Download or read book Structure and Thermodynamics of RNA protein Interactions written by Carolina Moises Reyes and published by . This book was released on 2000 with total page 446 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 2008-05-22 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides both in-depth background and up-to-date information in this area. The chapters are organized by general themes and principles, written by experts who illustrate topics with current findings. Topics covered include: - the role of ions and hydration in protein-nucleic acid interactions - transcription factors and combinatorial specificity - indirect readout of DNA sequence - single-stranded nucleic acid binding proteins - nucleic acid junctions and proteins, - RNA protein recognition - recognition of DNA damage. It will be a key reference for both advanced students and established scientists wishing to broaden their horizons.
Download or read book RNA Protein Interaction Protocols written by Susan R. Haynes and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 485 pages. Available in PDF, EPUB and Kindle. Book excerpt: The molecular characterization of RNA and its interactions with proteins is an important and exciting area of current research. Organisms utilize a variety of RNA–protein interactions to regulate the expression of their genes. This is particularly true for eukaryotes, since newly synthesized messenger RNA must be extensively modified and transported to the cytoplasm before it can be used for protein synthesis. The realization that posttranscriptional processes are critical components of gene regulation has sparked an explosion of interest in both stable ribonucleoprotein (RNP) complexes and transient RNA–protein interactions. RNA is conformationally flexible and can adopt complex structures that provide diverse surfaces for interactions with proteins. The fact that short RNA molecules (aptamers; see Chapter 16) can be selected to bind many different types of molecules is evidence of the structural variability of RNA. RNA molecules are rarely entirely single- or double-stranded, but usually contain multiple short duplexes interrupted by single-stranded loops and bulges; in some RNAs, such as tRNAs, the short duplexes stack on each other. Further variability is generated by the presence of non-Watson-Crick base pairs, modified nucleotides, and more complex structures, such as pseudoknots and triple-strand interactions.
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.
Download or read book Introduction to Protein DNA Interactions written by Gary Stormo and published by . This book was released on 2013 with total page 198 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the foundations of molecular biology is how the interactions of proteins with DNA control many aspects of gene expression. Since the mid-20th century discoveries of the lac repressor and operator and the competition between the cI and cro proteins for the same segment of DNA, we have learned an enormous amount about the interactions of proteins with DNA and their control of fundamental processes in the cell. Introduction to Protein-DNA Interactions: Structure, Thermodynamics, and Bioinformatics describes what we know about protein-DNA interactions from the complementary perspectives of molecular and structural biology and bioinformatics and how each perspective informs the others. A particular emphasis is on how insights from experimental work can be translated into specific computational approaches to create unified view of the field and a fuller understanding of protein-DNA interactions.
Download or read book RNA Protein Interactions A Practical Approach written by Christopher W.J. Smith and published by Oxford University Press, UK. This book was released on 1998-07-09 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-protein interactions play a fundamental role in gene expression and protein synthesis. Recent research into the role of RNA in cells has elucidated many more vital interactions with proteins. This book provides an up-to-date and comprehensive guide to a wide range of laboratory procedures to investigate the interactions between RNA and proteins. - ;RNA-protein interactions play a vital role in gene transcription and protein expression. Interactions such as the synthesis of mRNA by RNA polymerases, to the essential modification of RNA by the proteins of the spliceosome complex, and the highly catalytic action of the ribosome in protein synthesis, are established as being fundamental to the function of RNA. Recent research into, for example, the role of RNA as a catalyst, has elucidated many more interactions with proteins that are vital to cell function. RNA - Protein Interactions: A Practical Approach provides a clear and comprehensive guide to the experimental procedures used in studying RNA - protein interactions. The approaches covered range from those initially used to detect a novel RNA-protein interaction, various biochemical and genetic approaches to purifying and cloning RNA binding proteins, through to methods for an in depth analysis of the structural basis of the interaction. The volume includes a number of procedures that have not previously been covered in this type of manual. These include the production of site-specifically modified RNAs by enzymatic and chemical methods and in vivo screening for novel RNA - protein interactions in yeast and E. coli . This is the first volume to gather in one place this wide array of approaches for studying RNA - protein interactions. As is customary for the Practical Approach series, the writing is characterized by a clear explanatory style with many detailed protocols. This informative book will be a valuable aid to laboratory workers in biochemistry and molecular biology - graduate students, postdoctoral and senior scientists - whose research encompasses this field. -
Download or read book Biophysics of RNA Protein Interactions written by Chirlmin Joo and published by Springer Nature. This book was released on 2019-09-19 with total page 249 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA molecules play key roles in all aspects of cellular life, but to do so efficiently, they must work in synergism with proteins. This book addresses how proteins and RNA interact to carry out biological functions such as protein synthesis, regulation of gene expression, genome defense, liquid phase separation and more. The topics addressed in this volume will appeal to researchers in biophysics, biochemistry and structural biology. The book is a useful resource for anybody interested in elucidating the molecular mechanisms and discrete properties of RNA-protein complexes. Included are reviews of key systems such as microRNA and CRISPR/Cas that exemplify how RNA and proteins work together to perform their biological function. Also covered are techniques ranging from single molecule fluorescence and force spectroscopy to crystallography, cryo-EM microscopy, and kinetic modeling.
