Download or read book Single molecule Enzymology with a ClyA Nanopore written by and published by . This book was released on 2020 with total page 203 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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
Download or read book Single Molecule Enzymology Nanomechanical Manipulation and Hybrid Methods written by and published by Academic Press. This book was released on 2017-01-03 with total page 486 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-Molecule Enzymology, Part B, 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, and nanopore 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, and nanopore and tethered particle motion
Download or read book Single Molecule Tools for Bioanalysis written by Shuo Huang and published by CRC Press. This book was released on 2022-05-25 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last three decades, the fast development of single-molecule techniques has revolutionized the way we observe and understand biological processes. Some of these techniques have been further adapted as tools for bioanalysis. This book summarizes and details the frontiers of the development of these tools as well as their applications. The contributors are young and established researchers in their respective fields. The main content originates from the lecture notes of a chemistry graduate course taught by the book editor at Nanjing University. This book is suitable to be used as a textbook for a high-level undergraduate or an entry-level graduate course. The systematically written content provides a thorough illustration of the mechanisms of each methodology presented.
Download or read book High Resolution Single molecule Enzyme Dynamics Using Nanopores written by Jonathan M. Craig and published by . This book was released on 2017 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA is a molecule that contains the genetic information of all living organisms. DNA provides the instructions that the cell uses to construct the proteins which carry out the complex functions required for life to thrive. Enzymes are a class of proteins that use chemical potentials to catalyze energetically unfavorable chemical reactions to perform tasks ranging from muscle contraction to DNA packaging. In this thesis I focus on a class of enzymes called `motor enzymes' which use the energy provided by ATP hydrolysis to produce directed motion along a molecular track, such as DNA or RNA, and perform mechanical tasks such as unwinding double-stranded nucleic acids or building double stranded nucleic acids from single-stranded nucleic acids. Classically, enzyme reactions were studied by biochemical methods that monitor a large number of reactions simultaneously. These methods are limited because enzymes operate near thermal energies, leading to asynchronous progression of the chemical reaction. In the past 30 years, methods to monitor the reactions of single enzyme molecules have provided numerous insights into the function of motor enzymes, but these techniques lack the resolution to provide full details of how these molecules transduce chemical energy into mechanical work. In this thesis I present the development of Single-molecule Picometer Resolution Nanopore Tweezers (SPRNT), a method for monitoring the movement of single enzyme molecules on DNA at unprecedented spatiotemporal resolution using the biological nanopore MspA. In SPRNT, a single MspA protein pore (termed a `nanopore') in a phospholipid bilayer forms the only electrical connection between two salt solutions termed \textit{cis} and \textit{trans}. A voltage applied across the membrane causes an ion current to flow through the nanopore. Negatively charged single-stranded DNA complexed to a motor enzyme is attracted into the nanopore by the electric field. The DNA passes through the pore until the motor enzyme, which is too large to fit through the pore, comes to rest on the rim of MspA. The DNA bases in the pore reduce the ion current flowing through the pore depending on the bases therein. The motor enzyme then moves along the DNA, causing DNA to move through the pore, leading to a series of stochastic ion-current amplitudes which simultaneously provide measurements of the kinetics of the enzyme and the DNA sequence. This method leads to a higher spatiotemporal resolution than any other single-molecule technique. In this thesis I present my role in the development of SPRNT. In chapter 1 I introduce the relevant biomolecules and techniques used to examine them. In chapter 2 I discuss the development of SPRNT and quantify its spatiotemporal resolution. In chapters 3 and 4 I present the first enzyme dynamics studies done with SPRNT on the helicase Hel308, and use information from quantities that could not be measured previously to elucidate the precise details of Hel308 motion on DNA, and to determine the mechanism by which DNA modulates Hel308 translocation. Chapter 5 contains concluding remarks and a discussion of the future of SPRNT.
Download or read book Single Molecule Enzymology written by Gregory I. Mashanov and published by Humana Press. This book was released on 2011-08-04 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt: The last fifteen years have witnessed the birth and maturation of many original methods and the development of protocols specific to single molecule measurements and their analysis, including techniques involving optical imaging, electron microscopy, optical and magnetic trapping, and developments in atomic force microscopy. In Single Molecule Enzymology: Methods and Protocols, experts in the field provide procedures which enable the extraction of detailed information about enzyme work cycles, their static and kinetic properties, and information about their location and activity within cells. The detailed volume offers practical advice on many aspects of single molecule enzymology and includes strategic overviews of interconnected methods involved in sample preparation, single molecule measurements, and data analysis. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain 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 up-to-date, Single Molecule Enzymology: Methods and Protocols is intended for use within the diverse community of molecular biologists, biochemists, and biophysicists studying enzymes in detail and can be used by researchers planning their first single molecule study or to aid more experienced researchers in further developing their existing studies.
