Role of a Protein Cofactor in RNA-based Catalysis PDF Download
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Author: Aleks Schein
Publisher:
ISBN:
Category :
Languages : en
Pages : 56
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Book Description
Author: Aleks Schein
Publisher:
ISBN:
Category :
Languages : en
Pages : 56
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Book Description
Author: Hsin-Yue Tsai
Publisher:
ISBN:
Category : RNA-protein interactions
Languages : en
Pages : 123
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Book Description
Abstract: Ribonuclease P (RNase P) catalyzes the 5' maturation of tRNAs in all three domains of life and functions as a Mg2+-dependent ribonucleoprotein (RNP) complex. It is composed of one RNA subunit, essential for catalysis, and a varying number of protein cofactors depending on the source. We have now used bacterial and archaeal RNase P to understand how proteins aid RNA catalysis. Bacterial RNase P is composed of one catalytic RNA subunit and one protein cofactor, which is known to facilitate substrate binding and RNA catalysis. Although molecular modeling led to tertiary structure models of the RNA subunits, that were subsequently shown to be correct, and high-resolution studies established the structure of the protein subunit from bacterial RNase P, RNA-protein interactions in the holoenzyme were not established. Here, we have used a hydroxyl radical-mediated footprinting approach to generate this information which, together with results from other biochemical/biophysical studies, have furnished distance constraints for building three-dimensional models of the bacterial RNase P holoenzyme in the absence or presence of its precursor tRNA substrate. The model reveals how the protein subunit facilitates RNA catalysis by directly interacting with both the ptRNA substrate and the catalytic core of the RNA subunit. Unlike bacterial RNase P, both archaeal and eukaryal RNase P contain multiple protein subunits, whose roles are unclear largely due to the failure to reconstitute archaeal/eukaryal RNase P in vitro. Using recombinant subunits, we have now reconstituted functional RNase P from Pyroccocus furiosus, a thermophilic archaeon, and gained insights regarding its assembly pathway(s) and the contribution of its different protein subunits to RNA catalysis. The Pfu RNase P RNA is capable of multiple turnover catalysis with either of two pairs of protein subunits and becomes significantly more active, at lower magnesium concentrations, with addition of the remaining protein pair. These data support a central tenet of the RNA world hypothesis that the evolution of RNA enzymes to RNP complexes involved gradual recruitment of proteins to enhance biological function. Collectively, these two studies highlight the common strategies employed by protein cofactors to enhance RNA catalysis (i.e., enhanced substrate binding and improved affinity for Mg2+).
Author: Fritz Eckstein
Publisher: Springer Science & Business Media
ISBN: 3642612024
Category : Science
Languages : en
Pages : 416
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Book Description
In recent years, unprecedented advances in many aspects of the molecular biology of nucleic acids have been witnessed. The area of RNA chemistry has undergone a kind of explosion, with a huge interest in RNA-mediated catalysis. At the same time, our structural understanding of DNA-protein interactions has increased enormously, and the related area of RNA-protein interactions is beginning to gather pace. This softcover edition from the successful series Nucleic Acids and Molecular Biology is devoted to the structure and mechanism of ribozymes, and their potential exploitation. The subject has both important evolutionary implications and potential practical application in the development of therapeutic agents for diseases such as AIDS.
Author: David M J Lilley
Publisher: Royal Society of Chemistry
ISBN: 1847557988
Category : Science
Languages : en
Pages : 339
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Book Description
The discovery that RNA could act as a macromolecular catalyst in the cell, signified a paradigm shift in molecular biology. Ribozymes and RNA Catalysis takes the reader through the origins of catalysis in RNA and necessarily includes significant discussion of structure and folding. The main focus of the book concerns chemical mechanism with extensive comment on how, despite the importance of RNA catalysis in the cell, its origins are still poorly understood and often controversial. The reader is given an outline of the important role of RNA catalysis in many aspects of cell function, including RNA processing and translation. There has been a significant coming together in the field of RNA in recent years and this book offers a compelling review of the whole field to date. Written by leading experts in their field, who in turn review the structural and mechanistic data for all known ribozymes this book is well suited for undergraduates, postgraduates and researchers in catalytic chemistry as well as those in related fields who require a unique overview of the subject.
Author: Wen-Yi Chen
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Overall, my results demonstrate the functional coordination among the RPR and different RPPs, and help rationalize why distinct protein cofactors were recruited by an ancient RNA enzyme during the transition from a primordial RNA to the extant RNP world.
