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Download or read book PUF Proteins written by Laura J. Opperman and published by . This book was released on 2008 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book PUF Proteins written by Brad A. Hook and published by . This book was released on 2006 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Target Selection by Natural and Redesigned PUF Proteins by : Douglas F. Porter
Download or read book Target Selection by Natural and Redesigned PUF Proteins written by Douglas F. Porter and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-binding proteins define extensive, subtle networks of regulation in Eukaryotes. RNA-binding proteins control the amount of protein produced from mRNA, the location of translation and the protein isoform produced. Pumilio/PUF proteins are a family of RNA-binding protein families present in humans, as well as Eukaryotes in general, one of a limited number of such families. Pumilio/PUF proteins bind specific sequences in single-stranded RNA. The modular nature of the PUF-RNA interaction has led to the use of Pumilio/PUF proteins in reengineering RNA-binding proteins to recognize new RNA motifs. S. cerevisiae possesses a Pumilio/PUF protein representing a special subfamily we term the Puf2p family. The Puf2p family recognizes the unusual cognate motif of UAAU in RNA. We identify the RNA-binding map of S. cerevisiae Puf2p, determining that Puf2p binds roughly a fifth of the yeast genome and binds through clusters of UAAU motifs in 3'UTRs. In addition, we find that regions outside the PUF domain affect binding. Next, we reengineered Puf2p to recognize a UAAG site, and identified that the reengineered Puf2p binds its novel site in RNA with the same specificity as wild-type or greater. We evaluate the prediction of the RNA-binding map of a redesigned protein, and find that PUF-RNA interactions involve many factors beyond the binding site. We find that Puf2p is a repressor, and that reengineered Puf2p represses a novel RNA network. Our results suggest that direct RNA-binding by PUF proteins has small effects on many RNAs and large effects on a few RNAs. We find that, when redesigned to a new specificity, redesigned PUF proteins conserve targets, partly by finding new sites in the same mRNAs. Next, we identified the RNA binding specificity of the conserved stem cell regulator and PUF protein FBF in C. elegans. We find that FBF binds predominantly in mRNA 3'UTRs at its cognate motif, but that it also binds an alternative 7-mer site in the cell and that many FBF interaction sites are 'secondary' interactions near a stronger, primary interaction. Our results suggest a method for improving our understanding of RNA-protein interactions.
Book Synopsis Protein Structure and Modeling by : Natalya Kurochkina
Download or read book Protein Structure and Modeling written by Natalya Kurochkina and published by Springer. This book was released on 2019-06-04 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book will consider principles of the organization of protein molecules, the relationships between primary, secondary, and tertiary structure, the determinants of protein conformation, and the applications of structure determination and structure modeling in biomedical research.
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 Diverse PUFs with Distinct PBEs by : Craig Robert Stumpf
Download or read book Diverse PUFs with Distinct PBEs written by Craig Robert Stumpf and published by . This book was released on 2008 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The PUF Chronicles by : David S. Bernstein
Download or read book The PUF Chronicles written by David S. Bernstein and published by . This book was released on 2004 with total page 164 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Systems Biology of RNA Binding Proteins by : Gene W. Yeo
Download or read book Systems Biology of RNA Binding Proteins written by Gene W. Yeo and published by Springer. This book was released on 2014-09-08 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: After transcription in the nucleus, RNA binding proteins (RBPs) recognize cis-regulatory RNA elements within pre-mRNA sequence to form mRNA-protein (mRNP) complexes. Similarly to DNA binding proteins such as transcription factors that regulate gene expression by binding to DNA elements in the promoters of genes, RBPs regulate the fate of target RNAs by interacting with specific sequences or RNA secondary structural features within the transcribed RNA molecule. The set of functional RNA elements recognized by RBPs within target RNAs and which control the temporal, functional and spatial dynamics of the target RNA define a putative “mRNP code”. These cis-regulatory RNA elements can be found in the 5’ and 3’ untranslated regions (UTRs), introns, and exons of all protein-coding genes. RNA elements in 5’ and 3’ UTRs are frequently involved in targeting RNA to specific cellular compartments, affecting 3’ end formation, controlling RNA stability and regulating mRNA translation. RNA elements in introns and exons are known to function as splicing enhancers or silencers during the splicing process from pre-mRNA to mature mRNA. This book provides case studies of RNA binding proteins that regulate aspects of RNA processing that are important for fundamental understanding of diseases and development. Chapters include systems-level perspectives, mechanistic insights into RNA processing and RNA Binding proteins in genetic variation, development and disease. The content focuses on systems biology and genomics of RNA Binding proteins and their relation to human diseases.
