Download or read book Single Molecule Studies of RNA Unwinding and Ribosome Conformational Changes written by Dongmei Yu and published by . This book was released on 2014 with total page 237 pages. Available in PDF, EPUB and Kindle. Book excerpt: High-resolution structures of the ribosome have captured the endpoints of large-scale rearrangements of the ribosome. Direct observation of ribosome dynamics has been hindered by ensemble averaging in bulk solutions. Single-molecule methods, which eliminate these averaging effects, have emerged as powerful tools to probe many once-inaccessible biological processes. Here using single-molecule FRET, we observe the dynamic perturbation of the ribosome by structured mRNA, which renders the L1 stalk in an open state and induces a super-rotated conformation of the small subunit. We also found that when RNA structures are two nucleotide away from the mRNA entrance tunnel, the DNA:RNA structure still can induce the hyper rotated state and fluctuate among three different rotational state. The ability of inducing the hyper rotates state is correlated with RNA thermal stability and has nothing to do with the type of RNA structure. Ribosome can unwind RNA structure without the assistance of any other factors, which confirms the helicase function of ribosome. The advantage of single molecule is to follow the dynamics of single molecule in vitro. Single molecule techniques only can follow specific part or residues of large complex and it cannot give the information of all the atoms simultaneously. Solution NMR is not a single molecule technique and is a bulk dynamics basically. However, solution NMR can probe the dynamics of every atom and give you much more information even if they are averaged information. In the future, the complementary study of protein dynamics with both single molecule and NMR will provide more detail dynamics from protein in vitro.
Download or read book Single Molecule Studies of Ribosome Dynamics written by Peiwu Qin and published by . This book was released on 2013 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Ribosome is the protein factory with multiple coordinated components working together to translate the genetic code in the mRNA into protein sequence. Since it was discovered in 1955, the research around the ribosome has been pushed forward by hundreds of labs worldwide. In 2000, the breakthrough was marked by the publication of the ribosome structures at atomic resolution. Structures help people design and explain the biochemical data deeper and better. However, the ribosome is not static. It is a dynamic and highly regulated machine. The function of the ribosome can be understood further only if we can follow the dynamics of individual components in different functional states. Solution NMR is a powerful technique for studying protein dynamics. However, the gigantic nature of the ribosome makes this task daunting. Thanks to the development of single molecule techniques, the first real time ribosome dynamics was done in 2004 by Scott Blanchard when he was a post-doctorate with Steven Chu and Joseph Puglisi. After that, more than 300 research papers and reviews have been published about singe molecule ribosome studies. Both single molecule FRET and optical tweezers have been successfully used to address the dynamic process of protein translation. In 2008 and 2009, Dr. Peter Cornish and Dr. Dmitri Ermolenko followed the ribosome intersubunit rotation and L1 stalk dynamics in real time during the process of translocation, which was the first direct evidence of ribosome dynamics itself since the previous study inferred the ribosome dynamics from tRNA motion. The previous study could not exclude the possibility that the observed dynamics resulted purely from tRNA. Cornish and Ermolenko concluded that ribosome dynamics is a spontaneous process that is driven by thermodynamic Brownian motion. This pioneering study opened a window to address many unresolved problems such as the perturbation of the dynamic effects by structured RNA, mRNA unwinding, and ribosomal frameshifting. We found that the presence of RNA structure induces the ribosome into a new FRET state that we named super rotated state. The population distribution of the super rotated state is correlated with the thermostability and the distance of RNA structure to the ribosome. We can reduce the population of the super rotated state and reverse this change. Using other RNA structures like DNA:RNA hybrid and a pseudoknot, the ribosome can also be induced into the super rotated state. The different global conformations of ribosome when linear or structured RNA are present are shown by small angle X-ray scattering. The changes in the pair distance distribution function indicate the rotational change of ribosome theoretically. Structured RNA inhibits the regular intersubunit rotation and drives the ribosome into the super rotated state. However, the structured RNA cannot stop the open-to-close transition of the L1 stalk, which still can fluctuate between three different functional states. These results propose that ribosome dynamics is composed of several independent units with their own identity. Since the super rotated state also can be induced by DNA:RNA hybrid, we can investigate how far the RNA structure is away from the ribosome when the ribosome can sense the presence of these RNA structures.
