Download or read book Enzyme Mediated Ligation Methods written by Timo Nuijens and published by Springer Nature. This book was released on 2019-06-03 with total page 369 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume discusses different enzyme-catalyzed ligation methodologies for a variety of different chemical transformations. This book wants readers to view enzymes as a powerful tool in both academic and industrial research. Chapters in this book cover topics such as sortase A-mediated generation of site-specifically conjugated antibody-drug conjugates; omniligase-catalyzed inter- and intramolecular ligation; ligation catalyzed by microbial transglutaminase; peptide cyclization mediated by cyanobactin macrocyclases, butelase 1 and sortase A; using BioID as a tool for protein proximity labeling in living cells; and inducible, selective labeling of proteins via enzymatic oxidation of tyrosine. 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 thorough, Enzyme-Mediated Ligation Methods is a valuable resource for students and scientists from different disciplines who are interested in using enzymatic strategies to answer their research questions.
Download or read book Enzyme mediated Labeling of Proteins and Protein protein Interactions in Vitro and in Living Cells written by Sarah Ann Slavoff and published by . This book was released on 2010 with total page 250 pages. Available in PDF, EPUB and Kindle. Book excerpt: The E. coli biotin ligase enzyme, BirA, has been previously used by the Ting research group for site-specific labeling of peptide-tagged cell surface proteins. We sought to expand the utility of biotin ligase-mediated labeling to functional group handles, including azides and alkynes, for bio-orthogonal chemistry. Since the BirA and its point mutants were unable to ligate these probes to an acceptor peptide, we screened biotin ligases from multiple species to identify more permissive enzymes. We determined that the Pyrococcus horikoshii biotin ligase utilizes an azide-bearing biotin analog and that the Saccharomyces cerevisiae biotin ligase can utilize an alkyne-functionalized biotin analog. We subsequently demonstrated that the azidefunctionalized biotin analog can be derivatized with a phosphine probe via the Staudinger ligation. We next turned to the goal of delivering quantum dots to the cytosol of living cells, which in the future may permit intracellular single-molecule imaging. We investigated viral methods of delivery, but found that our protocol caused quantum dots to be trapped in endocytic vesicles. We then validated previous reports that the pore-forming toxin streptolysin 0 be used to deliver quantum dots to the cytosol of living cells. Lipoic acid ligase, or LpIA, has been previously applied to site-specific protein labeling of peptide-tagged proteins using small molecule probes including lipoic acid and coumarin fluorophores. We utilized LpIA and its substrate, the LAP peptide, to create sensors for proteinprotein interactions. If LpIA is fused to one protein and LAP is fused to another, only when the two proteins interact do LpIA and LAP come into proximity, allowing probe ligation onto the peptide to occur as a readout of the interaction. We demonstrate that proximity-dependent coumarin ligation detects protein-protein interactions in living mammalian cells with extremely low background, a signal-to-background ratio of at least 5:1, and sufficiently fast kinetics to label interactions with a half-life of at least 1 minute. The reporter quantitatively responds to subpopulations of interacting proteins, allowing dissociation constants to be measured. Coumarin fluorescence accurately reports the subcellular localization of the interaction under study. Finally, we applied proximity-dependent coumarin ligation to imaging of the interaction of PSD-95 and neuroligin-1, two proteins involved in synaptic maturation, in neurons.