Download or read book Biophysical Chemical and Functional Probes of RNA Structure Interactions and Folding Part A written by Daniel Herschlag and published by Academic Press. This book was released on 2009-11-16 with total page 491 pages. Available in PDF, EPUB and Kindle. Book excerpt: This MIE volume provides laboratory techniques that aim to predict the structure of a protein which can have tremendous implications ranging from drug design, to cellular pathways and their dynamics, to viral entry into cells. - Expert researchers introduce the most advanced technologies and techniques in protein structure and folding - Includes techniques on tiling assays
Download or read book RNA Biochemistry and Biotechnology written by Jan Barciszewski and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 373 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA Biochemistry and Biotechnology describes various aspects of nucleic acid and protein structure, mainly RNA structure and proteins, interacting with specific RNA species. Papers deal with DNA protein interactions, telomerase, aminoacyl-tRNA synthetases, elongation factor Tu, DNA repair, RNA structure, NMR technology, RNA aptamer interaction of biological macromolecules with metal ions. Two papers deal with theoretical aspects of RNA structure production and computer modelling. Many papers describe the possibility of commercial application of RNA biotechnology. One article discusses the impact of direct democracy on basic science supporting biotechnology. Readership: Advanced graduate students, Ph.D. students and young scientists as well as specialists in the field.
Download or read book The Interplay Between Single stranded Binding Proteins on RNA Secondary Structure written by Yi-Hsuan Lin and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Interactions between RNAs and RNA-binding proteins (RBPs) are significant in post-transcriptional regulation. In this process, an mRNA molecule is bound by many proteins and/or microRNAs to modulate its function. It is therefore an interesting question how these multiple RBPs collaborate to enable combinatorial gene regulation. Here, we propose a possible mechanism which can support this RBP-RBP collaboration, termed "cooperativity". Such a cooperativity can exist merely based on fundamental principles of statistical physics and thermodynamics of RNA structure folding, without considering any further details of RNA and RBP properties. The theory is based on the idea that a successfully binding RBP will prohibit the formation of some originally allowed RNA structures, thus changing the statistical properties of the RNA structure ensemble, as well as the binding probabilities of other RBPs on the same RNA. In addition, this mechanism does not require direct physical interactions between RBPs, and thus supports the long-range characteristic of the cooperativity. Focusing on an RNA with two binding sites, we first calculate the correlation function between the RBPs on the RNA-RBP complex, verifying that this cooperativity exists. We then derive a characteristic difference of free energy differences, i.e. delta delta G, as a quantitative measure of this structure-mediated cooperativity. We apply this measure to a large number of human mRNAs, and discover that this cooperativity is a generic feature. Interestingly, this cooperativity not only affects binding sites in close proximity along the sequence but also configurations in which one binding site is located in the 5'UTR and the other is located in the 3'UTR of the mRNA. Some intriguing interplays between RBPs, microRNA binding sites, and UTR sequences are also disclosed. In the last chapter, we extend our model to handle multiple sequence-specified protein binding sites. We apply this extended model to the binding reaction between the protein HuR and several RNA sequences, theoretically calculating their dissociation constants and comparing with experimental results. We discover that RNA secondary structures are crucial in the interplay between HuR and RNA sequences, verifying the importance of the structure-mediated cooperativity in realistic RNA-protein binding reactions.