Download or read book Single molecule Studies of RNA Conformations and Cotranscriptional Folding in Adenine Riboswitches written by Kirsten Linnea Frieda and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA--a ubiquitous and versatile type of biopolymer that is critically involved in many of life's molecular processes--is produced sequentially in single-stranded form during transcription by RNA polymerase and has the propensity to fold back on itself into interesting structures of functional import. In nature, riboswitches are elegant examples of structured RNA that adopt alternate conformations in response to ligand binding and thereby affect gene expression. We have been able to probe riboswitch conformations in novel detail using single-molecule optical-trapping techniques. These experimental approaches supply a unique perspective on folding since the ability to apply force provides an effective handle on the real-time state of individual RNA molecules and a means of modulating that state. In this dissertation, I focus on three studies that explore adenine riboswitch conformations and mechanisms. Specifically, in the first, we dissect the folding landscape of the aptamer (ligand-binding domain) of an adenine riboswitch. Extending this endeavor to full riboswitch sequences, we probe the interplay of a riboswitch aptamer with its downstream expression platform (which executes the switch's regulatory role), and develop methods to do so both during and after transcription. The second study takes full advantage of the latter ability: In a complete adenine riboswitch controlling transcription, we directly observe cotranscriptional folding of the nascent RNA in which the adopted conformation dictates whether or not to terminate transcription. Finally, in a different adenine riboswitch controlling translation, we investigate switch conformational changes and identify a series of competing structural elements that kinetically trap the riboswitch conformation, implying that the initial, cotranscriptional fold of the riboswitch may determine its gene regulatory state. These efforts enhance our understanding of folding architectures in riboswitches, specifically, and in RNA, more broadly. They further highlight the importance of cotranscriptional folding, providing a novel window into the nascent development of RNA conformations.
Download or read book The Ribosome written by Aleksandr S. Spirin and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 173 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph is neither a historical outline of the development of the concepts of protein biosynthesis and the structure and functions of the ribosomes, nor an exhaustive survey of the literature on these questions. The monograph is based upon an analysis of the modern trends in this field. The purpose of the monograph was to formulate more or less generalized representations of the structure and" function of the ribosome, as we envision it at the present day. It may be that this attempt is premature for a number of reasons, and the concepts outlined here will very soon be revised. Nonetheless, despite this risk, we believe it to be advisable to undertake this attempt for the following reasons: firstly, the undertaken analysis could aid in the comprehension of the substantial mass of extremely scattered experimental data on the ribosomes presently available; secondly, in any event, even if most of the concepts outlined rapidly become obselete, they can still serve as a stimulus for a whole series of experiments; and thirdly, we hope that some of the concepts outlined will still remain essentially correct and relatively stable. In view of the aforementioned, we should make the following reservations. First of all, we made no attempt to cite all the literature on the problems discussed, but considered it sufficient to illustrate the various premises with one or several sample references.
Download or read book Recoding Expansion of Decoding Rules Enriches Gene Expression written by John F. Atkins and published by Springer Science & Business Media. This book was released on 2010-03-10 with total page 473 pages. Available in PDF, EPUB and Kindle. Book excerpt: The literature on recoding is scattered, so this superb book ?lls a need by prov- ing up-to-date, comprehensive, authoritative reviews of the many kinds of recoding phenomena. Between 1961 and 1966 my colleagues and I deciphered the genetic code in Escherichia coli and showed that the genetic code is the same in E. coli, Xenopus laevis, and guinea pig tissues. These results showed that the code has been c- served during evolution and strongly suggested that the code appeared very early during biological evolution, that all forms of life on earth descended from a c- mon ancestor, and thus that all forms of life on this planet are related to one another. The problem of biological time was solved by encoding information in DNA and retrieving the information for each new generation, for it is easier to make a new organism than it is to repair an aging, malfunctioning one. Subsequently, small modi?cations of the standard genetic code were found in certain organisms and in mitochondria. Mitochondrial DNA only encodes about 10–13 proteins, so some modi?cations of the genetic code are tolerated that pr- ably would be lethal if applied to the thousands of kinds of proteins encoded by genomic DNA.