Download or read book Driving Sortase mediated Ligations Using Metal coordinating Peptides written by Sierra Reed and published by . This book was released on 2018 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: The versatility of sortase-mediated ligations as a protein modification technique has been well demonstrated, but the efficiency of these reactions suffers from inherent reversibility. Solutions to this issue have been reported, however these methods are accompanied by additional limitations of the sortase-mediated ligation (SML) strategy. A preferable methodology would include the smallest possible modification site without restricting the point of ligation. One promising solution to this issue is the expansion of the LPXTG SrtA recognition sequence to LPXTGGH, giving the excised fragment an N-terminal GGH motif. This minor alteration has been shown to allow complexation of the excised fragment with Ni2+ ions, thus sequestering this component from the reaction and improving yields through hindered reversibility. In this thesis, we explore the scope of this metal-assisted sortase-mediated ligation (MASML) approach, including the Ni2+-enhanced modification of full sized proteins with a number of useful chromophores. Furthermore, this approach was shown to be compatible with the installation of PEG and a cyclooctyne bioorthogonal ligation handle. In total, this work demonstrates that MASML is compatible with a range of high value protein targets and modifications, and shows how MASML is a straightforward method for improving the efficiency of sortase-mediated protein engineering strategies.
Download or read book Expressed Protein Ligation written by Miquel Vila-Perelló and published by Humana. This book was released on 2020-03-07 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive overview of Expressed Protein Ligation (EPL), detailing methods and protocols to generate site-specifically modified proteins. Chapters include an overview of the protein semi-synthesis field, as well as related areas that have contributed to the development of EPL such as protein splicing and peptide synthesis. Following the introductory chapters, the rest of the book guides readers through protocols to perform EPL reactions, methods to synthesize peptide thioesters and to perform peptide and protein ligations, label proteins inside living cells, protocols for the semi-synthesis of phorphorylated, glycosylated and ubiquitylated proteins, synthesis and assembly of assymetrically modified nucleosomes, use of ligation auxiliaries and synthesis of cyclic proteins, as well as novel desulfurization strategies and use of selective Cys side chain protection to obtain precisely modified 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. Authoritative and cutting-edge, Expressed Protein Ligation: Methods and Protocols will ensure successful implementation of protein semi-synthesis methods to further study the structure and function of proteins.
Download or read book Plant Cyclotides written by and published by Academic Press. This book was released on 2015-11-24 with total page 404 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Botanical Research publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences. Currently in its 76th volume, the series features several reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecology. - Publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences - Contains commentary by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology, and ecology - This volume features reviews of the fast moving field of plant cyclotides
Download or read book Chemoselective and Bioorthogonal Ligation Reactions written by W. Russ Algar and published by John Wiley & Sons. This book was released on 2017-06-19 with total page 766 pages. Available in PDF, EPUB and Kindle. Book excerpt: This timely, one-stop reference is the first on an emerging and interdisciplinary topic. Covering both established and recently developed ligation chemistries, the book is divided into two didactic parts: a section that focuses on the details of bioorthogonal and chemoselective ligation reactions at the level of fundamental organic chemistry, and a section that focuses on applications, particularly in the areas of chemical biology, biomaterials, and bioanalysis, highlighting the capabilities and benefits of the ligation reactions. With chapters authored by outstanding scientists who range from trailblazers in the field to young and emerging leaders, this book on a highly interdisciplinary topic will be of great interest for biochemists, biologists, materials scientists, pharmaceutical chemists, organic chemists, and many others.
Download or read book Organic Reactions Volume 97 written by and published by John Wiley & Sons. This book was released on 2019-01-14 with total page 718 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 97th volume in this series for organic chemists in industry presents critical discussions of widely used organic reactions or particular phases of a reaction. The material is treated from a preparative viewpoint, with emphasis on limitations, interfering influences, effects of structure and the selection of experimental techniques. The work includes tables that contain all possible examples of the reaction under consideration. Detailed procedures illustrate the significant modifications of each method.
Download or read book Non Ribosomal Peptide Biosynthesis and Engineering written by Michael Burkart and published by Springer Nature. This book was released on 2023-05-15 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides new technologies on NRPSs and related carrier protein dependent synthases, including polyketide synthases (PKS) and fatty acid synthases (FAS). Chapters detail enzymology, structural biology, proteopromics, chemical biology, natural product chemistry, and bioinformatics. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Non-Ribosomal Peptide Biosynthesis and Engineering: Methods and Protocols aims to feature methods that will be beneficial to new researchers, and those wanting to adopt new methodologies into their research.
