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New Mass Spectrometry Approaches To Investigate Proteins And Protein Interactions
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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 New Mass Spectrometry Approaches to Investigate Proteins and Protein Interactions by : Daniele Canzani
Download or read book New Mass Spectrometry Approaches to Investigate Proteins and Protein Interactions written by Daniele Canzani and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry (MS) is essential for understanding the composition, structures, and interactions of proteins. There are various forms of MS that can be used to obtain valuable information about proteins and protein interactions. In native MS, intact protein ions are generated from a solution that maintains the non-covalent protein interactions into the gas-phase environment of a mass spectrometer. MS is frequently coupled liquid chromatography (LC), which is an analytical technique that is used to separate proteins or peptides before they enter the mass spectrometer. LC can improve the sensitivity of an MS analysis and increase the amount of information that can be obtained from a sample. Ion mobility (IM) is a gas-phase separation technique that occurs after a protein sample has been ionized. IM-MS measurements can provide simultaneous details about the mass and size of a protein ion, which is useful for structural biology applications. In the following chapters of this dissertation, various MS, LC, and IM techniques were used to study protein composition, interactions, and structure. In Chapter 2, native anion exchange chromatography (AEX), which uses a low-pressure and bioinert workflow with ammonium acetate mobile phases, is used to enhance native MS by removing common contaminants that interfere with MS, separating protein variants based on their charge, and isolating proteins from complex mixtures. Those capabilities demonstrate that native AEX is a valuable tool for overcoming common challenges that are associated with native MS, and that native AEX has distinct advantages over other conventional sample preparation methods. In Chapter 3, an integrative MS strategy was developed to identify binding interactions that essential proteins called E3 ligases have in cells. Eukaryotic cells use hundreds of unique E3 ligases to control cellular functions through protein degradation. E3 ligases selectively bind to protein substrates through recognition motifs known as degrons. The integrative MS strategy, which uses a combination of native MS, native top-down MS, MS of destabilized samples, and LC-MS, is called "degronomics" and will be useful for uncovering degron motifs that other E3s can recognize in cells. Results from that study demonstrate that an E3 ligase called KLHDC2 binds to C-terminus diglycine degrons by uncovering KLHDC2-peptide binding interactions from cells. In Chapter 4, a combination of IM-MS experiments and computational tools was used to characterize the effects of charge state, charge distribution, and structure on the ion mobility of proteins in nitrogen gas. The results from Chapter 4 have implications for interpreting protein structures from IM-MS experiments and for comparing nitrogen gas-based measurements against measurements taken with helium gas.
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 Introduction to Proteomics by : Daniel Liebler
Download or read book Introduction to Proteomics written by Daniel Liebler and published by Springer Science & Business Media. This book was released on 2001-12-04 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: Daniel C. Liebler masterfully introduces the science of proteomics by spelling out the basics of how one analyzes proteins and proteomes, and just how these approaches are then employed to investigate their roles in living systems. He explains the key concepts of proteomics, how the analytical instrumentation works, what data mining and other software tools do, and how these tools can be integrated to study proteomes. Also discussed are how protein and peptide separation techniques are applied in proteomics, how mass spectrometry is used to identify proteins, and how data analysis software enables protein identification and the mapping of modifications. In addition, there are proteomic approaches for analyzing differential protein expression, characterizing proteomic diversity, and dissecting protein-protein interactions and networks.
Download or read book Proteomics written by Timothy Palzkill and published by Springer Science & Business Media. This book was released on 2007-05-08 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomics is an introduction to the exciting new field of proteomics, an interdisciplinary science that includes biology, bioinformatics, and protein chemistry. The purpose of this book is to provide the active researcher with an overview of the types of questions being addressed in proteomics studies and the technologies used to address those questions. Key subjects covered in this book include: an assessment of the limitations of this approach and outlines new developments in mass spectrometry that will advance future research high-throughput recombinant DNA cloning methods used to systematically clone all of the open reading frames of an organism into plasmid vectors for large scale protein expression and functional studies such as protein-protein interactions with the two-hybrid system protein structure an overview of large-scale experimental attempts to determine the three-dimensional structures of representative sets of proteins computational approaches to determining the three-dimensional structure of proteins. Proteomics provides a starting point for researchers who would like a theoretical understanding of the new technologies in the field, and obtain a solid grasp of the fundamentals before integrating new tools into their experiments. Written with attention to detail, but without being overwhelmingly technical, Proteomics is a user-friendly guide needed by most biologists today.
