Author : Ronny Lorenz
Publisher : Springer Nature
Page : 407 pages
File Size : 51,9 Mb
Release : 2024-07-01
Category : Electronic
ISBN : 9781071635193
RNA Folding
Ronny Lorenz
Rna Folding
Rna Folding Book in PDF, ePub and Kindle version is available to download in english. Read online anytime anywhere directly from your device. Click on the download button below to get a free pdf file of Rna Folding book. This book definitely worth reading, it is an incredibly well-written.
Biophysics of RNA Folding
Rick Russell
Author : Rick Russell
Publisher : Springer Science & Business Media
Page : 238 pages
File Size : 43,9 Mb
Release : 2012-12-09
Category : Science
ISBN : 9781461449546
Biophysics of RNA Folding by Rick Russell Pdf
This volume, written by experts in the field, discusses the current understanding of the biophysical principles that govern RNA folding, with featured RNAs including the ribosomal RNAs, viral RNAs, and self-splicing introns. In addition to the fundamental features of RNA folding, the central experimental and computational approaches in the field are presented with an emphasis on their individual strengths and limitations, and how they can be combined to be more powerful than any method alone; these approaches include NMR, single molecule fluorescence, site-directed spin labeling, structure mapping, comparative sequence analysis, graph theory, course-grained 3D modeling, and more. This volume will be of interest to professional researchers and advanced students entering the field of RNA folding.
Markov State Models for Protein and RNA Folding
Gregory Ross Bowman
Author : Gregory Ross Bowman
Publisher : Stanford University
Page : 279 pages
File Size : 47,8 Mb
Release : 2010
Category : Electronic
ISBN : STANFORD:ky974bm1455
Markov State Models for Protein and RNA Folding by Gregory Ross Bowman Pdf
Understanding the molecular bases of human health could greatly augment our ability to prevent and treat diseases. For example, a deeper understanding of protein folding would serve as a reference point for understanding, preventing, and reversing protein misfolding in diseases like Alzheimer's. Unfortunately, the small size and tremendous flexibility of proteins and other biomolecules make it difficult to simultaneously monitor their thermodynamics and kinetics with sufficient chemical detail. Atomistic Molecular Dynamics (MD) simulations can provide a solution to this problem in some cases; however, they are often too short to capture biologically relevant timescales with sufficient statistical accuracy. We have developed a number of methods to address these limitations. In particular, our work on Markov State Models (MSMs) now makes it possible to map out the conformational space of biomolecules by combining many short simulations into a single statistical model. Here we describe our use of MSMs to better understand protein and RNA folding. We chose to focus on these folding problems because of their relevance to misfolding diseases and the fact that any method capable of describing such drastic conformational changes should also be applicable to less dramatic but equally important structural rearrangements like allostery. One of the key insights from our folding simulations is that protein native states are kinetic hubs. That is, the unfolded ensemble is not one rapidly mixing set of conformations. Instead, there are many non-native states that can each interconvert more rapidly with the native state than with one another. In addition to these general observations, we also demonstrate how MSMs can be used to make predictions about the structural and kinetic properties of specific systems. Finally, we explain how MSMs and other enhanced sampling algorithms can be used to drive efficient sampling.
Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding:
Daniel Herschlag
Author : Daniel Herschlag
Publisher : Academic Press
Page : 496 pages
File Size : 48,8 Mb
Release : 2009-11-16
Category : Science
ISBN : 0080922139
Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding: by Daniel Herschlag Pdf
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
Folding and Self-assembly of Biological Macromolecules
Noah Hardy,Eric Westhof
Author : Noah Hardy,Eric Westhof
Publisher : World Scientific
Page : 424 pages
File Size : 45,5 Mb
Release : 2004
Category : Mathematics
ISBN : 9812703055
Folding and Self-assembly of Biological Macromolecules by Noah Hardy,Eric Westhof Pdf
Organized by Alessandra Carbone ( IHeS, Bures-sur-Yvette, France ) Organized by Misha Gromov ( IHeS, Bures-sur-Yvette, France ) Organized by Fran ois K(r)p s ( CNRS-Genopole-, evry, France ) Organized by Eric Westhof ( Universit(r) Louis-Pasteur, Strasbourg, France ). This proceedings volume explores the pathways and mechanisms by which constituent residues interact and fold to yield native biological macromolecules (catalytic RNA and functional proteins), how ribosomes and other macromolecular complexes self-assemble, and relevant energetics considerations. At the week-long interactive conference, some 20 leading researchers reported their most pertinent results, confronting each other and an audience of more than 150 specialists from a wide range of scientific disciplines, including structural and molecular biology, biophysics, computer science, mathematics, and theoretical physics. The fourteen papers OCo and audience interaction OCo are edited and illustrated versions of the transcribed oral presentations. The proceedings have been selected for coverage in: . OCo Biochemistry & Biophysics Citation Index(tm). OCo Index to Scientific & Technical Proceedings (ISTP CDROM version / ISI Proceedings). OCo CC Proceedings OCo Biomedical, Biological & Agricultural Sciences. Contents: Evolution-Based Genome Analysis: An Alternative to Analyze Folding and Function in Proteins (S Benner); Conformation of Charged Polymers: Polyelectrolytes and Polyampholytes (J-F Joanny); Statistically Derived Rules for RNA Folding (M Zuker); Experimental Approaches to RNA Folding (S Woodson); Some Questions Concerning RNA Folding (F Michel); RNA Folding in Ribosome Assembly (J R Williamson); From RNA Sequences to Folding Pathways and Structures: A Perspective (H Isamber t); An Evolutionary Perspective on the Determinants of Protein Function and Assembly (O Lichtarg e); Some Residues are more Equal than Others: Application to Protein Classification and Structure Prediction (A Kister & I Gelfan d); Structure-Function Relationships in Polymerases (M Delarue); The Protein-Folding Nucleus: From Simple Models to Real Proteins (L Mirn y); Chaperonin-Mediated Protein Folding (D Thirumalai); Virus Assembly and Maturation (J E Johnson); The Animal in the Machine: Is There a Geometric Program in the Genetic Program? (A Danchin). Readership: Researchers, academics and graduate students in structural biology, cellular and molecular biology, biophysics, biochemistry and biomathematics/bioinformatics."
Structural and Catalytic Roles of Metal Ions in RNA
Astrid Sigel,Helmut Sigel,Roland K. O. Sigel
Author : Astrid Sigel,Helmut Sigel,Roland K. O. Sigel
Publisher : Royal Society of Chemistry
Page : 425 pages
File Size : 54,5 Mb
Release : 2011
Category : Science
ISBN : 9781849730945
Structural and Catalytic Roles of Metal Ions in RNA by Astrid Sigel,Helmut Sigel,Roland K. O. Sigel Pdf
The discovery of ribozymes triggered a huge interest in the chemistry and biology of RNAs. Much of the recently made progress focusing on metal ions is addressed in Volume 9. This book, written by 28 internationally recognized experts, provides a most up-to-date view and it is thus of special relevance for colleagues teaching courses in biological inorganic chemistry and for researchers dealing, e.g., with nucleic acids, gene expression, and enzymology, but also for those in analytical and bioinorganic chemistry or biophysics. Structural and Catalytic Roles of Metal Ions in RNA describes metal ion-binding motives, methods to detect and characterize metal ion binding sites, and the role of metal ions in folding and catalysis. It deals with diffuse metal ion binding, RNA quadruplexes, the regulation of riboswitches, metal ions and ribozymes, including artificial ribozymes. The ribosome, ribozymes and redox cofactors, as well as the binding of kinetically inert metal ions to RNA are also considered.