Download or read book Engineering the Genetic Code written by Nediljko Budisa and published by John Wiley & Sons. This book was released on 2006-05-12 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ability to introduce non-canonical amino acids in vivo has greatly expanded the repertoire of accessible proteins for basic research and biotechnological application. Here, the different methods and strategies to incorporate new or modified amino acids are explained in detail, including a lot of practical advice for first-time users of this powerful technique. Novel applications in protein biochemistry, genomics, biotechnology and biomedicine made possible by the expansion of the genetic code are discussed and numerous examples are given. Essential reading for all molecular life scientists who want to stay ahead in their research.
Download or read book Total Chemical Synthesis of Proteins written by Ashraf Brik and published by John Wiley & Sons. This book was released on 2021-06-08 with total page 626 pages. Available in PDF, EPUB and Kindle. Book excerpt: How to synthesize native and modified proteins in the test tube With contributions from a panel of experts representing a range of disciplines, Total Chemical Synthesis of Proteins presents a carefully curated collection of synthetic approaches and strategies for the total synthesis of native and modified proteins. Comprehensive in scope, this important reference explores the three main chemoselective ligation methods for assembling unprotected peptide segments, including native chemical ligation (NCL). It includes information on synthetic strategies for the complex polypeptides that constitute glycoproteins, sulfoproteins, and membrane proteins, as well as their characterization. In addition, important areas of application for total protein synthesis are detailed, such as protein crystallography, protein engineering, and biomedical research. The authors also discuss the synthetic challenges that remain to be addressed. This unmatched resource: Contains valuable insights from the pioneers in the field of chemical protein synthesis Presents proven synthetic approaches for a range of protein families Explores key applications of precisely controlled protein synthesis, including novel diagnostics and therapeutics Written for organic chemists, biochemists, biotechnologists, and molecular biologists, Total Chemical Synthesis of Proteins provides key knowledge for everyone venturing into the burgeoning field of protein design and synthetic biology.
Download or read book Cancer Biology and the Nuclear Envelope written by Eric C. Schirmer and published by Springer Science & Business Media. This book was released on 2014-02-22 with total page 610 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Nuclear envelope (NE) defects have been linked to cancer biology since the mid-1800s, but it was not until the last few years that we have begun to understand these historical links and to realize that there are myriad ways that the NE impacts on tumorigenesis. The NE is a complex double membrane system that encloses the genome while providing structural support through the intermediate filament lamin polymer and regulating protein/ mRNA trafficking and signaling between the nucleus and cytoplasm via the nuclear pore complexes (NPCs). These functions already provide some mechanisms for NE influences on cancer biology but work in the past few years has elucidated many others. Lamins and many recently identified NE transmembrane proteins (NETs) have been now shown to function in DNA repair, regulation of cell cycle and signaling, apoptosis, cell migration in metastasis and nuclear architecture and morphology. This volume presents a comprehensive overview of the wide range of functions recently identified for NE proteins and their relevance in cancer biology, providing molecular mechanisms and evidence of their value as prognostic and diagnostic markers and suggesting new avenues for the treatment of cancer. Indeed some of these recent links are already yielding promising therapies, such as the current clinical trial of selective inhibitors of the nuclear export factor exportin in certain types of leukemia, melanoma and kidney cancer."
Download or read book The Handbook of Plant Mutation Screening written by Khalid Meksem and published by John Wiley & Sons. This book was released on 2009-12-21 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: Induced mutagenesis is a common and promising method for screening for new crops with improved properties. This title introduces the different methods and then focuses on the screening, detection and analysis of the novel mutations. Written by a global team of authors the book is an indispensable tool for all scientists working on crop breeding in industry and academia.
