrometry to the characterization of crosslinked peptide-nucleic acid hybrids isolated from a photochemically crosslinked protein-nucleic acid complex demonstrate that the new protocol can be used to identify nucleic acid binding domains in proteins.
Book Synopsis Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics by : M. Chance
Download or read book Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics written by M. Chance and published by John Wiley & Sons. This book was released on 2008-09-22 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents a wide variety of mass spectrometry methods used to explore structural mechanisms, protein dynamics and interactions between proteins. Preliminary chapters cover mass spectrometry methods for examining proteins and are then followed by chapters devoted to presenting very practical, how-to methods in a detailed way. Includes footprinting and plistex specifically, setting this book apart from the competition.
Book Synopsis Mapping Protein-DNA Interactions Using UV Cross-linking and Mass Spectrometry by : Fiona Jane Flett
Download or read book Mapping Protein-DNA Interactions Using UV Cross-linking and Mass Spectrometry written by Fiona Jane Flett and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Mass Spectrometry of Protein Interactions by : Kevin Downard
Download or read book Mass Spectrometry of Protein Interactions written by Kevin Downard and published by John Wiley & Sons. This book was released on 2007-08-24 with total page 153 pages. Available in PDF, EPUB and Kindle. Book excerpt: The authoritative guide to analyzing protein interactions by mass spectrometry Mass spectrometry (MS) is playing an increasingly important role in the study of protein interactions. Mass Spectrometry of Protein Interactionspresents timely and definitive discussions of the diverse range of approaches for studying protein interactions by mass spectrometry with an extensive set of references to the primary literature. Each chapter is written by authors or teams of authors who are international authorities in their fields. This leading reference text: * Discusses the direct detection of protein interactions through electrospray ionization (ESI-MS); ion mobility analysis; and matrix-assisted laser desorption/ionization (MALDI-MS) * Covers the indirect analysis of protein interactions through hydrogen-deuterium exchange (HX-MS); limited proteolysis; cross-linking; and radial probe (RP-MS) * Guides researchers in the use of mass spectrometry in structural biology, biochemistry, and protein science to map and define the huge number and diversity of protein interactions * Reviews the latest discoveries and applications and addresses new and ongoing challenges This is a comprehensive reference for researchers in academia and industry engaged in studies of protein interactions and an excellent text for graduate and postgraduate students.
Book Synopsis Quantitative Mass Spectrometry to Study Nucleic Acid-protein Interactions by : Falk Butter
Download or read book Quantitative Mass Spectrometry to Study Nucleic Acid-protein Interactions written by Falk Butter and published by . This book was released on 2010 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Mass Spectrometric Analysis of UV-crosslinked Protein-nucleic Acid Complexes by : Catalin E. Doneanu
Download or read book Mass Spectrometric Analysis of UV-crosslinked Protein-nucleic Acid Complexes written by Catalin E. Doneanu and published by . This book was released on 2002 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Quantitative Methods in Proteomics by : Katrin Marcus
Download or read book Quantitative Methods in Proteomics written by Katrin Marcus and published by Humana Press. This book was released on 2012-06-08 with total page 539 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein modifications and changes made to them, as well as the quantities of expressed proteins, can define the various functional stages of the cell. Accordingly, perturbations can lead to various diseases and disorders. As a result, it has become paramount to be able to detect and monitor post-translational modifications and to measure the abundance of proteins within the cell with extreme sensitivity. While protein identification is an almost routine requirement nowadays, reliable techniques for quantifying unmodified proteins (including those that escape detection under standard conditions, such as protein isoforms and membrane proteins) is not routine. Quantitative Methods in Proteomics gives a detailed survey of topics and methods on the principles underlying modern protein analysis, from statistical issues when planning proteomics experiments, to gel-based and mass spectrometry-based applications. The quantification of post-translational modifications is also addressed, followed by the “hot” topics of software and data analysis, as well as various overview chapters which provide a comprehensive overview of existing methods in quantitative proteomics. Written in the successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Quantitative Methods in Proteomics serves as a comprehensive and competent overview of the important and still growing field of quantitative proteomics.
Book Synopsis Mass Spectrometry of Nucleosides and Nucleic Acids by : Joseph H Banoub
Download or read book Mass Spectrometry of Nucleosides and Nucleic Acids written by Joseph H Banoub and published by CRC Press. This book was released on 2019-08-30 with total page 504 pages. Available in PDF, EPUB and Kindle. Book excerpt: Assembling the work of an international panel of researchers, Mass Spectrometry of Nucleosides and Nucleic Acids summarizes and reviews the latest developments in the field and provides a window on the next generation of analysis. Beginning with an overview of recent developments, the book highlights the most popular ionization methods and illustrates the diversity of strategies employed in the characterization and sequencing of DNA and RNA oligomers, nucleosides, nucleotides, and adducts. It describes studies performed on deoxyinosine and its analogues and provides an introduction to tandem mass spectrometry (MS/MS). Next, the contributors examine mass spectrometric application in the study of cyclic nucleotides in biochemical signal transduction. They analyze urinary modified nucleosides and explore DNA adducts. They discuss isotope labeling of DNA-mass spectrometry (ILD-MS) and examine various uses of electrospray ionization mass spectrometry (ESI-MS). The book reviews recent progress in the direct MS characterization of noncovalent nucleic acid-protein complexes, explores the interaction and ionization of guanidine-derived compounds with highly acidic biomolecules, and examines quantitative identification of nucleic acids via signature digestion products detected using mass spectrometry. The book describes a direct-infusion ESI-MS approach that can serve as a screening technique for the presence of modified nucleosides from small RNAs. Lastly, it discusses the LC-MS/MS method for the in vitro replication studies on damage-containing DNA substrates, and concludes with an examination of the influence of metal ions on the structure and reactivity of nucleic acids. The exciting developments in mass spectrometry technology have fueled incredible advances in our understanding of nucleic acids and their complexes. The contributions presented in this volume capture the range of these advances, helping to inspire new findings a
Book Synopsis Advancing Chemical Cross-linking Mass Spectrometry for Protein Structure and Interaction Analysis by : Bingqing Zhao (Bioanalytical chemist)
Download or read book Advancing Chemical Cross-linking Mass Spectrometry for Protein Structure and Interaction Analysis written by Bingqing Zhao (Bioanalytical chemist) and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical cross-linking mass spectrometry elucidates protein structures and protein-protein interactions by establishing distance constraints between residues pairs. Interpreting the mass spectra of covalently linked peptide pairs is more challenging than identifying peptides in proteomics. This dissertation presents improvements in methodology for identifying cross-linked peptides and their application to probing protein interacting surfaces.