Reviews in Fluorescence 2005
Chris D. Geddes,Joseph R. Lakowicz
Author : Chris D. Geddes,Joseph R. Lakowicz
Publisher : Springer Science & Business Media
Page : 453 pages
File Size : 43,5 Mb
Release : 2007-12-31
Category : Science
ISBN : 9780387236902
Reviews in Fluorescence 2005 by Chris D. Geddes,Joseph R. Lakowicz Pdf
Last year we launched Volume 1 of the Reviews in Fluorescence series. The volume was well-received by the fluorescence community, with many e-mails and letters providing valuable feedback, we subsequently thank you all for your continued support. After the volume was published we were most pleased to learn that the volume is to be citable and indexed, appearing on the ISI database. Subsequently, as well as the series having an impact number in due course, individual chapters will appear on the database and be both citable and keyword searchable. We feel that this will be a powerful resource to both authors and readers, further disseminating leading-edge fluorescence based material. Our intention with this new series is to both disseminate and archive the most recent developments in both past and emerging fluorescence based disciplines. While all chapters are invited, we welcome and indeed encourage the fluorescence community to suggest areas of interest that they feel need to be covered by the series. In this new volume. Reviews in Fluorescence 2005, Volume 2, we have invited reviews in areas such as: Multi-dimensional Time-correlated Single Photon Counting; Fluorescence Correlation Spectroscopy; RNA folding; Lanthanide Probes and Fluorescent Biosensors to name but just a few. We hope you find this volume a useful resource and we look forward to receiving any suggestions you may have. Finally we would like to thank the authors for their timely articles, Caroleann Aitken for the fi-ont cover design, Kadir Asian for typesetting and Mary Rosenfeld for administrative support.
RNA Folding
Christina Waldsich
Author : Christina Waldsich
Publisher : Humana
Page : 0 pages
File Size : 49,5 Mb
Release : 2016-08-23
Category : Medical
ISBN : 149396058X
RNA Folding by Christina Waldsich Pdf
Focusing on in vitro and intracellular RNA structure formation, RNA Folding: Methods and Protocols provides a comprehensive collection of experimental protocols which are suitable to dissect RNA folding pathways and to characterize the structure of RNA folding intermediates at nucleotide or even atomic resolution. The presented techniques include powerful tools with a long tradition in RNA research as well as more advanced, novel methods, thus the methods span multiple disciplines, including molecular biology, biochemistry, biophysics, and computational biology. 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. Practical and authoritative, RNA Folding: Methods and Protocols serves as a vital reference for researchers attempting to gain insights into the secrets of this astounding macromolecule.
The Many Faces of RNA
D. S. Eggleston,Catherine D. Prescott,Neil D. Pearson
Author : D. S. Eggleston,Catherine D. Prescott,Neil D. Pearson
Publisher : Elsevier
Page : 228 pages
File Size : 53,5 Mb
Release : 1997-12-19
Category : Science
ISBN : 0080542557
The Many Faces of RNA by D. S. Eggleston,Catherine D. Prescott,Neil D. Pearson Pdf
The Many Faces of RNA is the subject for the eighth SmithKline Beecham Pharmaceuticals Research Symposia. It highlights a rapidly developing area of scientific investigation. The style and format are deliberately designed to promote in-depth presentations and discussions and to facilitate the forging of collaborations between academic and industrial partners. This symposium focuses on several of the many fundamental, advancing strategies for exploring RNA and its functions. It emphasizes the interplay between biology, chemistry, genomics, and molecular biology which is leading to exciting new insights and avenues of investigation. The book explores RNA as a therapeutic target, RNA as a tool, RNA and its interactions, along with chemical, computational, and structural investigations.
