Comprehensive Analysis Of Wrn Protein Interaction Network By Mass Spectrometry
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Comprehensive Analysis Of Wrn Protein Interaction Network By Mass Spectrometry
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Author : Veronika A. Glukhova
language : en
Publisher:
Release Date : 2014
Comprehensive Analysis Of Wrn Protein Interaction Network By Mass Spectrometry written by Veronika A. Glukhova and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with categories.
Cells that have lost WRN function exhibit a shortened replicative lifespan, accumulation of chromosomal aberrations, and demonstrate sensitivity to a number of chemotherapeutic agents, including DNA Topoisomerase I inhibitor camptothecin (CPT). On organismal level, the lack of this protein results in the progeroid syndrome Werner Syndrome, which is characterized by increased incidence of cancers, cardiovascular disease, cataracts, and other age-associated pathologies. In this study we examined the network of proteins that associate with WRN protein, and then expanded this picture when the cells were challenged with CPT. We detail the profiling analysis used for unbiased detection of all interacting proteins using LC-MS/MS, followed by data analysis and selection of targets for follow-up. We then focus on the method development, complexities of data analysis, and application of selected reaction monitoring (SRM), a method for targeted MS. Using RNAi we demonstrate the power of this technique for relative protein quantitation of human proteins WRN and TP53, and a number of small, low-abundance seminal fluid proteins from D.melanogaster flies. SRM was applied for two studies of the WRN interactome: 1) to partially validate findings of the profiling screen after short-term treatment with CPT, and 2) to describe the dynamics of association of these proteins with WRN as a function of time, by expanding the treatment time course to 6 and 12 hours. We report on our description of WRN protein interaction complexes in unperturbed cells, and how these interaction complexes become reorganized in response to DNA damage. Our results demonstrate that the newly recruited proteins participate in chromatin remodeling, negative regulation of cell cycle progression, and double-strand break repair. We focus on 40 proteins to test their differential interaction with WRN after 1, 6, and 12 hours of treatment with CPT. We specifically focus on the functional importance of the chromatin-remodeling factors, and present the list of WRN interacting proteins that have emerged as high-priority targets for functional validation. Finally, we discuss how our work has expanded the understanding of the functional roles of WRN, and how targeted, hypothesis-driven application of mass spectrometry can be used to answer complex questions about protein interaction.
Protein Protein Interactions And Networks
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Author : Anna Panchenko
language : en
Publisher: Springer Science & Business Media
Release Date : 2010-04-06
Protein Protein Interactions And Networks written by Anna Panchenko and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-04-06 with Science categories.
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.
Protein Interaction Networks
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Author : Aidong Zhang
language : en
Publisher: Cambridge University Press
Release Date : 2009-04-06
Protein Interaction Networks written by Aidong Zhang and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-04-06 with Computers categories.
The analysis of protein-protein interactions is fundamental to the understanding of cellular organization, processes, and functions. Proteins seldom act as single isolated species; rather, proteins involved in the same cellular processes often interact with each other. Functions of uncharacterized proteins can be predicted through comparison with the interactions of similar known proteins. Recent large-scale investigations of protein-protein interactions using such techniques as two-hybrid systems, mass spectrometry, and protein microarrays have enriched the available protein interaction data and facilitated the construction of integrated protein-protein interaction networks. The resulting large volume of protein-protein interaction data has posed a challenge to experimental investigation. This book provides a comprehensive understanding of the computational methods available for the analysis of protein-protein interaction networks. It offers an in-depth survey of a range of approaches, including statistical, topological, data-mining, and ontology-based methods. The author discusses the fundamental principles underlying each of these approaches and their respective benefits and drawbacks, and she offers suggestions for future research.
Mass Spectrometry Of Protein Interactions
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Author : Kevin Downard
language : en
Publisher: Wiley-Interscience
Release Date : 2007-08-10
Mass Spectrometry Of Protein Interactions written by Kevin Downard and has been published by Wiley-Interscience this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-08-10 with Science categories.
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.
Stable Isotope Labeling By Amino Acids In Cell Culture Silac
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Author : Bettina Warscheid
language : en
Publisher: Humana Press
Release Date : 2014-07-25
Stable Isotope Labeling By Amino Acids In Cell Culture Silac written by Bettina Warscheid and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-07-25 with Science categories.
Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC): Methods and Protocols provides a synopsis of a large array of different SILAC methods by presenting a set of protocols that have been established by renowned scientists and their working groups. These include methods and protocols for the labeling of various model organisms as well as advanced strategies relying on SILAC, e.g. for the analysis of protein interactions, the mapping of posttranslational modifications or the characterization of subcellular proteomes. 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. Authoritative and practical, Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC): Methods and Protocols will serve students and experienced scientists alike as a valuable reference of how to make use of the SILAC technology for their own research.
Systems Biology Of Cancer
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Author : Sam Thiagalingam
language : en
Publisher: Cambridge University Press
Release Date : 2015-04-09
Systems Biology Of Cancer written by Sam Thiagalingam and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-04-09 with Mathematics categories.
An overview of the current systems biology-based knowledge and the experimental approaches for deciphering the biological basis of cancer.
Proteins Involved In Dna Replication
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Author : Ulrich Huebscher
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-06-29
Proteins Involved In Dna Replication written by Ulrich Huebscher and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-06-29 with Science categories.
