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Engineering Rna Binding Proteins
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Book Synopsis Engineering RNA-binding Proteins by : Muhammad Fazril Mohamad Razif
Download or read book Engineering RNA-binding Proteins written by Muhammad Fazril Mohamad Razif and published by . This book was released on 2012 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-protein interactions have key roles in the regulation of gene expression and are vital for many cellular processes and complex developmental programs in eukaryotes. Proteins that have the ability to bind RNAs tend to do so in various modes that are often difficult to predict, limiting the ability to engineer these RNA-binding proteins for medical and biotechnological use. Hence, engineering proteins that can bind a specific RNA sequence has many potential applications, analogous to that of siRNAs and miRNAs, with even more potential benefits. The ability to fuse RNA-binding proteins to any desired effector domain, in turn enabling the manipulation of any aspect of the target RNA's metabolism makes engineering these proteins highly appealing. Here, the recognition of PUF repeats beyond adenine, guanine and uracil has been achieved through directed evolution, enabling them to specifically bind cytosine. With this code, PUF domains capable of selectively binding RNA targets of diverse sequence and structure can be designed. Unlike the PUFs, the basis for nucleotide RNA recognition by pentatricopeptide repeat (PPR) proteins, another RNA-binding protein, remains ambiguous. Here, computational methods have been used to create a stable, highly reduced PPR architecture for the study of RNA-binding specificity and the design of specific tools to manipulate RNA metabolism. We used these synthetic PPRs to examine the amino acid codes for nucleotide recognition by PPRs, which also revealed that PPRs have a modular recognition mechanism similar to that of PUFs. These findings provide a significant step towards predicting native binding sites of the vast number of PPR proteins found in nature. It also highlights the possibility of a PPR scaffold to be engineered for new functions and sequence specificities.
Book Synopsis RNA Binding Proteins by : Zdravko Lorkovic
Download or read book RNA Binding Proteins written by Zdravko Lorkovic and published by CRC Press. This book was released on 2012-08-10 with total page 174 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene expression in eukaryotes is regulated at different levels, which need to be coordinated to implement the information in the genome. Now it is clear that post-transcriptional regulation of gene expression such as pre-mRNA splicing, mRNA transport, editing, turnover and translation are as important as the control of transcription. In all aspects
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 Biophysics of RNA-Protein Interactions by : Chirlmin Joo
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.
Book Synopsis Nucleic Acids by : Victor A. Bloomfield
Download or read book Nucleic Acids written by Victor A. Bloomfield and published by Sterling Publishing Company. This book was released on 2000-04-17 with total page 854 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text has been organized to meet the needs of those who have only a basic understanding of physical chemistry and molecular biology.
Download or read book RNA Processing written by Gene W. Yeo and published by Springer. This book was released on 2016-06-02 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ribonucleic acid (RNA) binding proteins currently number in the thousands and defects in their function are at the heart of diseases such as cancer and neurodegeneration. RNA binding proteins have become implicated in the intricate control of surprisingly diverse biological settings, such as circadian rhythm, stem cell self-renewal, oncogenesis and germ cell development. This book surveys a range of genome-wide and systems approaches to studying RNA binding proteins, the importance of RNA binding proteins in development, cancer and circadian rhythm.
Book Synopsis Engineering RNA Base-editing Tools and Uncovering Post-transcriptional Regulatory Roles of RNA-binding Proteins in Neurodegeneration by : Ryan Jared Marina
Download or read book Engineering RNA Base-editing Tools and Uncovering Post-transcriptional Regulatory Roles of RNA-binding Proteins in Neurodegeneration written by Ryan Jared Marina and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-binding proteins (RBPs) play integral roles in mediating all cellular functions through RNA processing. Given the importance of post-transcriptional gene regulation in maintaining cellular function, and the role that RNA processing dysregulation plays in disease causation, it is of critical importance to understand the underlying biology of RNA-RBP interactions. At the same time, engineered RBP paradigms offer tremendous potential to increase our ability to both further probe and manipulate the transcriptome. In this dissertation, we aim to explore both natural and synthetic RBP systems and the role they play on cellular function. We begin by describing molecular tools developed to perform site-directed RNA editing using CRISPR/Cas technologies and natural adenosine-deaminase enzymes. We demonstrate efficacy of our new platform, as well as perform a systematic evaluation of similar editing platforms in both on- and off-target efficiency. We then describe a novel and simplified sequencing-based platform (STAMP) that demonstrates how RNA editing enzymes can be leveraged to characterize global RNA-RBP interactions both at bulk and single-cell levels. Next, to explore the regulatory roles of a specific RBP in disease modification, we profile the functional landscape of ataxin-2 (ATXN2) in spinal cord harvested from a mouse model of amyotrophic lateral sclerosis (ALS) using RNA sequencing and enhanced CLIP. In doing so, we uncover hundreds of differentially expressed transcripts of moderate fold-change affected by ataxin-2 knockout, the majority of which occur in a dose-dependent manner and can be explained by direct ataxin-2 binding. We also discover a subset of genes whose signatures can be reversed in the context of ALS with ataxin-2 deletion, corresponding to suppression of neuroinflammatory pathways and promotion of neuronal processes, supporting the notion that depletion of ataxin-2 levels may be protective against progression of ALS pathogenesis. Lastly, we describe efforts to further characterize regulatory roles of ataxin-2 in disease susceptibility using newly engineered human stem cell models.