Download or read book Nanoscale Electrochemistry written by Andrew J. Wain and published by Elsevier. This book was released on 2021-09-14 with total page 580 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nanoscale Electrochemistry focuses on challenges and advances in electrochemical nanoscience at solid–liquid interfaces, highlighting the most prominent developments of the last decade. Nanotechnology has had a tremendous effect on the multidisciplinary field of electrochemistry, yielding new fundamental insights that have broadened our understanding of interfacial processes and stimulating new and diverse applications. The book begins with a tutorial chapter to introduce the principles of nanoscale electrochemical systems and emphasize their unique behavior compared with their macro/microscopic counterparts. Building on this, the following three chapters present analytical applications, such as sensing and electrochemical imaging, that are familiar to the traditional electrochemist but whose extension to the nanoscale is nontrivial and reveals new chemical information. The subsequent three chapters present exciting new electrochemical methodologies that are specific to the nanoscale, including "single entity"-based methods and surface-enhanced electrochemical spectroscopy. These techniques, now sufficiently mature for exposition, have paved the way for major developments in our understanding of solid–liquid interfaces and continue to push electrochemical analysis toward atomic-length scales. The final three chapters address the rich overlap between electrochemistry and nanomaterials science, highlighting notable applications in energy conversion and storage. This is an important reference for both academic and industrial researchers who are seeking to learn more about how nanoscale electrochemistry has developed in recent years. Outlines the major applications of nanoscale electrochemistry in energy storage, spectroscopy and biology Summarizes the major principles of nanoscale electrochemical systems, exploring how they differ from similar system types Discusses the major challenges of electrochemical analysis at the nanoscale
Download or read book Pore Forming Toxins written by and published by Academic Press. This book was released on 2021-03-10 with total page 672 pages. Available in PDF, EPUB and Kindle. Book excerpt: Pore Forming Toxins, Volume 649 in the Methods in Enzymology series continues the legacy of this premier serial with quality chapters authored by field leaders. Chapters in this new release include X-ray crystallography shines a light on pore-forming toxins, Giant unilamellar vesicles for studying activity of pore forming proteins, Combined applications of fluorescence spectroscopy and molecular dynamics simulations in studies of Diphtheria Toxin translocation domain, Biophysical approaches to study actinoporin-lipid interactions, Molecular basis for activation of Actinoporins by lipids, Engineered ClyA for detection of biological molecules, Pore-forming Toxins for the Size-Discrimination of Polymers and Biopolymers: Towards Biomolecules Sequencing, 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
Download or read book Single molecule Enzymology written by Maria Spies and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Nanopore Technology written by Monifa A. V. Fahie and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Single Molecule Tools Part A Fluorescence Based Approaches written by and published by Academic Press. This book was released on 2010-06-28 with total page 528 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
Download or read book Single molecule Enzymology of Alpha chymotrypsin Using Microfabricated Arrays of Cylindrical Wells written by Angela Y. Chen and published by . This book was released on 2009 with total page 94 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-molecule enzymatic studies have introduced ways to identify and track the distributions of individual enzyme's reaction rates that are averaged in ensemble kinetics. We describe a simple method that combines the use of a microfabricated array of wells, a protease assay, and fluorescence microscopy to study our model enzyme alpha-chymotrypsin at the single-molecule level. The microfabrication process for the silicon wafer mold is outlined in detail, and the enzymatic assay is compared between ensemble and single-molecule experiments. In our method, PDMS wells are designed 2micron in diameter and 1.35micron in height. We isolate alpha-chymotrypsin into single molecules inside the cylindrical wells with an enzyme-to-substrate ratio of 1: 6,666 molecules. This method allows for the simultaneous tracking of hundreds of individual enzyme molecules over time. In our analysis of single-enzyme kinetics, we incorporate orange fluorescent microspheres (540/560nm) as the reference standard and correct for photobleaching of the dye in the protease assay. Our results show that single alpha-chymotrypsin molecules exhibit heterogeneous product formation rates that are stable for long durations.
