Download or read book Probing RNA Dynamics and Protein ligand Interactions Using Fluorescence Spectroscopy written by Andrew Myles Parrott and published by . This book was released on 1999 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Probing RNA Structure and RNA protein Interactions Using Nanopore Force Spectroscopy written by Jianxun Lin and published by . This book was released on 2012 with total page 236 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Biophysical Chemical and Functional Probes of RNA Structure Interactions and Folding Part B written by Daniel Herschlag and published by Academic Press. This book was released on 2009-11-16 with total page 567 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 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 Ligand Interactions Part A Structural Biology Methods written by and published by Elsevier. This book was released on 2000-05-30 with total page 583 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-Ligand Interactions, Part A focuses on structural biology methods. Major topics covered include semisynthetic methodologies (RNA synthetic methods and derivatization of RNA); RNA structure determination (X-ray crystallography, NMR, EM); techniques for monitoring RNA conformation and dynamics (solution methods and electrophoretic and spectroscopic methods); and modeling tertiary structure: Part B, its companion Volume 318 of Methods in Enzymology, focuses on molecular 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 Fluorescence Spectroscopy as a Tool for Probing DNA protein Interactions written by Heather Marie Watrob Hargett and published by . This book was released on 2003 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Probing the Conformational Dynamics of Membrane associated Proteins Using Single Molecule Fluorescence written by Devdoot Majumdar and published by . This book was released on 2009 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Riboswitch Discovery Structure and Function written by and published by Academic Press. This book was released on 2014-11-21 with total page 595 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 riboswitch discovery and validation, synthesis and sample prep methods for large RNAs, riboswitch structure and function methods, folding pathways and dynamics, and ligand interactions and thermodynamics. - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers research methods in riboswitch discovery, structure and function - Contains sections on such topics as riboswitch discovery and validation, synthesis and sample prep methods for large RNAs, riboswitch structure and function methods, folding pathways and dynamics, ligand interactions and thermodynamics
Download or read book Investigating the Conformational Dynamics of RNA Molecules and Their Interaction Modes written by Niyati Jain and published by . This book was released on 2010 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA is a structurally flexible and dynamic molecule, and rapidly interconverts between multiple conformations. Despite the significant advances in traditional biophysical techniques like NMR spectroscopy and X-ray crystallography it is difficult to resolve the structures of dynamically inter-converting states as these methods measure the average property of an ensemble of molecules. It is necessary to resolve and get detailed descriptions of the multiple conformational structures, their quantitative distribution and their related dynamics in order to understand the ruggedness of the energy landscape. The present study attempts to link the conformational dynamics of RNA to its structure and biological function. Ultrafast time-resolved fluorescence spectroscopy is used to probe the distribution of multiple conformations and their dynamics that occur on a very fast timescales. This tool uses the resolution of time domain behavior of 2-aminopurine fluorescence decay on the ultrafast timescale to capture the characteristics of different structures. The RNAs are labeled with the fluorescent base analog 2-aminopurine to probe the base stacking patterns in RNA. Base stacking interactions is a unique feature that defines nucleic acid structures compared to proteins and are the major stabilizing force in RNA. Chapter 1 discusses the RNA folding mechanism and the relationships between sequence, structure, dynamics and function and explains the advantage of using ultrafast time resolved spectroscopy in defining structure-function relationships in RNA. Chapter 2 discusses the conformational heterogeneity and dynamics in purine-sensing riboswitches. We observed multiple conformations where the ligand is significantly stacked with the bases of the binding pocket and shows a dynamic balance between base stacking interactions and hydrogen bonding to achieve specificity and high affinity by the aptamer domain. Chapter 3 explores the conformational heterogeneity of GAAA tetraloop receptor and the impacts of the tertiary interactions between the receptor and the GAAA tetraloop, where we probe the isolated and GAAA-tetraloop bound receptor. The presence of any bound conformation in the free receptor state leads us to propose the conformational capture mechanism in tetraloop-receptor recognition. Chapter 4 summarizes findings of employing the ultrafast spectroscopy approach in studying riboswitches and the GAAA tetraloop-receptor. Overall our research is an effort to understand the role of conformational dynamics in RNA folding, tertiary interactions, recognition and functions.
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 Fluorescence Spectroscopy written by and published by Academic Press. This book was released on 2011-09-06 with total page 403 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fluorescence spectroscopy is a type of electromagnetic spectroscopy, using a beam of light, which analyzes fluorescence from a sample. Given its extremely high sensitivity and selectivity, it is an important investigational tool in many areas including material sciences, analytical sciences, and across a broad range of chemical, biochemical and medical research. It has become an essential investigational technique allowing detailed, real-time observation of the structure and dynamics of intact biological systems. The pharmaceutical industry uses it heavily and it has become a dominating technique in biochemistry and molecular genetics. - Keeps MIE buyers and online subscribers up-to-date with the latest research with this highly used technique - Provides tried and tested techniques which eliminate searching through many different sources
Download or read book Protein ligand Interactions Structure and Spectroscopy written by Stephen E. Harding and published by Practical Approach (Hardcover). This book was released on 2001 with total page 436 pages. Available in PDF, EPUB and Kindle. Book excerpt: X-ray crystallographic studies of protein-ligand interactions (R. A. Palmer). Molecular modeling (R. T. Kroemer). Circular dichroism (A. F. Drake). Genetic techniques for fluorescence measurements of protein-ligand interactions; real time kinetics and spatial imaging (J. Cladera, P. O'Shea). Stopped-flow techniques (J. F. Eccleston, J. P. Hutchinson, H. D. White). Protein-ligand interactions studied by FTIR spectroscopy: methodological aspects (M. J., H. H. Mantsch). Protein-ligand interactions studied by raman and resonance raman spectroscopy (R. Withnall). Electrospary ionization mass spectrometry (T. J. Hill, D. Lafitte, P. J. Derrick). Nitroxide spin labels as paramagnetic probes (D. A. Middleton). NMR studies of protein-ligand interactions (Lu-Yun Lian). Quantification and mapping of protein-ligand interactions at the single molecule level by atomic force microscopy (C. J. Roberts, S. Allen, M. C. Davies, S. J. B. Tendler, M. Williams). List of suppliers. Index.