Book Synopsis RNA-Binding Proteins: Advances in Research and Application: 2011 Edition by :
Download or read book RNA-Binding Proteins: Advances in Research and Application: 2011 Edition written by and published by ScholarlyEditions. This book was released on 2012-01-09 with total page 49 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-Binding Proteins: Advances in Research and Application: 2011 Edition is a ScholarlyBrief™ that delivers timely, authoritative, comprehensive, and specialized information about RNA-Binding Proteins in a concise format. The editors have built RNA-Binding Proteins: Advances in Research and Application: 2011 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about RNA-Binding Proteins in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of RNA-Binding Proteins: Advances in Research and Application: 2011 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.
Book Synopsis RNA-Binding Proteins—Advances in Research and Application: 2012 Edition by :
Download or read book RNA-Binding Proteins—Advances in Research and Application: 2012 Edition written by and published by ScholarlyEditions. This book was released on 2012-12-26 with total page 73 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-Binding Proteins—Advances in Research and Application: 2012 Edition is a ScholarlyBrief™ that delivers timely, authoritative, comprehensive, and specialized information about RNA-Binding Proteins in a concise format. The editors have built RNA-Binding Proteins—Advances in Research and Application: 2012 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about RNA-Binding Proteins in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of RNA-Binding Proteins—Advances in Research and Application: 2012 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.
Book Synopsis Protein Engineering by : Huimin Zhao
Download or read book Protein Engineering written by Huimin Zhao and published by John Wiley & Sons. This book was released on 2021-08-23 with total page 41 pages. Available in PDF, EPUB and Kindle. Book excerpt: A one-stop reference that reviews protein design strategies to applications in industrial and medical biotechnology Protein Engineering: Tools and Applications is a comprehensive resource that offers a systematic and comprehensive review of the most recent advances in the field, and contains detailed information on the methodologies and strategies behind these approaches. The authors—noted experts on the topic—explore the distinctive advantages and disadvantages of the presented methodologies and strategies in a targeted and focused manner that allows for the adaptation and implementation of the strategies for new applications. The book contains information on the directed evolution, rational design, and semi-rational design of proteins and offers a review of the most recent applications in industrial and medical biotechnology. This important book: Covers technologies and methodologies used in protein engineering Includes the strategies behind the approaches, designed to help with the adaptation and implementation of these strategies for new applications Offers a comprehensive and thorough treatment of protein engineering from primary strategies to applications in industrial and medical biotechnology Presents cutting edge advances in the continuously evolving field of protein engineering Written for students and professionals of bioengineering, biotechnology, biochemistry, Protein Engineering: Tools and Applications offers an essential resource to the design strategies in protein engineering and reviews recent applications.
Book Synopsis Protein Engineering by : Caroline Koehrer
Download or read book Protein Engineering written by Caroline Koehrer and published by Springer Science & Business Media. This book was released on 2009-01-07 with total page 351 pages. Available in PDF, EPUB and Kindle. Book excerpt: Site-specific mutagenesis of DNA, developed some thirty years ago, has proven to be one of the most important advances in biology. By allowing the site-specific replacement of any amino acid in a protein with one of the other nineteen amino acids, it ushered in the new era of "Protein Engineering". The field of protein engineering has, however, evolved rapidly since then and the last fifteen years have witnessed remarkable advances through the use of new chemical, biochemical and molecular biological tools towards the synthesis and manipulation of proteins. The chapters included in this book reflect the rapid evolution of protein engineering and its many applications in basic research, biotechnology, material sciences and therapy. This book will provide the reader with an introduction to state-of the-art concepts and methods and will be of use to anyone interested in the study of proteins, in academia as well as in industry.
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 Discovery and Engineering of RNA-binding Proteins that Activate Alternative Exon Inclusion by : Jonathan Schmok
Download or read book Discovery and Engineering of RNA-binding Proteins that Activate Alternative Exon Inclusion written by Jonathan Schmok and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we evaluated 718 human RBPs with tethered function luciferase-based splicing reporter assays to identify 58 candidates, including known splicing factors such as RBFOX and serine-arginine proteins. We performed enhanced CLIP, RNA-seq, and affinity purification-mass spectrometry to investigate a subset of the 11 candidates with no prior association with splicing. Integrative analysis of these assays indicated the surprising roles of TRNAU1AP, SCAF8, and RTCA in modulating hundreds of endogenous splicing events. We also leveraged our tethering assays and top candidates to identify potent and compact exon inclusion activation domains for splicing modulation applications. Using identified domains, we engineered programmable fusion proteins which outperformed current artificial splicing factors at manipulating inclusion of reporter and endogenous exons. Altogether, our tethering approach characterized the ability of RBPs to induce exon inclusion and yielded new molecular parts for programmable splicing control.
Book Synopsis RNA-Protein Interactions : A Practical Approach by : Christopher W.J. Smith
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. -
Book Synopsis Computational Design of Ligand Binding Proteins by : Barry L. Stoddard
Download or read book Computational Design of Ligand Binding Proteins written by Barry L. Stoddard and published by . This book was released on 2016 with total page 375 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a collection of protocols and approaches for the creation of novel ligand binding proteins, compiled and described by many of today's leaders in the field of protein engineering. Chapters focus on modeling protein ligand binding sites, accurate modeling of protein-ligand conformational sampling, scoring of individual docked solutions, structure-based design program such as ROSETTA, protein engineering, and additional methodological approaches. Examples of applications include the design of metal-binding proteins and light-induced ligand binding proteins, the creation of binding proteins that also display catalytic activity, and the binding of larger peptide, protein, DNA and RNA ligands. 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.
Book Synopsis Concepts in Protein Engineering and Design by : Paul Wrede
Download or read book Concepts in Protein Engineering and Design written by Paul Wrede and published by Walter de Gruyter GmbH & Co KG. This book was released on 2020-10-12 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: No detailed description available for "Concepts in Protein Engineering and Design".
Book Synopsis RNA-Ligand Interactions, Part B: Molecular Biology Methods by :
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.