Book Synopsis Bioconjugate Techniques by : Greg T. Hermanson
Download or read book Bioconjugate Techniques written by Greg T. Hermanson and published by Academic Press. This book was released on 2010-07-26 with total page 1233 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioconjugate Techniques, 2nd Edition, is the essential guide to the modification and cross linking of biomolecules for use in research, diagnostics, and therapeutics. It provides highly detailed information on the chemistry, reagent systems, and practical applications for creating labeled or conjugate molecules. It also describes dozens of reactions with details on hundreds of commercially available reagents and the use of these reagents for modifying or cross linking peptides and proteins, sugars and polysaccharides, nucleic acids and oligonucleotides, lipids, and synthetic polymers. A one-stop source for proven methods and protocols for synthesizing bioconjugates in the lab Step-by-step presentation makes the book an ideal source for researchers who are less familiar with the synthesis of bioconjugates More than 600 figures that visually describe the complex reactions associated with the synthesis of bioconjugates Includes entirely new chapters on the latest areas in the field of bioconjugation as follows: Microparticles and nanoparticlesSilane coupling agentsDendrimers and dendronsChemoselective ligationQuantum dotsLanthanide chelatesCyanine dyesDiscrete PEG compoundsBuckyballs,fullerenes, and carbon nanotubesMass tags and isotope tagsBioconjugation in the study of protein interactions
Book Synopsis RNA-RNA Interactions by : Frank J. Schmidt
Download or read book RNA-RNA Interactions written by Frank J. Schmidt and published by Humana Press. This book was released on 2014-10-29 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this volume expert researchers in the field detail many of the methods which are now commonly used to study RNA. These methods are presented as a guidebook to scientists who are experienced with RNA research and want to brush up on a new technique. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Thorough and intuitive, RNA-RNA Interactions: Methods and Protocols guides scientists investigating biological systems and studying RNA.
Book Synopsis Strategies for the Analysis of Protein Interactions by Chemical Cross-linking and Tandem Mass Spectrometry and Diastereoselective Synthesis of the Pectenotoxin 2 Non-anomeric AB Spiroacetal by : Danielle Vellucci
Download or read book Strategies for the Analysis of Protein Interactions by Chemical Cross-linking and Tandem Mass Spectrometry and Diastereoselective Synthesis of the Pectenotoxin 2 Non-anomeric AB Spiroacetal written by Danielle Vellucci and published by . This book was released on 2010 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical cross-linking coupled with mass spectrometry is a potentially powerful method for mapping protein-protein interactions. This strategy is currently limited by challenges associated with the effective isolation and identification of cross-linked peptides. Novel azide-labeled cross-linking reagents have been developed that enable selective enrichment of cross-linked products by Staudinger ligation. Additionally, a cross-linking strategy has been explored using a newly designed MS-cleavable cross-linker (DSSO) for effective identification of cross-linked peptides based on their distinct fragmentation patterns. These combined advancements have enabled rapid and efficient analysis of cross-linked products of model peptides, proteins, and the yeast 20S proteasome complex. The reductive cyclization reaction of a cyanoacetal has been used to prepare the pectenotoxin 2 (PTX-2) AB spiroacetal with high diastereoselectively for the first time. The strategy is convergent and makes use of the axial-selective reductive lithiation of 2-cyano tetrahydropyran rings to introduce the spiroacetal center with the desired non-anomeric selectivity.
Book Synopsis RNA-protein Interactions by : Kiyoshi Nagai
Download or read book RNA-protein Interactions written by Kiyoshi Nagai and published by Oxford University Press, USA. This book was released on 1994 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
Book Synopsis Measuring Protein-protein Interactions in Complex Samples by Targeted Chemical Cross-linking Mass Spectrometry by : Hamed Khakzad
Download or read book Measuring Protein-protein Interactions in Complex Samples by Targeted Chemical Cross-linking Mass Spectrometry written by Hamed Khakzad and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Integrative Structural Biology with Hybrid Methods by : Haruki Nakamura
Download or read book Integrative Structural Biology with Hybrid Methods written by Haruki Nakamura and published by Springer. This book was released on 2019-01-08 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a new emerging concept of "Integrative Structural Biology". It covers current trends of the molecular and cellular structural biology, providing new methods to observe, validate, and keep the structural models of the large cellular machines with recent scientific results. Structures of very large macromolecular machines in cells are being determined by combining observations from complementary experimental methods. Thus, this volume presents the each methods such as X-ray crystallography, NMR spectroscopy, 3DEM, small-angle scattering (SAS), FRET, crosslinking, and enables the readers to understand the hybrid methods. This book discusses how those integrative models should be represented, validated and archived. A unique highlight of this book is discussion of the data validation and archive, which are big problems in this filed along with the progress of this field. The researchers in biology will be interested in this book as a guide book for learning the current structure biology, but also those in structure biology may use this book as a comprehensive reference to cover broad topics.