Book Synopsis Germline Stem Cells by : Steven X. Hou
Download or read book Germline Stem Cells written by Steven X. Hou and published by Humana Press. This book was released on 2014-10-15 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this comprehensive and cutting-edge book, leading experts explore the parameters that define germline stem cells and the mechanisms that regulate the cell behavior in order to better isolate, characterize and maintain them. The volume begins by providing protocols for germline stem cell identification and regulation in model organisms, and concludes with detailed chapters covering current techniques involving in vitro culture and the applications of the cells.
Book Synopsis Protein-Nucleic Acid Interactions by : Phoebe A Rice
Download or read book Protein-Nucleic Acid Interactions written by Phoebe A Rice and published by Royal Society of Chemistry. This book was released on 2008-04-22 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: The structural biology of protein-nucleic acid interactions is in some ways a mature field and in others in its infancy. High-resolution structures of protein-DNA complexes have been studied since the mid 1980s and a vast array of such structures has now been determined, but surprising and novel structures still appear quite frequently. High-resolution structures of protein-RNA complexes were relatively rare until the last decade. Propelled by advances in technology as well as the realization of RNA's importance to biology, the number of example structures has ballooned in recent years. New insights are now being gained from comparative studies only recently made possible due to the size of the database, as well as from careful biochemical and biophysical studies. As a result of the explosion of research in this area, it is no longer possible to write a comprehensive review. Instead, current review articles tend to focus on particular subtopics of interest. This makes it difficult for newcomers to the field to attain a solid understanding of the basics. One goal of this book is therefore to provide in-depth discussions of the fundamental principles of protein-nucleic acid interactions as well as to illustrate those fundamentals with up-to-date and fascinating examples for those who already possess some familiarity with the field. The book also aims to bridge the gap between the DNA- and the RNA- views of nucleic acid - protein recognition, which are often treated as separate fields. However, this is a false dichotomy because protein - DNA and protein - RNA interactions share many general principles. This book therefore includes relevant examples from both sides, and frames discussions of the fundamentals in terms that are relevant to both. The monograph approaches the study of protein-nucleic acid interactions in two distinctive ways. First, DNA-protein and RNA-protein interactions are presented together. Second, the first half of the book develops the principles of protein-nucleic acid recognition, whereas the second half applies these to more specialized topics. Both halves are illustrated with important real life examples. The first half of the book develops fundamental principles necessary to understand function. An introductory chapter by the editors reviews the basics of nucleic acid structure. Jen-Jacobsen and Jacobsen discuss how solvent interactions play an important role in recognition, illustrated with extensive thermodynamic data on restriction enzymes. Marmorstein and Hong introduce the zoology of the DNA binding domains found in transcription factors, and describe the combinational recognition strategies used by many multiprotein eukaryotic complexes. Two chapters discuss indirect readout of DNA sequence in detail: Berman and Lawson explain the basic principles and illustrate them with in-depth studies of CAP, while in their chapter on DNA bending and compaction Johnson, Stella and Heiss highlight the intrinsic connections between DNA bending and indirect readout. Horvath lays out the fundamentals of protein recognition of single stranded DNA and single stranded RNA, and describes how they apply in a detailed analysis of telomere end binding proteins. Nucleic acids adopt more complex structures - Lilley describes the conformational properties of helical junctions, and how proteins recognize and cleave them. Because RNA readily folds due to the stabilizing role of its 2'-hydroxyl groups, Li discusses how proteins recognize different RNA folds, which include duplex RNA. With the fundamentals laid out, discussion turns to more specialized examples taken from important aspects of nucleic acid metabolism. Schroeder discusses how proteins chaperone RNA by rearranging its structure into a functional form. Berger and Dong discuss how topoisomerases alter the topology of DNA and relieve the superhelical tension introduced by other processes such as replication and transcription. Dyda and Hickman show how DNA transposes mediate genetic mobility and Van Duyne discusses how site-specific recombinases "cut" and "paste" DNA. Horton presents a comprehensive review of the structural families and chemical mechanisms of DNA nucleases, whereas Li in her discussion of RNA-protein recognition also covers RNA nucleases. Lastly, FerrÚ-D'AmarÚ shows how proteins recognize and modify RNA transcripts at specific sites. The book also emphasises the impact of structural biology on understanding how proteins interact with nucleic acids and it is intended for advanced students and established scientists wishing to broaden their horizons.
