Read Books Online and Download eBooks, EPub, PDF, Mobi, Kindle, Text Full Free.
Single Molecule Spectroscopy Studies Of The Conformational Dynamics Of Enzymes
Download Single Molecule Spectroscopy Studies Of The Conformational Dynamics Of Enzymes full books in PDF, epub, and Kindle. Read online Single Molecule Spectroscopy Studies Of The Conformational Dynamics Of Enzymes ebook anywhere anytime directly on your device. Fast Download speed and no annoying ads. We cannot guarantee that every ebooks is available!
Book Synopsis Single-Molecule Spectroscopy Studies of the Conformational Dynamics of Enzymes by : Maolin Lu
Download or read book Single-Molecule Spectroscopy Studies of the Conformational Dynamics of Enzymes written by Maolin Lu and published by . This book was released on 2014 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: Conformational motions of enzymes are highly dynamic and intrinsically stochastic. Obtaining molecular level insights into conformational dynamics of enzymes is critical for unraveling the complex intimate structure-to-function relationship. This dissertation describes the investigation of conformational dynamics of HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) and T4 lysozyme by single-molecule FRET (Forster/fluorescence resonance energy transfer) spectroscopy and photon stamping spectroscopy. This dissertation also demonstrates the developments of corresponding single-molecule spectroscopic approaches to serve scientifically experimental demands. This dissertation also demonstrates the developments of corresponding single-molecule spectroscopic approaches to serve scientifically experimental demands. Multiple conformational intermediate states and multi-dimensional conformational motions of T4 lysozyme have been observed. The Markov process has successfully reproduced the experimental observations, suggesting that T4 lysozyme hinge-bending open-close conformational changes follow multiple pathways involving multiple intermediate states. The combination of lifetime and anisotropy results presents a whole picture of multi-dimensional conformational dynamics in the process of T4 lysozyme open-close hinge-bending. The non-exponential features of both lifetime and anisotropy autocorrelation functions reveal dynamic and static inhomogeneity/complexity of multi-dimensional conformational fluctuations. The investigations of probing and manipulating HPPK conformational dynamics has been described. The consistency between the decay rate of donor lifetime and rising rate of acceptor lifetime gives a direct observation of FRET dynamic process at single-molecule level. The autocorrelation analysis of donor lifetimes have revealed intermittent conformational coherence of multiple HPPK Loop3-active site conformational states, regulated by substrate-enzyme interactions. Mechanically manipulating a targeted dye-labeled single HPPK in pinpoint nano-scale precision and simultaneously monitoring the conformational changes during the AFM pulling event has been achieved. The observed results of different lifetime fluctuations, distinct anisotropy fluctuations and various dynamic rates have suggested the existence of function-inert and function-active scenarios of HPPK Loop 3-active site conformational dynamic motions. The developments of single-molecule spectroscopic approaches have been demonstrated, including 1) single molecule photon stamping FRET spectroscopy, on the basis of only measuring the donor's lifetime trajectory; 2) single-molecule AFM-FRET nanoscopy, capable of effectively pinpointing and mechanically manipulating a targeted dye-labeled single protein in a large sampling area; and 3) single-molecule multi-parameter photon stamping spectroscopy system, integrating fluorescence anisotropy-FRET-lifetime and capable of observing single-molecule multi-dimensional conformational motions.
Book Synopsis Single Molecule Spectroscopy by : R. Rigler
Download or read book Single Molecule Spectroscopy written by R. Rigler and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 375 pages. Available in PDF, EPUB and Kindle. Book excerpt: The topics range from single molecule experiments in quantum optics and solid-state physics to analogous investigations in physical chemistry and biophysics.