Download or read book Single Molecule Dynamics in Life Science written by Toshio Yanagida and published by John Wiley & Sons. This book was released on 2008-12-04 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this first comprehensive resource to cover the application of single molecule techniques to biological measurements, the pioneers in the field show how to both set up and interpret a single molecule experiment. Following an introduction to single molecule measurements and enzymology, the expert authors consider molecular motors and mechanical properties before moving on to the applications themselves. Detailed discussions of studies on protein enzymes, ribozymes and nucleic acids are also included.
Download or read book Nanotechnology Tools for the Study of RNA written by and published by Academic Press. This book was released on 2016-02-23 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume of Progress in Molecular Biology and Translational Science introduces emerging strategies of studying RNA structure and function using nanotechnological tools. The volume aims to provide the readers with a novel view and give them opportunities to think about how to incorporate the new technologies into their own research. This book informs and updates on strategies to take advantages of nanotechnological tools to answer to fundamental questions in RNA science Collection of reviews written by the leading scientists from the field The book covers a range of topics, from single molecule analyses using nanomaterials to gene regulation using RNA nanostructures
Download or read book RNA Nanotechnology written by Bin Wang and published by CRC Press. This book was released on 2014-04-02 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the past few decades there has been incredible growth in "bionano"-related research, which has been accompanied by numerous publications in this field. Although various compilations address topics related to deoxyribonucleic acid (DNA) and protein, there are few books that focus on determining the structure of ribonucleic acid (RNA) and using RNA as building blocks to construct nanoarchitectures for biomedical and healthcare applications. RNA Nanotechnology is a comprehensive volume that details both the traditional approaches and the latest developments in the field of RNA-related technology. This book targets a wide audience: a broad introduction provides a solid academic background for students, researchers, and scientists who are unfamiliar with the subject, while the in-depth descriptions and discussions are useful for advanced professionals. The book opens with reviews on the basic aspects of RNA biology, computational approaches for predicting RNA structures, and traditional and emerging experimental approaches for probing RNA structures. This section is followed by explorations of the latest research and discoveries in RNA nanotechnology, including the design and construction of RNA-based nanostructures. The final segment of the book includes descriptions and discussions of the potential biological and therapeutic applications of small RNA molecules, such as small/short interfering RNAs (siRNAs), microRNAs (miRNAs), RNA aptamers, and ribozymes.
Download or read book RNA and Protein Synthesis written by Kivie Moldave and published by . This book was released on 1981 with total page 838 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA and Protein Synthesis ...
Download or read book Organelles Advances in Research and Application 2012 Edition written by and published by ScholarlyEditions. This book was released on 2012-12-26 with total page 728 pages. Available in PDF, EPUB and Kindle. Book excerpt: Organelles—Advances in Research and Application: 2012 Edition is a ScholarlyEditions™ eBook that delivers timely, authoritative, and comprehensive information about Organelles. The editors have built Organelles—Advances in Research and Application: 2012 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about Organelles 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 Organelles—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/.