This book collects the Proceedings of a workshop sponsored by the European Molecular Biology Organization (EMBO) entitled "Pro teins Involved in DNA Replication" which was held September 19 to 23,1983 at Vitznau, near Lucerne, in Switzerland. The aim of this workshop was to review and discuss the status of our knowledge on the intricate array of enzymes and proteins that allow the replication of the DNA. Since the first discovery of a DNA polymerase in Escherichia coli by Arthur Kornberg twenty eight years ago, a great number of enzymes and other proteins were des cribed that are essential for this process: different DNA poly merases, DNA primases, DNA dependent ATPases, helicases, DNA liga ses, DNA topoisomerases, exo- and endonucleases, DNA binding pro teins and others. They are required for the initiation of a round of synthesis at each replication origin, for the progress of the growing fork, for the disentanglement of the replication product, or for assuring the fidelity of the replication process. The number, variety and ways in which these proteins inter act with DNA and with each other to the achievement of replication and to the maintenance of the physiological structure of the chromo somes is the subject of the contributions collected in this volume. The presentations and discussions during this workshop reinforced the view that DNA replication in vivo can only be achieved through the cooperation of a high number of enzymes, proteins and other cofactors.
Post Transcriptional Gene Regulation
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Author : Erik Dassi
language : en
Publisher: Humana
Release Date : 2022-11-09
Post Transcriptional Gene Regulation written by Erik Dassi and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-11-09 with Science categories.
This volume presents the most recent advances in techniques for studying the post-transcriptional regulation of gene expression (PTR). With sections on bioinformatics approaches, expression profiling, the protein and RNA interactome, the mRNA lifecycle, and RNA modifications, the book guides molecular biologists toward harnessing the power of this new generation of techniques, while also introducing the data analysis skills that these high-throughput techniques require. Written for the highly successful Methods in Molecular Biology series, 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 up-to-date, Post-Transcriptional Gene Regulation, Third Edition serves as a versatile resource for researchers studying post-transcriptional regulation by both introducing the most recent techniques and providing a comprehensive guide to their implementation. Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Gene Mapping Discovery And Expression
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Author : Minou Bina
language : en
Publisher: Springer Science & Business Media
Release Date : 2008-02-04
Gene Mapping Discovery And Expression written by Minou Bina and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-02-04 with Science categories.
Completion of the sequence of the human genome represents an unpar- leled achievement in the history of biology. The project has produced nearly complete, highly accurate, and comprehensive sequences of genomes of s- eral organisms including human, mouse, drosophila, and yeast. Furthermore, the development of high-throughput technologies has led to an explosion of projects to sequence the genomes of additional organisms including rat, chimp, dog, bee, chicken, and the list is expanding. The nearly completed draft of genomic sequences from numerous species has opened a new era of research in biology and in biomedical sciences. In keeping with the interdisciplinary nature of the new scientific era, the chapters in Gene Mapping, Discovery, and Expression: Methods and Protocols recapitulate the necessity of integration of experimental and computational tools for solving - portant research problems. The general underlying theme of this volume is DNA sequence-based technologies. At one level, the book highlights the importance of databases, genome-browsers, and web-based tools for data access and ana- sis. More specifically, sequencing projects routinely deposit their data in p- licly available databases including GenBank, at the National Center of Biotechnology (NCBI) in the United States; EMBL, maintained by the European Bioinformatics Institute; and DDBJ, the DNA Data Bank of Japan. Currently, several browsers offer facile access to numerous genomic DNA sequences for gene mapping and data retrieval.
Rna Metabolism In Neurodegenerative Diseases
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Author : Rita Sattler
language : en
Publisher: Springer
Release Date : 2018-06-18
Rna Metabolism In Neurodegenerative Diseases written by Rita Sattler and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-06-18 with Medical categories.
It has become evident over the last years that abnormalities in RNA processing play a fundamental part in the pathogenesis of neurodegenerative diseases. Cellular viability depends on proper regulation of RNA metabolism and subsequent protein synthesis, which requires the interplay of many processes including transcription, pre--‐mRNA splicing, mRNA editing as well as mRNA stability, transport and translation. Dysfunction in any of these processes, often caused by mutations in the coding and non--‐ coding RNAs, can be very destructive to the cellular environment and consequently impair neural viability. The result of this RNA toxicity can lead to a toxic gain of function or a loss of function, depending on the nature of the mutation. For example, in repeat expansion disorders, such as the newly discovered hexanucleotide repeat expansion in theC9orf72 gene found in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), a toxic gain of function leads to the formation of RNA foci and the sequestration of RNA binding proteins (RBPs). This in return leads to a loss of function of those RBPs, which is hypothesized to play a significant part in the disease progression of ALS and FTD. Other toxicities arising from repeat expansions are the formation of RNA foci, bi--‐directional transcription and production of repeat associated non--‐ATG (RAN) translation products. This book will touch upon most of these disease mechanisms triggered by aberrant RNA metabolism and will therefore provide a broad perspective of the role of RNA processing and its dysfunction in a variety of neurodegenerative disorders, including ALS, FTD, Alzheimer’s disease, Huntington’s disease, spinal muscular atrophy, myotonic dystrophy and ataxias. The proposed authors are leading scientists in the field and are expected to not only discuss their own work, but to be inclusive of historic as well as late breaking discoveries. The compiled chapters will therefore provide a unique collection of novel studies and hypotheses aimed to describe the consequences of altered RNA processing events and its newest molecular players and pathways.