Book Synopsis Methods in Proteome and Protein Analysis by : Roza Maria Kamp
Download or read book Methods in Proteome and Protein Analysis written by Roza Maria Kamp and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 429 pages. Available in PDF, EPUB and Kindle. Book excerpt: Following the succesful publication of "Proteome and Protein Analysis" in 2000, which was based on a former MPSA (Methods in Protein Structure Analysis) conference, Methods in Proteome and Protein Analysis presents the most interesting papers from the 14th MPSA meeting. Major topics include: protein and peptide sample preparation and separation; new reagent for protein sequence analysis; mass spectrometry in protein research; analysis of posttranslational modification; protein-protein interaction using MALDI-MS; manipulation of genome or functional compositon trap; structure-function correlation study using optical biosensors of microcolorimetrical techniques; structural proteomics as NMR or fluorescence polarization study; the classification and prediction of structure or functional sites; in silico analysis of proteins and proteomes; increasing throughput and data quality for proteomics.
Book Synopsis Mass Spectrometry of Proteins by : Caroline A. Evans
Download or read book Mass Spectrometry of Proteins written by Caroline A. Evans and published by Humana Press. This book was released on 2019-06-16 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: New insights into modern medicine and systems biology are enabled by innovative protocols and advanced technologies in mass spectrometry-based proteomics. This volume details new pipelines, workflows, and ways to process data that allow for new frontiers in proteomics to be pushed forward. With applications to biomarker discovery, interactions between proteins, between biological systems, dynamics of post-translational modifications among others, new protocols have been developed and iteratively refined to probe the endless complexity of the proteome in ever greater details. This volume deals with methods for data dependent and data independent mass spectrometry analyses. Valuable, first-hand information is provided from designing experiments, sample preparation and analysis, exploitation of public datasets and carrying out reproducible data pipelines, using modern computational tools such as Galaxy or Jupyter. 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 tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Mass Spectrometry of Proteins: Methods and Protocols aims to ensure successful results in the further study of this vital field.
Book Synopsis Protein and Peptide Mass Spectrometry in Drug Discovery by : Michael L. Gross
Download or read book Protein and Peptide Mass Spectrometry in Drug Discovery written by Michael L. Gross and published by John Wiley & Sons. This book was released on 2011-09-26 with total page 484 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book that highlights mass spectrometry and its application in characterizing proteins and peptides in drug discovery An instrumental analytical method for quantifying the mass and characterization of various samples from small molecules to large proteins, mass spectrometry (MS) has become one of the most widely used techniques for studying proteins and peptides over the last decade. Bringing together the work of experts in academia and industry, Protein and Peptide Mass Spectrometry in Drug Discovery highlights current analytical approaches, industry practices, and modern strategies for the characterization of both peptides and proteins in drug discovery. Illustrating the critical role MS technology plays in characterizing target proteins and protein products, the methods used, ion mobility, and the use of microwave radiation to speed proteolysis, the book also covers important emerging applications for neuroproteomics and antigenic peptides. Placing an emphasis on the pharmaceutical industry, the book stresses practice and applications, presenting real-world examples covering the most recent advances in mass spectrometry, and providing an invaluable resource for pharmaceutical scientists in industry and academia, analytical and bioanalytical chemists, and researchers in protein science and proteomics.