Author: Sabine Müller
Publisher: John Wiley & Sons
ISBN: 3527814531
Category : Science
Languages : en
Pages : 81
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Book Description
Ribozymes Provides comprehensive coverage of a core field in the molecular biosciences, bringing together decades of knowledge from the world’s top professionals in the field Timely and unique in its breadth of content, this all-encompassing and authoritative reference on ribozymes documents the great diversity of nucleic acid-based catalysis. It integrates the knowledge gained over the past 35 years in the field and features contributions from virtually every leading expert on the subject. Ribozymes is organized into six major parts. It starts by describing general principles and strategies of nucleic acid catalysis. It then introduces naturally occurring ribozymes and includes the search for new catalytic motifs or novel genomic locations of known motifs. Next, it covers the development and design of engineered ribozymes, before moving on to DNAzymes as a close relative of ribozymes. The next part examines the use of ribozymes for medicinal and environmental diagnostics, as well as for therapeutic tools. It finishes with a look at the tools and methods in ribozyme research, including the techniques and assays for structural and functional characterization of nucleic acid catalysts. The first reference to tie together all aspects of the multi-faceted field of ribozymes Features more than 30 comprehensive chapters in two volumes Covers the chemical principles of RNA catalysis; naturally occurring ribozymes, engineered ribozymes; DNAzymes; ribozymes as tools in diagnostics and therapy, and tools and methods to study ribozymes Includes first-hand accounts of concepts, techniques, and applications by a team of top international experts from leading academic institutions Dedicates half of its content to methods and practical applications, ranging from bioanalytical tools to medical diagnostics to therapeutics Ribozymes is an unmatched resource for all biochemists, biotechnologists, molecular biologists, and bioengineers interested in the topic.
Author: Pierre Pontarotti
Publisher: Springer Nature
ISBN: 3030572463
Category : Science
Languages : en
Pages : 389
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Book Description
This book includes 16 selected contributions presented at the 23rd Evolutionary Biology Meeting, which took place in Marseille in September 2019. The annual Evolutionary Biology Meetings in Marseille serve to gather leading evolutionary biologists and other scientists using evolutionary biology concepts, e.g. for medical research. The aim of these meetings is to promote the exchange of ideas to encourage interdisciplinary collaborations. Offering an up-to-date overview of recent findings in the field of evolutionary biology, this book is an invaluable source of information for scientists, teachers and advanced students.
Author: Ren-Jang Lin
Publisher: Springer Nature
ISBN: 1071631918
Category : Science
Languages : en
Pages : 349
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Book Description
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.
Author:
Publisher:
ISBN:
Category : Nucleoproteins
Languages : en
Pages :
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Book Description
Abstract: Ribonuclease P (RNase P) is a ribonucleoprotein involved in tRNA biosynthesis in all living organisms. Bacterial RNase P is comprised of a catalytic RNA subunit and a lone protein cofactor which plays a supporting, albeit essential, role in the tRNA processing reaction in vivo. In this study, we have searched various databases to identify homologs of the protein subunit of RNase P from diverse bacteria and generated an alignment of their primary sequences to determine the most highly conserved residues. Such an approach has helped us to extend earlier predictions of which residues might play an important role in RNase P catalysis. The amino acid residues identified as important for RNase P catalysis could be categorized in three groups: (i) the RNR motif in helix alpha 2, (ii) the substrate binding cleft, and (iii) amino acid residues involved in the overall stability of the bacterial RNase P protein subunit. By employing site-directed mutagenesis and a genetic complementation assay, we have also gained insights into structure-function relationships in the protein subunit of bacterial RNase P. Specifically, we were able to demonstrate that the bacterial RNase P protein uses one domain to recognize its cognate catalytic RNA subunit and another domain to recognize the 5' leader sequences of its precursor tRNA substrates. The plasticity of the substrate-binding cleft has also been demonstrated by both chemical and genetic rescue experiments. These results, taken together with earlier kinetic studies, have enabled us to understand how the bacterial RNase P protein subunit is able to enhance the rate of chemical cleavage 10-fold and enhance substrate binding 10,000-fold over the RNA alone ptRNA-processing reaction. Finally, we report an interesting study that demonstrates how the Escherichia coli RNase P protein subunit lacking a metal affinity tag can be purified under denaturing conditions using immobilized metal affinity chromatography (IMAC). We are not aware of a precedent in this regard and report these results as a potential new method for the purification of a protein lacking metal affinity tags under denaturing conditions using IMAC.
Author:
Publisher: Elsevier
ISBN: 0080522572
Category : Science
Languages : en
Pages : 555
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Book Description
This second volume on ribonucleases provides up-to-date, methods-related information on these enzymes. Of particular interest to researchers will be the discussion of artificial and engineered ribonucleases, as well as the application of ribonucleases in medicine and biotechnology.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.