Download or read book Single molecule Fluorescence Spectroscopy of Protein Folding written by Sonja Müller-Späth and published by . This book was released on 2010 with total page 99 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Exploring the Conformational Dynamics of Functional RNA Molecules by Ultrafast Time resolved Spectroscopy written by Beena Mary Kadakkuzha and published by . This book was released on 2009 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA has the intrinsic property to adopt multiple conformations through very fast independent as well as coupled motions. Resolving the high-resolution structures of dynamically inter-converting states is a major challenge for traditional biophysical techniques such as NMR spectroscopy and X-ray crystallography which provide an averaged structure of well folded conformations. It has been shown that the presence of multiple conformations contributes to the ruggedness of the RNA energy landscape, and the functionally relevant conformations could be less populated or transiently present in the ensemble of structure. In two different RNA molecules; a ribozyme with an asymmetric internal loop and a protein binding RNA with a trinucleotide bulge, the conformational dynamics and the structure-function correlation are explored by time-resolved ultrafast fluorescence spectroscopy. Here, RNAs are labeled with one of the most extensively studied fluorescent nucleic acid probes 2-aminopurine, to probe the base stacking patterns in specific motifs in RNA. Base stacking interactions are the major stabilizing force in RNA and the base stacking motions contribute to the local dynamics in RNA. Chapter 1 reviews the broad picture of RNA beyond the static structures and the role of conformational dynamics in defining structure-function relationships in RNA. Chapter 2 explains the basic principles and experimental set-up of ultrafast spectroscopy approach used in our lab and a brief discussion of other spectroscopic techniques that complement the time-resolved spectroscopy. Chapter 3 discusses the conformational dynamics and heterogeneity of leadzyme. We observed a highly unique asymmetric loop structure in leadzyme that lacks orderliness in the catalytic loop. Chapter 4 reviews the heterogeneity of HIV-1 TAR RNA, where we probe the free and ligand bound TAR to capture any bound conformation in the free state that can lead to the proposal of a possible conformational capture mechanism in TAR-Tat recognition. Chapter 5 summarizes our findings and the future prospects of employing time-resolved approach to study the dynamics of biomolecules. In conclusion, we observed RNA as an ensemble of structures in different structural context rather than a single rigid static structure.
Download or read book Probing the Protein Dynamics by a Combination Approach of Molecular Dynamics Simulation with Time resolved Fluorescence Spectroscopy and X ray Scattering written by 楊承翰 and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Fuzziness written by Monika Fuxreiter and published by Springer Science & Business Media. This book was released on 2012-03-07 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: Detailed characterization of fuzzy interactions will be of central importance for understanding the diverse biological functions of intrinsically disordered proteins in complex eukaryotic signaling networks. In this volume, Peter Tompa and Monika Fuxreiter have assembled a series of papers that address the issue of fuzziness in molecular interactions. These papers provide a broad overview of the phenomenon of fuzziness and provide compelling examples of the central role played by fuzzy interactions in regulation of cellular signaling processes and in viral infectivity. These contributions summarize the current state of knowledge in this new field and will undoubtedly stimulate future research that will further advance our understanding of fuzziness and its role in biomolecular interactions.
Download or read book Mass Spectrometry in Biophysics written by Igor A. Kaltashov and published by John Wiley & Sons. This book was released on 2005-05-06 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first systematic summary of biophysical mass spectrometrytechniques Recent advances in mass spectrometry (MS) have pushed the frontiersof analytical chemistry into the biophysical laboratory. As aresult, the biophysical community's acceptance of MS-based methods,used to study protein higher-order structure and dynamics, hasaccelerated the expansion of biophysical MS. Despite this growing trend, until now no single text has presentedthe full array of MS-based experimental techniques and strategiesfor biophysics. Mass Spectrometry in Biophysics expertly closesthis gap in the literature. Covering the theoretical background and technical aspects of eachmethod, this much-needed reference offers an unparalleled overviewof the current state of biophysical MS. Mass Spectrometry inBiophysics begins with a helpful discussion of general biophysicalconcepts and MS-related techniques. Subsequent chaptersaddress: * Modern spectrometric hardware * High-order structure and dynamics as probed by various MS-basedmethods * Techniques used to study structure and behavior of non-nativeprotein states that become populated under denaturingconditions * Kinetic aspects of protein folding and enzyme catalysis * MS-based methods used to extract quantitative information onprotein-ligand interactions * Relation of MS-based techniques to other experimental tools * Biomolecular properties in the gas phase Fully referenced and containing a helpful appendix on the physicsof electrospray mass spectrometry, Mass Spectrometry in Biophysicsalso offers a compelling look at the current challenges facingbiomolecular MS and the potential applications that will likelyshape its future.