Book Synopsis Single Molecule Spectroscopy for Studying Conformational Dynamics of Short Oligonucleotides by : Ron Reuven Lin
Download or read book Single Molecule Spectroscopy for Studying Conformational Dynamics of Short Oligonucleotides written by Ron Reuven Lin and published by . This book was released on 2012 with total page 66 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding biology at the molecular level has been driving technological advances in biological and medical science for many years. Methods for probing molecular systems are often dependent on sampling the concerted actions of large assemblies of molecules rather than for studying individual molecules operating in isolation. Most methods used in experimental biology are largely insensitive to the activity of a single molecule. Over the past twenty five years, advances in a variety of disciplines have been employed which allow researchers to use single molecule approaches to for examining biomolecules, a development which has had remarkable implications for advancing the understanding of cellular processes. Single molecule techniques have been used to resolve questions about everything from replication, recombination, transcription and translation and protein folding, among other subjects. The structure-function relationship in biology is central to the understanding of cellular processes, and has provided one of the most significant intellectual frameworks for understanding molecular pathways. Its success is validated by numerous studies using X-ray crystallography that now routinely allow researchers to make rational predictions explaining why and how biomolecules interact. The famous "lock and key" model for enzymatic function perhaps best exemplifies this framework. Despite their predictive power, structure-functional relationships often gloss over a basic fact of biological systems--both structure and function may in fact possess a remarkable degree of dynamism. This dissertation summarizes my efforts to develop and refine methods for interrogating the dynamical properties of single molecules, with a particular emphasis on studying structural properties of DNA and examining protein-DNA interactions. I provide an overview of fluorescence, FRET and fluorescence lifetime spectroscopy in Chapter 1, and discuss the methods I developed using fluorescence lifetime to examine conformational fluctuations of sub-persistence length segments of DNA. In Chapter 2, I describe a microfluidic-based platform developed in the Shimon Weiss Lab for conducting single molecule FRET assays, which was used to exploit persistence length changes in DNA upon hybridization to screen context-dependent RNA polymerase transcription. Finally, in Chapter 3, I describe a new detector with improved red spectrum sensitivity, which provides a foundation for further work applying fluorescence lifetime analysis to studying structural perturbations in DNA on nanosecond timescales.
Book Synopsis Single Molecule Optical Magnetic Tweezers Microscopy Studies of Protein Dynamics by : Qing Guo
Download or read book Single Molecule Optical Magnetic Tweezers Microscopy Studies of Protein Dynamics written by Qing Guo and published by . This book was released on 2015 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation presents our research work aiming at conformational manipulation of single enzyme protein molecules, performed by single molecule magnetic tweezers correlated with optical fluorescence spectroscopy. To experimentally investigate the enzyme-substrate interactions and the related conformational fluctuations, we have developed a new approach to manipulate the enzymatic conformation and enzyme-substrate interaction at the single-molecule level by using a combined magnetic tweezers and simultaneous fluorescence resonance energy transfer (FRET) spectroscopic microscopy. By a repetitive pulling-releasing manipulation of a Cy3-Cy5 dye labeled 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) molecule under the conditions with and without enzymatic substrates, we have probed and analyzed the enzymatic conformational dynamics. Our results indicate that the enzymatic conformational flexibility can be regulated by enzyme-substrate interactions: (1) the enzyme at its conformation-perturbed state has less flexibility when binding substrates, and (2) substrate binding to the enzyme significantly changes the enzyme conformational flexibility, experimental evidence of so called entropy trapping in and enzyme-substrate reactive transition state. Furthermore, our results provide significant experimental analysis of folding-binding interactions of the enzyme-substrate interactions, and reveal the dynamic nature of the enzyme-substrate interactions. We also find supportive results from Steered Molecular Dynamics (SMD) Simulation, showing that in our studies, conformational manipulation by magnetic tweezers is able to distort the active domain of the enzyme molecules to an extent that significantly beyond thermal conformational fluctuations. Furthermore, we have also revealed the impact of partially unfolding the enzyme molecules on their activity by using single-molecule TIRF-magnetic tweezers spectroscopy to manipulate conformation of the enzyme molecules to a partially unfolded, yet not fully denatured condition. By conformationally distorting horseradish peroxidase (HRP) molecules via magnetic tweezers at the single molecule level, we successfully manipulated and examined the activity changes of the HRP catalyzed H2O2-Amplex Red reaction. We have observed significant tolerance of the enzyme activity to the enzyme conformation in its deformed or partially-unfolded states. We have identified that (1) enzymatic activity can be manipulated by our TIRF-magnetic tweezers at single molecule level; and (2) enzyme molecules in partially unfolded conformation are still capable of showing significant activity, although at a lower but measurable level, due to the enzymatic active site conformational fluctuation and substrate binding induced folding-binding conformational changes. We further provide our understanding of the enzyme behavior based on enzymatic conformational fluctuation, enzyme-substrate interactions, enzyme-substrate active complex formation, and protein folding-binding interactions.