Book Synopsis Proteomics and Protein-Protein Interactions by : Gabriel Waksman
Download or read book Proteomics and Protein-Protein Interactions written by Gabriel Waksman and published by Springer Science & Business Media. This book was released on 2005-12-21 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: The rapidly evolving field of protein science has now come to realize the ubiquity and importance of protein-protein interactions. It had been known for some time that proteins may interact with each other to form functional complexes, but it was thought to be the property of only a handful of key proteins. However, with the advent of high throughput proteomics to monitor protein-protein interactions at an organism level, we can now safely state that protein-protein interactions are the norm and not the exception. Thus, protein function must be understood in the larger context of the various binding complexes that each protein may form with interacting partners at a given time in the life cycle of a cell. Proteins are now seen as forming sophisticated interaction networks subject to remarkable regulation. The study of these interaction networks and regulatory mechanism, which I would like to term "systems proteomics," is one of the thriving fields of proteomics. The bird-eye view that systems proteomics offers should not however mask the fact that proteins are each characterized by a unique set of physical and chemical properties. In other words, no protein looks and behaves like another. This complicates enormously the design of high-throughput proteomics methods. Unlike genes, which, by and large, display similar physico-chemical behaviors and thus can be easily used in a high throughput mode, proteins are not easily amenable to the same treatment. It is thus important to remind researchers active in the proteomics field the fundamental basis of protein chemistry. This book attempts to bridge the two extreme ends of protein science: on one end, systems proteomics, which describes, at a system level, the intricate connection network that proteins form in a cell, and on the other end, protein chemistry and biophysics, which describe the molecular properties of individual proteins and the structural and thermodynamic basis of their interactions within the network. Bridging the two ends of the spectrum is bioinformatics and computational chemistry. Large data sets created by systems proteomics need to be mined for meaningful information, methods need to be designed and implemented to improve experimental designs, extract signal over noise, and reject artifacts, and predictive methods need to be worked out and put to the test. Computational chemistry faces similar challenges. The prediction of binding thermodynamics of protein-protein interaction is still in its infancy. Proteins are large objects, and simplifying assumptions and shortcuts still need to be applied to make simulations manageable, and this despite exponential progress in computer technology. Finally, the study of proteins impacts directly on human health. It is an obvious statement to say that, for decades, enzymes, receptors, and key regulator proteins have been targeted for drug discovery. However, a recent and exciting development is the exploitation of our knowledge of protein-protein interaction for the design of new pharmaceuticals. This presents particular challenges because protein-protein interfaces are generally shallow and interactions are weak. However, progress is clearly being made and the book seeks to provide examples of successes in this area.
Book Synopsis Proteomics Today by : Mahmoud H. Hamdan
Download or read book Proteomics Today written by Mahmoud H. Hamdan and published by John Wiley & Sons. This book was released on 2005-05-13 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: The last few years have seen an unprecedented drive toward theapplication of proteomics to resolving challenging biomedical andbiochemical tasks. Separation techniques combined with modern massspectrometry are playing a central role in this drive. This bookdiscusses the increasingly important role of mass spectrometry inproteomic research, and emphasizes recent advances in the existingtechnology and describes the advantages and pitfalls as well. * Provides a scientifically valid method for analyzing theapproximatey 500,000 proteins that are encoded in the humangenome * Explains the hows and whys of using mass spectrometry inproteomic analysis * Brings together the latest approaches combining separationtechniques and mass spectrometry and their application in proteomeanalysis * Comments on future challenges and how they may be addressed * Includes sections on troubleshooting
Book Synopsis Proteomics for Biological Discovery by : Timothy D. Veenstra