Download or read book The Study of Single Molecule Protein Biophysics Using a Solid State Nanopore written by Kevin J. Freedman and published by . This book was released on 2013 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt: The kinetics of protein folding and binding has been studied for several decades and continues to reveal links to overall cellular health,cell functionality, and responses to therapeutic agents. Despite numerous methods to purify and detect proteins, there is still a growing need to develop technology that can enhance sensing and reveal potentially hidden properties of proteins. This is important not only from a scientific perspective but also in practically achieving the goals of personalized healthcare. Next generation sensors should ideally have three main characteristics: (1) high resolution sensing, (2) high-throughput sensing, and (3) the potential to be automated and used by untrained personnel. Future devices will revolutionize the healthcare industry by decreasing both the time and cost to do basic scientific research, diagnostic testing, and drug development. A likely candidate for next-generation protein sensing is solid-state nanopores. The pores developed here are fabricated in a 50 nm thick silicon nitride membrane and a single nanopore is drilled using a focused ion beam or a focused electron beam. The detection method employed is largely based on resistive pulse sensing where analytes are electrokinetically transported through a pore and identified by their unique modulation of ionic current (i.e. an ionic blockade). Since the dimensions of the nanopore are on the same scale as the molecule being sensed, only a single molecule can enter the pore allowing individual protein kinetics to be probed. Traditionally proteins are detected by ensemble averaging which hides important kinetics and sub-populations of molecules that may be important to understanding the early stages of a disease or detect a disease early. In the first section of this study, the prominent issue of protein adsorption onto the sensing device (i.e. the nanopore) is addressed and resolved by using a modified voltage protocol. The rationale behind the new sensing scheme is explained in terms of the interplay of diffusive and entropic (barrier-dominated) forces on a protein. In the second section, we discovered that the voltage which drives the protein through the pore also has denaturing effects. The unfolding data supports a gradual unfolding mechanism rather than the cooperative transition observed by classical urea denaturation experiments. Lastly it is shown that the voltage-mediated unfolding is a function of the stability of the protein by comparing two mutationally destabilized variants of the protein. In the final section of this study, voltage-mediated unbinding of a single protein complex is studied. We argue that determining the unbinding forces between two proteins adds an additional level of specificity which is needed for eventual use as a diagnostic tool. In this study, nanopores are developed not only as a sensor but also a single molecule or protein complex manipulator that can locally unfold or unbind molecules.
Download or read book Polymer Translocation written by M. Muthukumar and published by CRC Press. This book was released on 2016-04-19 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: Polymer translocation occurs in many biological and biotechnological phenomena where electrically charged polymer molecules move through narrow spaces in crowded environments. Unraveling the rich phenomenology of polymer translocation requires a grasp of modern concepts of polymer physics and polyelectrolyte behavior. Polymer Translocation discusse
Download or read book Dynamics in Enzyme Catalysis written by Judith Klinman and published by Springer. This book was released on 2013-09-14 with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt: Christopher M. Cheatum and Amnon Kohen, Relationship of Femtosecond–Picosecond Dynamics to Enzyme-Catalyzed H-Transfer. Cindy Schulenburg and Donald Hilvert, Protein Conformational Disorder and Enzyme Catalysis. A. Joshua Wand, Veronica R. Moorman and Kyle W. Harpole, A Surprising Role for Conformational Entropy in Protein Function. Travis P. Schrank, James O. Wrabl and Vincent J. Hilser, Conformational Heterogeneity Within the LID Domain Mediates Substrate Binding to Escherichia coli Adenylate Kinase: Function Follows Fluctuations. Buyong Ma and Ruth Nussinov, Structured Crowding and Its Effects on Enzyme Catalysis. Michael D. Daily, Haibo Yu, George N. Phillips Jr and Qiang Cui, Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations. Karunesh Arora and Charles L. Brooks III, Multiple Intermediates, Diverse Conformations, and Cooperative Conformational Changes Underlie the Catalytic Hydride Transfer Reaction of Dihydrofolate Reductase. Steven D. Schwartz, Protein Dynamics and the Enzymatic Reaction Coordinate.
Download or read book Bionanotechnology written by David S. Goodsell and published by John Wiley & Sons. This book was released on 2004-04-16 with total page 351 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discussions of the basic structural, nanotechnology, and system engineering principles, as well as an introductory overview of essential concepts and methods in biotechnology, will be included. Text is presented side-by-side with extensive use of high-quality illustrations prepared using cutting edge computer graphics techniques. Includes numerous examples, such applications in genetic engineering. Represents the only available introduction and overview of this interdisciplinary field, merging the physical and biological sciences. Concludes with the authors' expert assessment of the future promise of nanotechnology, from molecular "tinkertoys" to nanomedicine. David Goodsell is author of two trade books, Machinery of Life and Our Molecular Nature, and Arthur Olson is the world's leader in molecular graphics and nano-scale representation.
Download or read book Protocells written by Steen Rasmussen and published by MIT Press. This book was released on 2022-06-07 with total page 723 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first comprehensive general resource on state-of-the-art protocell research, describing current approaches to making new forms of life from scratch in the laboratory. Protocells offers a comprehensive resource on current attempts to create simple forms of life from scratch in the laboratory. These minimal versions of cells, known as protocells, are entities with lifelike properties created from nonliving materials, and the book provides in-depth investigations of processes at the interface between nonliving and living matter. Chapters by experts in the field put this state-of-the-art research in the context of theory, laboratory work, and computer simulations on the components and properties of protocells. The book also provides perspectives on research in related areas and such broader societal issues as commercial applications and ethical considerations. The book covers all major scientific approaches to creating minimal life, both in the laboratory and in simulation. It emphasizes the bottom-up view of physicists, chemists, and material scientists but also includes the molecular biologists' top-down approach and the origin-of-life perspective. The capacity to engineer living technology could have an enormous socioeconomic impact and could bring both good and ill. Protocells promises to be the essential reference for research on bottom-up assembly of life and living technology for years to come. It is written to be both resource and inspiration for scientists working in this exciting and important field and a definitive text for the interested layman.