Book Synopsis Spectroscopy and Dynamics of Single Molecules by :
Download or read book Spectroscopy and Dynamics of Single Molecules written by and published by Elsevier. This book was released on 2019-08-14 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: Spectroscopy and Dynamics of Single Molecules: Methods and Applications reviews the most recent developments in spectroscopic methods and applications. Spectroscopic techniques are the chief experimental methods for testing theoretical models and research in this area plays an important role in stimulating new theoretical developments in physical chemistry. This book provides an authoritative insight into the latest advances in the field, highlighting new techniques, current applications, and potential future developments An ideal reference for chemists and physicists alike, Spectroscopy and Dynamics of Single Molecules: Methods and Applications is a useful guide for all those working in the research, design, or application of spectroscopic tools and techniques across a wide range of fields. Includes the latest research on ultrafast vibrational and electronic dynamics, nonlinear spectroscopies, and single-molecule methods Makes the content accessible to researchers in chemistry, biophysics, and chemical physics through a rigorous multi-disciplinary approach Provides content edited by a world-renowned chemist with more than 30 years of experience in research and instruction
Book Synopsis Protein Conformational Dynamics by : Ke-li Han
Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.
Book Synopsis Single-molecule Studies of Proteins by : Andres F. Oberhauser
Download or read book Single-molecule Studies of Proteins written by Andres F. Oberhauser and published by Springer Science & Business Media. This book was released on 2012-11-09 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Single Molecule Studies of Proteins, expert researchers discuss the successful application of single-molecule techniques to a wide range of biological events, such as the imaging and mapping of cell surface receptors, the analysis of the unfolding and folding pathways of single proteins, the analysis interaction forces between biomolecules, the study of enzyme catalysis or the visualization of molecular motors in action. The chapters are aimed at established investigators and post-doctoral researchers in the life sciences wanting to pursue research in the various areas in which single-molecule approaches are important; this volume also remains accessible to advanced graduate students seeking similar research goals.
Book Synopsis Single Molecule Dynamics in Life Science by : Toshio Yanagida
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.
Book Synopsis High-resolution Single-molecule Spectroscopy to Probe Conformational Dynamics of Proteins by : Christian Gebhardt
Download or read book High-resolution Single-molecule Spectroscopy to Probe Conformational Dynamics of Proteins written by Christian Gebhardt and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Single Molecule Tools, Part A: Fluorescence Based Approaches by :
Download or read book Single Molecule Tools, Part A: Fluorescence Based Approaches written by and published by Academic Press. This book was released on 2010-08-17 with total page 559 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single molecule tools have begun to revolutionize the molecular sciences, from biophysics to chemistry to cell biology. They hold the promise to be able to directly observe previously unseen molecular heterogeneities, quantitatively dissect complex reaction kinetics, ultimately miniaturize enzyme assays, image components of spatially distributed samples, probe the mechanical properties of single molecules in their native environment, and "just look at the thing" as anticipated by the visionary Richard Feynman already half a century ago. Single Molecule Tools, Part A: Fluorescence Based Approaches captures a snapshot of this vibrant, rapidly expanding field, presenting articles from pioneers in the field intended to guide both the newcomer and the expert through the intricacies of getting single molecule tools. Includes time-tested core methods and new innovations applicable to any researcher employing single molecule tools Methods included are useful to both established researchers and newcomers to the field Relevant background and reference information given for procedures can be used as a guide to developing protocols in a number of disciplines
Book Synopsis SINGLE MOLECULE STUDIES OF ENZYMES HORSERADISH PEROXIDASE AND ALKALINE PHOSPHATASE USING TOTAL INTERNAL REFLECTION FLUORESCENCE MICROSCOPY AND CONFOCAL MICROSCOPY by : Leonora Kaldaras