Download or read book Proteomics for Biological Discovery written by Timothy D. Veenstra and published by John Wiley & Sons. This book was released on 2019-04-26 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: An update to the popular guide to proteomics technology applications in biomedical research Building on the strength of the original edition, this book presents the state of the art in the field of proteomics and offers students and scientists new tools and techniques to advance their own research. Written by leading experts in the field, it provides readers with an understanding of new and emerging directions for proteomics research and applications. Proteomics for Biological Discovery begins by discussing the emergence of proteomics technologies and summarizing the potential insights to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are thoroughly covered, from underlying concepts to limitations and future directions. Later chapters provide an overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, applied proteomics, and bioinformatics relevant to proteomics. Chapters cover: Quantitative Proteomics for Differential Protein Expression Profiling; Protein Microarrays; Protein Biomarker Discovery; Biomarker Discovery using Mass Spectrometry Imaging; Protein-Protein Interactions; Mass Spectrometry Of Intact Protein Complexes; Crosslinking Applications in Structural Proteomics; Functional Proteomics; High Resolution Interrogation of Biological Systems via Mass Cytometry; Characterization of Drug-Protein Interactions by Chemoproteomics; Phosphorylation; Large-Scale Phosphoproteomics; and Probing Glycoforms of Individual Proteins Using Antibody-Lectin Sandwich Arrays. Presents a comprehensive and coherent review of the major issues in proteomic technology development, bioinformatics, strategic approaches, and applications Chapters offer a rigorous overview with summary of limitations, emerging approaches, questions, and realistic future industry and basic science applications Features new coverage of mass spectrometry for high throughput proteomic measurements, and novel quantitation strategies such as spectral counting and stable isotope labeling Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Offers new chapters on biomarker discovery, global phosphorylation analysis, proteomic profiling using antibodies, and single cell mass spectrometry Proteomics for Biological Discovery is an excellent advanced resource for graduate students, postdoctoral fellows, and scientists across all the major fields of biomedical science.
Book Synopsis Protein-protein Interactions and Networks by : Anna Panchenko
Download or read book Protein-protein Interactions and Networks written by Anna Panchenko and published by Springer Science & Business Media. This book was released on 2010-04-06 with total page 198 pages. Available in PDF, EPUB and Kindle. Book excerpt: The biological interactions of living organisms, and protein-protein interactions in particular, are astonishingly diverse. This comprehensive book provides a broad, thorough and multidisciplinary coverage of its field. It integrates different approaches from bioinformatics, biochemistry, computational analysis and systems biology to offer the reader a comprehensive global view of the diverse data on protein-protein interactions and protein interaction networks.
Download or read book Neuroproteomics written by Oscar Alzate and published by CRC Press. This book was released on 2009-10-26 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this, the post-genomic age, our knowledge of biological systems continues to expand and progress. As the research becomes more focused, so too does the data. Genomic research progresses to proteomics and brings us to a deeper understanding of the behavior and function of protein clusters. And now proteomics gives way to neuroproteomics as we beg
Book Synopsis Protein Mass Spectrometry by : Julian Whitelegge
Download or read book Protein Mass Spectrometry written by Julian Whitelegge and published by Elsevier. This book was released on 2008-10-09 with total page 563 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is designed to be a central text for young graduate students interested in mass spectrometry as it relates to the study of protein structure and function as well as proteomics. It is a definite must-have work for:- libraries at academic institutions with Master and Graduate programs in biochemistry, molecular biology, structural biology and proteomics- individual laboratories with interests covering these areas - libraries and individual laboratories in the pharmaceutical and biotechnology industries. *Serves as an essential reference to those working in the field*Incorporates the contributions of prominent experts *Features comprehensive coverage and a logical structure
Book Synopsis Protein Purification and Analysis I by : IConcept Press Staff
Download or read book Protein Purification and Analysis I written by IConcept Press Staff and published by CreateSpace. This book was released on 2013-12 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chapter 1 is a review of the bioinformatics literature on protein-protein interactions (PPIs). A protein-protein interaction network (PPIN) is a collection of PPIs, often deposited in online databases. PPINs may complement other datasets, such as protein structural information. Chapter 2 describes the usability and advantages of the micro-patterning technique to study protein-protein interactions in a live cell context. It summarizes results achieved so far, discusses latest technical developments and describes potential future applications. Chapter 3 describes a strategy for identification of protein peptides cross-linked to