Download or read book Route Maps in Gene Technology written by Mark Walker and published by John Wiley & Sons. This book was released on 2009-07-17 with total page 336 pages. Available in PDF, EPUB and Kindle. Book excerpt: Route Maps in Gene Technology is an exciting new introductory textbook for first-year undergraduates in molecular biology and molecular genetics. The subject is broken down into 140 to 150 key concepts or topics, each of which is dealt with in one doublepaged spread. These range from basic introductory principles to applied topics at the cutting edge of research. A control strip along the top of the page shows the student which pages need to have been read beforehand and which topics may be followed afterward. In addition, at the front of the book are a selection of 'routes,' which the student or teacher may choose in order to study a particular topic. Because courses have become more 'modular' and many students arrive at college with little or no biology background, this approach enables teachers and students to structure a course of study to best suit their disparate exposure to biology. An exciting new concept in textbook design, allowing unparalleled flexibility on the part of the student and the teacher Covers the full range of modern molecular biology, from basic principles to the latest applications Attractive, clear and simple presentation with copious two-colour illustrations
Download or read book Proximity Labeling written by Murat Sunbul and published by Humana. This book was released on 2020-08-14 with total page 231 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides detailed protocols and untold tips and tricks regarding the most well-known examples of proximity labeling methods, in which the protein of interest is genetically fused to or labeled with an enzyme that can generate short-lived reactive species to non-specifically label molecules within a certain radius of up to twenty nanometers. Beginning with peroxidase-based proximity labeling methods, the volume continues with BioID, proximity labeling methods that describe the proximity ligation assay to detect RNA-DNA interactions, UV cross-linking to demonstrate RNA-protein interactions, and how chemical and enzymatic reactivities can be improved upon DNA-DNA and protein-protein interactions, as well as “proximity-induced self-labeling,” where the radius of labeling is zero. 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 practical, Proximity Labeling: Methods and Protocols serves as an ideal guide for researchers exploring the crucial roles that proximity-driven reactions play in biological systems.
Download or read book Enzymes of Epigenetics written by and published by Academic Press. This book was released on 2016-06-29 with total page 554 pages. Available in PDF, EPUB and Kindle. Book excerpt: Enzymes of Epigenetics, one of two new volumes in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods that are employed to study epigenetic regulation and includes structural, biochemical, molecular, biological, cellular, computational, and systems approaches. Topics include chromatin structure and histones, posttranslational histone modification enzymes and complexes, histone modification binders, DNA modifications and nucleic acid regulators, epigenetic technologies and small molecule epigenetic regulators, and biological connections - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Contains two new volumes covering research methods in enzymes of epigenetics - Covers topics such as chromatin structure and histones, posttranslational histone modification enzymes and complexes, histone modification binders, DNA modifications and nucleic acid regulators, epigenetic technologies and small molecule epigenetic regulators and biological connections
Download or read book Synthetic Biology written by Maxim Ryadnov and published by Royal Society of Chemistry. This book was released on 2014-06-30 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: Leading researchers draw on the recent literature in Synthetic Biology, from both dedicated journals and broader sources, making this an essential reference to any library supporting this research in this emerging field.
Download or read book DNA Nanotechnology written by Chunhai Fan and published by Springer Nature. This book was released on 2020-09-07 with total page 406 pages. Available in PDF, EPUB and Kindle. Book excerpt: The series Topics in Current Chemistry Collections presents critical reviews from the journal Topics in Current Chemistry organized in topical volumes. The scope of coverage is all areas of chemical science including the interfaces with related disciplines such as biology, medicine and materials science. The goal of each thematic volume is to give the non-specialist reader, whether in academia or industry, a comprehensive insight into an area where new research is emerging which is of interest to a larger scientific audience. Each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years are presented using selected examples to illustrate the principles discussed. The coverage is not intended to be an exhaustive summary of the field or include large quantities of data, but should rather be conceptual, concentrating on the methodological thinking that will allow the non-specialist reader to understand the information presented. Contributions also offer an outlook on potential future developments in the field. The chapter "DNA-Programmed Chemical Synthesis of Polymers and Inorganic Nanomaterials" is available open access under a CC BY 4.0 License via link.springer.com.