Download or read book Structures of Large RNA Molecules and Their Complexes written by and published by Academic Press. This book was released on 2015-06-06 with total page 675 pages. Available in PDF, EPUB and Kindle. Book excerpt: This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in RNA folding and dynamics, RNA-protein interactions and large RNPs. Continues the legacy of this premier serial with quality chapters on structures of large RNA molecules and their complexes
Download or read book Biocalorimetry 2 written by John E. Ladbury and published by John Wiley & Sons. This book was released on 2005-07-15 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the last decade, high-sensitivity calorimetry has developed from a specialist method used mainly by dedicated experts to a major, commercially available tool in the arsenal directed at understanding molecular interactions and stability. Calorimeters have now become commonplace in bioscience laboratories. As a result, the number of those proficient in experimentation in this field has risen dramatically, as has the range of experiments to which these methods have been applied. Applications extend from studies in small molecule and solvent biophysics, through drug screening to whole cell assays. The technology has developed to include higher levels of sensitivity (and hence smaller sample size requirements) and a drive towards high-throughput technology, creating a very large user base in both academia and the pharmaceutical industry. This book is a fully revised and updated edition of the successful Biocalorimetry: Applications of Calorimetry in the Biological Sciences, published in 1998. Since then, there have been many advances in the instrumentation as well as in its applications and methodology. There are general chapters highlighting the usage of the isothermal titration calorimeter and the differential scanning calorimeter, more advanced chapters on specific applications and tutorials that cover the idiosyncrasies of experimental methods and data analysis. The book draws these together to create the definitive biological calorimetric text book. This book both explains the background to the method and describes novel, high-impact applications. It features works of interest to the experienced calorimetrist and the enthusiastic dilettante. The book should be of interest to all working in the field of biocalorimetry, from graduate students to researchers in academia and in industry.
Download or read book RNA Structure and Folding written by Dagmar Klostermeier and published by Walter de Gruyter. This book was released on 2013-10-14 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: While structure-function relationships of proteins have been studied for a long time, structural studies of RNA face additional challenges. Nevertheless, with the continuous discovery of novel RNA molecules with key cellular functions and of novel pathways and interaction networks, the need for structural information of RNA is still increasing. This volume provides an introduction into techniques to assess structure and folding of RNA. Each chapter explains the theoretical background of one technique, and illustrates possibilities and limitations in selected application examples.
Download or read book Thermodynamics of RNA Structural Changes written by Peter J. Mikulecky and published by . This book was released on 2005 with total page 564 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book RNA Ligand Interactions Part B Molecular Biology Methods written by and published by Elsevier. This book was released on 2000-06-26 with total page 579 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-Ligand Interactions, Part B focuses on molecular biology methods. Major topics covered include: solution probe methods, tethered-probe methodologies, in vitro affinity selection methodologies, genetic methodologies for detecting RNA-protein interactions, protein engineering methodologies useful for RNA-protein interaction studies, and cell biology methods.RNA-Ligand Interactions, Part A, its companion, VOLUME 317 focuses on structural biology methods.The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with more than 300 volumes (all of them still in print), the series contains much material still relevant today--truly an essential publication for researchers in all fields of life sciences.
Download or read book RNA Protein Complexes and Interactions written by Ren-Jang Lin and published by Springer Nature. This book was released on 2023-05-11 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second edition updates, complements, and expands upon the first edition by providing a collection of cutting-edge techniques developed or refined in the past few years along with tried-and-true methods. Chapters explore the isolation and characterization of RNA-protein complexes, the analysis and measurement of RNA-protein interaction, and related novel techniques and strategies. Written in the highly successful Methods in Molecular Biology series format, the chapters include brief introductions to the material, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and a Notes section which highlights tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA-Protein Complexes and Interactions: Methods and Protocols, Second Edition aims to be comprehensive guide for researchers in the field.
Download or read book New Insights Into the Determinants of Protein RNA Interactions A Structural Thermodynamic and Kinetic Investigation of the HnRNP C and UNR Proteins written by Zuzana Cienikova and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