radiolabeled RNA derivatives in specific complexes of proteins or ribonucleoproteins with these derivatives. This strategy is alternative to the identification based on mass-spectrometry and can be used for determination of protein sites involved in interactions with specific RNAs when mass-spectrometry is not applicable. Chapter 4 describes biochemical methods for assessing interaction between distinct ligand-gated channels. This chapter proposes also methods to examine functional impact of these receptor-receptor interactions in the nervous system. Chapter 5 proposes a statistical approach based on Structural Equation Modeling, in combination with step-wise factor analysis, to infer protein-DNA interactions for gene transcriptional control in the absence of protein information. Such approach only uses gene expression profiles. Chapter 6 describes procedures for the biochemical analysis of amyloid proteins in transgenic Drosophila, specifically the prion protein. The authors show that protocols from the mammalian literature can be easily adapted and scaled to these small flies and by ensuring robust expression of the prion protein and proper handling of these delicate samples. Chapter 7 discusses DEAD-box proteins. DEAD-box protein family members participate in many aspects of RNA metabolism, particularly in the ATP-driven disruption of secondary structures of RNA. Genes coding for these types of proteins are recognised in all free living bacteria. Chapter 8 provides an experimental model of restriction-modification enzyme fusion and proposes a molecular mechanism for appearance of type IIC restriction-modification and M.SsoII-related enzymes, as well as other multifunctional proteins. Chapter 9 describes the role of branched chain amino acids, leucine, isoleucine and valine, in exercise with respect to performance, muscle kinetics, fatigue and immunity. It also discusses the existing evidence on any superior benefits of branched chain amino acid supplements to exercising individuals and athletes. Chapter 10 provides an overview of the protein-peptide based research in dermatology and the recent emergence of many new dermatologic therapeutic modalities. Chapter 11 summarizes the adverse health effects of prenatal or early postnatal exposure to environmental pollutants (lead, arsenic and dioxins are the best known), pharmaceuticals, some food additives, and other chemicals through the mechanism of cell deprogramming or imprinting. Chapter 12 put forward 2D-PAGE as an important tool, especially for clinical laboratories involved in the determination of protein expression levels and disease biomarker discovery. Chapter 13 shows how to investigate and characterize an open reading frame, from exploiting the similarity in amino acid sequence, until the cloning, expression, purification and activity of the protein and its biological partners. Chapter 14 focuses on the cloning, heterologous expression and physicochemical characterization of Als5, one of the GPI-anchored adhesins from Candida albicans.
Book Synopsis Lipid-Protein Interactions by : Jörg H. Kleinschmidt
Download or read book Lipid-Protein Interactions written by Jörg H. Kleinschmidt and published by Humana. This book was released on 2019-06-25 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second edition volume expands all chapters of the previous edition, which have been enhanced to cover the most recent developments, the current state of method research, and applications. Additional protocols were added to examine lipid-protein interactions by mass spectrometry, to use protein microarrays to investigate large sets of various proteins, to study membrane protein dynamics by UV resonance Raman spectroscopy, to analyze peptide-induced pore formation in membranes, and to investigate folding and insertion of membrane proteins. 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 tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Lipid-Protein Interactions: Methods and Protocols, Second Edition is an essential resource for all researchers who are interested in obtaining up-to-date and comprehensive information about membrane structure and function.
Book Synopsis New Frontiers of Network Analysis in Systems Biology by : Avi Ma'ayan
Download or read book New Frontiers of Network Analysis in Systems Biology written by Avi Ma'ayan and published by Springer Science & Business Media. This book was released on 2012-06-25 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt: The rapidly developing field of systems biology is influencing many aspects of biological research and is expected to transform biomedicine. Some emerging offshoots and specialized branches in systems biology are receiving particular attention and are becoming highly active areas of research. This collection of invited reviews describes some of the latest cutting-edge experimental and computational advances in these emerging sub-fields of systems biology. In particular, this collection focuses on the study of mammalian embryonic stem cells; new technologies involving mass-spectrometry proteomics; single cell measurements; methods for modeling complex stochastic systems; network-based classification algorithms; and the revolutionary emerging field of systems pharmacology.