Book Synopsis Evolution of RNA-PUF Protein Networks by :
Download or read book Evolution of RNA-PUF Protein Networks written by and published by . This book was released on 2015 with total page 200 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins bind and control mRNAs, directing their localization, translation, and stability. Members of the PUF family of RNA-binding proteins control multiple mRNAs in a single cell, and play key roles in development, stem cell maintenance and memory formation. Here we demonstrate the conservation of PUF regulatory networks by bioinformatic analysis. We identified the mRNA targets of two Saccharomyces cerevisiae PUF proteins, Puf3p and Puf5p, and two Neurospora crassa PUF proteins, PUF3 and PUF5, by UV-crosslinking-affinity purification and high-throughput sequencing (HITS-CLIP). Taken together these data allowed us to elucidate a rewiring of a nulcear-endcoded circuit of mitochondrial related mRNAs. S. cerevisiae Puf5p associates with ~1,000 RNAs, suggesting that it is a broad spectrum regulator. The binding sites recognized by both Puf5 proteins are diverse, with variable spacer lengths between two specific sequences. S. cerevisiae Puf3p binds a group of RNAs significantly enriched for nuclear encoded RNAs that code for mitochondrial proteins. Many of these orthologous RNAs are bound by N. crassa PUF5. This constitutes a switch, from Puf3p to Puf5, regulation, when comparing S. cerevisiae and N. crassa PUF regulatory networks. Crystal structures of S. cerevisiae Puf5p-RNA complexes reveal that the protein scaffold presents an exceptionally flat and extended interaction surface relative to other PUF proteins. A single PUF protein repeat is sufficient to induce broadening of specificity. Changes in protein architecture, such as alterations in curvature, may have led to evolution of mRNA regulatory networks which we observe.
Book Synopsis Inducing Targeted Protein Degradation by : Philipp Cromm
Download or read book Inducing Targeted Protein Degradation written by Philipp Cromm and published by John Wiley & Sons. This book was released on 2022-11-15 with total page 389 pages. Available in PDF, EPUB and Kindle. Book excerpt: Inducing Targeted Protein Degradation Enables drug developers in academia and industry to expand the range of accessible drug targets through induced protein degradation Since the breakthrough of the PROTAC technology in 2015, targeted protein degradation has revolutionized drug discovery, enabling pharma companies to develop completely novel therapeutics. Inducing Targeted Protein Degradation is a timely guide to navigating the complexities of the subject and understanding its practical application, with an eye on expanding the druggable space. In Inducing Targeted Protein Degradation, readers will find the most recent information on: Cellular mechanisms of targeted protein degradation and current approaches to utilize these mechanisms for drug discovery A comparison of different induced degradation approaches, including PROTAC, molecular glues, LYTACs and ATTECs as well as additional post translational modifications Drug development aspects such as DMPK optimization and criteria for the selection of clinical candidates A discussion of the potential of targeted degradation for expanding the druggable space Inducing Targeted Protein Degradation will serve as a practice-oriented reference on induced protein degradation for drug discovery professionals and for researchers employing chemical biology approaches.