Download or read book Brookhaven Symposia in Biology written by Brookhaven National Laboratory and published by . This book was released on 1948 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Optical Tweezers written by Arne Gennerich and published by Humana. This book was released on 2016-11-15 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this volume is to provide a comprehensive overview of optical tweezers setups, both in practical and theoretical terms, to help biophysicists, biochemists, and cell biologists to build and calibrate their own instruments and to perform force measurements on mechanoenzymes both in isolation in vitro and in living cells. Chapters have been divided in three parts focusing on theory and practical design of optical tweezers, detailed protocols for performing force measurements on single DNA- and microtubule/actin-associated mechanoenzymes in isolation, and describing recent advances that have opened up quantitative force measurements in living cells. 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, Optical Tweezers: Methods and Protocols aims help to further expand the accessibility and use of optical traps by scientists of diverse disciplines.
Download or read book Single Molecule Studies of Enzyme Kinetics and Mechanism written by Jue Shi and published by . This book was released on 2006 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Fundamental Molecular Biology written by Lizabeth A. Allison and published by John Wiley & Sons. This book was released on 2021-04-21 with total page 816 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fundamental Molecular Biology Discover a focused and up to date exploration of foundational and core concepts in molecular biology The newly revised Third Edition of Fundamental Molecular Biology delivers a selective and precise treatment of essential topics in molecular biology perfect for allowing students to develop an accurate understanding of the applications of the field. The book applies the process of discovery-observations, questions, experimental designs, results, and conclusions-with an emphasis on the language of molecular biology. Readers will easily focus on the key ideas they need to succeed in any introductory molecular biology course. Fundamental Molecular Biology provides students with the most up to date techniques and research used by molecular biologists today. Readers of the book will have the support and resources they need to develop a concrete understanding of core and foundational concepts of molecular biology, without being distracted by outdated or peripheral material. Readers will also benefit from the inclusion of: A thorough introduction to and comparison of eukaryotic and prokaryotic organisms illustrating the variation of cellular processes across organisms Tool boxes exploring up to date experimental methods and techniques used by molecular biologists Focus boxes providing detailed treatment of topics that delve further into experimental strategies Disease boxes placing complex regulatory pathways in their relevant context and illustrating key principles of molecular biology Perfect for instructors and professors of introductory molecular biology courses, Fundamental Molecular Biology will also earn a place in the libraries of anyone seeking to improve their understanding of molecular biology with an insightful and well-grounded treatment of the core principles of the subject.
Download or read book Single stranded RNA phages written by Paul Pumpens and published by CRC Press. This book was released on 2020-02-03 with total page 1832 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a comprehensive guide to single-stranded RNA phages (family Leviviridae), first discovered in 1961. These phages played a unique role in early studies of molecular biology, the genetic code, translation, replication, suppression of mutations. Special attention is devoted to modern applications of the RNA phages and their products in nanotechnology, vaccinology, gene discovery, evolutionary and environmental studies. Included is an overview of the generation of novel vaccines, gene therapy vectors, drug delivery, and diagnostic tools exploring the role of RNA phage-derived products in the revolutionary progress of the protein tethering and bioimaging protocols. Key Features Presents the first full guide to single-stranded RNA phages Reviews the history of molecular biology summarizing the role RNA phages in the development of the life sciences Demonstrates how RNA phage-derived products have resulted in nanotechnological applications Presents an up-to-date account of the role played by RNA phages in evolutionary and environmental studies
Download or read book Laser Physics at the Limits written by Hartmut Figger and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 525 pages. Available in PDF, EPUB and Kindle. Book excerpt: Published on the occasion of Theodor Hänsch's 60th Birthday emphasis is placed on precision related to results in a variety of fields, such as atomic clocks, frequency standards, and the measurement of physical constants in atomic physics. Furthermore, illustrations and engineering applications of the fundamentals of quantum mechanics are widely covered. It has contributions by Nobel prize winners Norman F. Ramsey, Steven Chu, and Carl E. Wieman.
Download or read book Viral Replication Enzymes and their Inhibitors Part A written by and published by Academic Press. This book was released on 2021-10-23 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: Viral Replication Enzymes and their Inhibitors Part A, Volume 49, the latest release in the Enzymes series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of related topics. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in The Enzymes series