RNA Folding
Joseph Daniel Puglisi
Author : Joseph Daniel Puglisi
Publisher : Unknown
Page : 750 pages
File Size : 46,9 Mb
Release : 1989
Category : Electronic
ISBN : UCAL:$C73483
RNA Folding by Joseph Daniel Puglisi Pdf
Handbook of RNA Biochemistry
Roland K. Hartmann,Albrecht Bindereif,Astrid Schön,Eric Westhof
Author : Roland K. Hartmann,Albrecht Bindereif,Astrid Schön,Eric Westhof
Publisher : John Wiley & Sons
Page : 1368 pages
File Size : 51,7 Mb
Release : 2015-10-06
Category : Science
ISBN : 9783527650545
Handbook of RNA Biochemistry by Roland K. Hartmann,Albrecht Bindereif,Astrid Schön,Eric Westhof Pdf
The second edition of a highly acclaimed handbook and ready reference. Unmatched in its breadth and quality, around 100 specialists from all over the world share their up-to-date expertise and experiences, including hundreds of protocols, complete with explanations, and hitherto unpublished troubleshooting hints. They cover all modern techniques for the handling, analysis and modification of RNAs and their complexes with proteins. Throughout, they bear the practising bench scientist in mind, providing quick and reliable access to a plethora of solutions for practical questions of RNA research, ranging from simple to highly complex. This broad scope allows the treatment of specialized methods side by side with basic biochemical techniques, making the book a real treasure trove for every researcher experimenting with RNA.
RNA Recognition
Anonim
Author : Anonim
Publisher : Academic Press
Page : 468 pages
File Size : 54,5 Mb
Release : 2019-06-23
Category : Science
ISBN : 9780128168325
RNA Recognition by Anonim Pdf
RNA Recognition, Volume 623, the latest volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This updated volume covers a variety of topics, including The Preparation of cooperative RNA recognition complexes for crystallographic structural studies, Methods for thermal denaturation studies of fluorogenic aptamers, Dynamic combinatorial chemistry as a rapid, fragment-based approach to RNA-targeted compound discovery, Using a click chemistry assay to identify natural product ligands for pre-microRNAs, Lessons from exploration of chemical and structural small molecule:RNA space, Using ligand-observed NMR to study RNA-small molecule interactions, and much more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology series Includes the latest information on RNA Recognition
Non-Protein Coding RNAs
Nils Walter,Sarah A. Woodson,Robert T. Batey
Author : Nils Walter,Sarah A. Woodson,Robert T. Batey
Publisher : Springer Science & Business Media
Page : 400 pages
File Size : 47,6 Mb
Release : 2008-11-18
Category : Science
ISBN : 9783540708407
Non-Protein Coding RNAs by Nils Walter,Sarah A. Woodson,Robert T. Batey Pdf
The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, Andrew Fire and Craig Mello. This prize, which follows “RNA” Nobels for splicing and RNA catalysis, highlights just one class of recently discovered non-protein coding RNAs. Remarkably, non-coding RNAs are thought to outnumber protein coding genes in mammals by perhaps as much as four-fold. In fact, it appears that the complexity of an organism correlates with the fraction of its genome devoted to non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic tra- posons, higher-level organization of eukaryotic chromosomes, and gene expression are found to be largely directed by non-protein coding RNAs. Currently, bioinformatic, high-throughput sequencing, and biochemical approaches are identifying an increasing number of these RNAs. Unfortunately, our ability to characterize the molecular details of these RNAs is significantly lacking. The biophysical study of these RNAs is an emergent field that is unraveling the molecular underpinnings of how RNA fulfills its multitude of roles in sustaining cellular life. The resulting understanding of the physical and chemical processes at the molecular level is critical to our ability to harness RNA for use in biotechnology and human therapy, a prospect that has recently spawned a multi-billion dollar industry.
Ribozymes and RNA Catalysis
David Malcolm James Lilley,Fritz Eckstein
Author : David Malcolm James Lilley,Fritz Eckstein
Publisher : Royal Society of Chemistry
Page : 339 pages
File Size : 42,9 Mb
Release : 2008
Category : Science
ISBN : 9780854042531
Ribozymes and RNA Catalysis by David Malcolm James Lilley,Fritz Eckstein Pdf
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.
RNA 3D Structure Analysis and Prediction
Neocles Leontis,Eric Westhof
Author : Neocles Leontis,Eric Westhof
Publisher : Springer Science & Business Media
Page : 402 pages
File Size : 44,5 Mb
Release : 2012-06-05
Category : Science
ISBN : 9783642257407
RNA 3D Structure Analysis and Prediction by Neocles Leontis,Eric Westhof Pdf
With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.