Download or read book SINGLE MOLECULE STUDIES OF ENZYMES HORSERADISH PEROXIDASE AND ALKALINE PHOSPHATASE USING TOTAL INTERNAL REFLECTION FLUORESCENCE MICROSCOPY AND CONFOCAL MICROSCOPY written by Leonora Kaldaras and published by . This book was released on 2013 with total page 46 pages. Available in PDF, EPUB and Kindle. Book excerpt: Conformational dynamics plays an important role in determining protein reactivity including affinity to substrate and product, catalytic rate constant and product release process. Whereas the influence of conformational dynamics on kinetic parameters of enzymatic reaction have been widely studied by ensemble averaging techniques, in these experiments conformational variations tend to average out and therefore ensemble averaging methods lack the level of resolution necessary to characterize time dependent behavior of individual enzyme molecules, which is essential to understanding enzymatic catalysis. This thesis consists of two parts. The first part focuses on the new development of integrated spectroscopy system, which combined the advantages of wide plane view field of objective-type TIRFM imaging with high time-resolution confocal single-molecule spectroscopy to address the challenge of probing both temporally and spatially stochastic events of the single-molecule reactions, such as fluorogenic enzymatic reactions with enzyme tethered to a solution/glass interface. Tthe calibration of this integrated apparatus is demonstrated with fluorescence microspheres and the feasibility by spectroscopy measurement of single molecule Rhodamine 6G on glass surface. Finally, the application of the apparatus is demonstrated by studying spatially and temporally randomly distributed single-molecule enzymatic reaction of fluorogenic substrate, horseradish peroxidase-catalyzed oxidation of amplex red. The second part focuses on exploratory studies of enzyme Alkaline Phosphatase from E. coli and its potential to be studied on single molecule level using fluorogenic substrate 3-o-methylfluorescein phosphate (MFP) and two polarization total internal reflection fluorescence microscopy apparatus. Ensemble averaged kinetics data and several single molecule trajectories are presented here.
Book Synopsis Single Molecule Spectroscopy in Chemistry, Physics and Biology by : Astrid Graslund
Download or read book Single Molecule Spectroscopy in Chemistry, Physics and Biology written by Astrid Graslund and published by Springer Science & Business Media. This book was released on 2010-04-17 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by the leading experts in the field, this book describes the development and current state of the art in single molecule spectroscopy. The application of this technique, which started 1989, in physics, chemistry and biosciences is displayed.
Book Synopsis Single-Molecule Enzymology: Fluorescence-Based and High-Throughput Methods by :
Download or read book Single-Molecule Enzymology: Fluorescence-Based and High-Throughput Methods written by and published by Academic Press. This book was released on 2016-10-28 with total page 618 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-Molecule Enzymology, Part A, 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 volume covers research methods in single-molecule enzymology, and includes sections on such topics as force-based and hybrid approaches, fluorescence, high-throughput sm enzymology, nanopores, and tethered particle motion. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods in single-molecule enzymology Contains sections on such topics as force-based and hybrid approaches, fluorescence, high-throughput sm enzymology, nanopores, and tethered particle motion
Book Synopsis Photon-counting Single-molecule Spectroscopy for Studying Conformational Dynamics and Macromolecular Interactions by : Ted Alfred Laurence
Download or read book Photon-counting Single-molecule Spectroscopy for Studying Conformational Dynamics and Macromolecular Interactions written by Ted Alfred Laurence and published by . This book was released on 2002 with total page 390 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Single Molecule Studies of Enzyme Kinetics and Mechanism by : Jue Shi
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:
Book Synopsis Single Molecule Spectroscopy in Chemistry, Physics and Biology by : Astrid Gräslund
Download or read book Single Molecule Spectroscopy in Chemistry, Physics and Biology written by Astrid Gräslund and published by Springer Science & Business Media. This book was released on 2009-12-09 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: With a foreword written by a Nobel Laureate, this book describes the development and current state-of-the-art in single molecule spectroscopy. The application of this technique, which started 1989, in physics, chemistry and biosciences is displayed.
Book Synopsis Single-Molecule/Entity Spectroscopy by : Anne Myers Kelley
Download or read book Single-Molecule/Entity Spectroscopy written by Anne Myers Kelley and published by American Chemical Society. This book was released on 2023-11-01 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-Molecule/Entity Spectroscopy is an indispensable resource for scientists interested in understanding single-molecule spectroscopy comprehensively. By presenting detailed information on the technique’s principles, discussing its diverse applications, and providing insights into future developments, researchers can acquire a holistic overview of this dynamic field without the need to consult an extensive array of individual papers. This primer bridges the gap between standard undergraduate coursework to practical implementation in the research lab for single-molecule spectroscopy.