Book Synopsis Introduction to Proteins by : Amit Kessel
Download or read book Introduction to Proteins written by Amit Kessel and published by CRC Press. This book was released on 2018-03-22 with total page 1423 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the structure, function, and motion of proteins for students, faculty, and researchers at all levels. The book covers proteins and enzymes across a wide range of contexts and applications, including medical disorders, drugs, toxins, chemical warfare, and animal behavior. Each chapter includes a Summary, Exercies, and References. New features in the thoroughly-updated second edition include: A brand-new chapter on enzymatic catalysis, describing enzyme biochemistry, classification, kinetics, thermodynamics, mechanisms, and applications in medicine and other industries. These are accompanied by multiple animations of biochemical reactions and mechanisms, accessible via embedded QR codes (which can be viewed by smartphones) An in-depth discussion of G-protein-coupled receptors (GPCRs) A wider-scale description of biochemical and biophysical methods for studying proteins, including fully accessible internet-based resources, such as databases and algorithms Animations of protein dynamics and conformational changes, accessible via embedded QR codes Additional features Extensive discussion of the energetics of protein folding, stability and interactions A comprehensive view of membrane proteins, with emphasis on structure-function relationship Coverage of intrinsically unstructured proteins, providing a complete, realistic view of the proteome and its underlying functions Exploration of industrial applications of protein engineering and rational drug design Each chapter includes a Summary, Exercies, and References Approximately 300 color images Downloadable solutions manual available at www.crcpress.com For more information, including all presentations, tables, animations, and exercises, as well as a complete teaching course on proteins' structure and function, please visit the author's website: http://ibis.tau.ac.il/wiki/nir_bental/index.php/Introduction_to_Proteins_Book. Praise for the first edition "This book captures, in a very accessible way, a growing body of literature on the structure, function and motion of proteins. This is a superb publication that would be very useful to undergraduates, graduate students, postdoctoral researchers, and instructors involved in structural biology or biophysics courses or in research on protein structure-function relationships." --David Sheehan, ChemBioChem, 2011 "Introduction to Proteins is an excellent, state-of-the-art choice for students, faculty, or researchers needing a monograph on protein structure. This is an immensely informative, thoroughly researched, up-to-date text, with broad coverage and remarkable depth. Introduction to Proteins would provide an excellent basis for an upper-level or graduate course on protein structure, and a valuable addition to the libraries of professionals interested in this centrally important field." --Eric Martz, Biochemistry and Molecular Biology Education, 2012
Book Synopsis Multifunctional Proteins by : James F. Kane
Download or read book Multifunctional Proteins written by James F. Kane and published by CRC Press. This book was released on 2019-06-04 with total page 132 pages. Available in PDF, EPUB and Kindle. Book excerpt: First Published in 1983, this book offers a full, comprehensive guide into proteins and their functions. Carefully compiled and filled with a vast repertoire of notes, diagrams, and references this book serves as a useful reference for Students of Alternative Medicine, and other practitioners in their respective fields.
Book Synopsis New and Developing Sources of Food Proteins by : B.J.F. Hudson
Download or read book New and Developing Sources of Food Proteins written by B.J.F. Hudson and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 377 pages. Available in PDF, EPUB and Kindle. Book excerpt: The recent series of texts 'Developments in Food Proteins' comprised in all seven volumes which were published in the course of the decade 1982-1991. Each volume contained inter alia one or more chapters that were concerned with new or developing sources of food proteins. Most of these have now been collected together in an up dated and re-evaluated form for the present volume. 'New' sources of food proteins includes those sources that are unconventional, that are still of very limited significance in market terms, or that are at present of very localized use. Several of these were included in 'Developments in Food Proteins'. One of them, algae, appeared both in Volume 1 and in an up-dated form in Volume 7. It is therefore not included here. Others, such as yeasts and bacteria, have not yet increased in practical importance as potential food components beyond the long-term promise already evident at that time. However, leaf protein, as described in the present Chapter 10, has moved from the original rather crude concept to a much more sophisticated product in the form of Rubisco. Fungal protein, as Quorn (Chapter 11), has also proved to be potentially of real food value. 'Developing' sources of food protein are those sources that have always been basic items in human diets.
Book Synopsis Protein Research Progress by : Alan B. Boscoe
Download or read book Protein Research Progress written by Alan B. Boscoe and published by Nova Publishers. This book was released on 2008 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by a gene and encoded in the genetic code. Although this genetic code specifies 20 'standard' amino acids, the residues in a protein are often chemically altered in post-translational modification: either before the protein can function in the cell, or as part of control mechanisms. Proteins can also work together to achieve a particular function, and they often associate to form stable complexes. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in every process within cells. Many proteins are enzymes that catalyse biochemical reactions, and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle, and the proteins in the cytoskeleton, which forms a system of scaffolding that maintains cell shape. Other proteins are important in cell signalling, immune responses, cell adhesion, and the cell cycle. Protein is also a necessary part of animals' diets, since they cannot synthesise all the amino acids and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that can be used for protein synthesis. This new book presents the latest research in the field.
Book Synopsis Food Proteins and Their Applications by : Srinivasan Damodaran
Download or read book Food Proteins and Their Applications written by Srinivasan Damodaran and published by CRC Press. This book was released on 1997-03-12 with total page 696 pages. Available in PDF, EPUB and Kindle. Book excerpt: Reviews the physiochemical properties of the main food proteins and explores the interdependency between the structure-function relationship of specific protein classes and the processing technologies applied to given foods. The book offers solutions to current problems related to the complexity of food composition, preparation and storage, and includes such topics as foams, emulsions, gelation by macromolecules, hydrolysis, microparticles/fat replacers, protein-based edible films, and extraction procedures.