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High Resolution Single Molecule Spectroscopy To Probe Conformational Dynamics Of Proteins
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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 Probing the Conformational Dynamics of Membrane-associated Proteins Using Single Molecule Fluorescence by : Devdoot Majumdar
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:
Book Synopsis Single-Molecule Spectroscopy And Imaging Studies Of Protein Folding-Unfolding Conformational Dynamics by : Zijan Wang
Download or read book Single-Molecule Spectroscopy And Imaging Studies Of Protein Folding-Unfolding Conformational Dynamics written by Zijan Wang and published by . This book was released on 2016 with total page 132 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein conformational dynamics often plays a critical role in protein functions. We have characterized the spontaneous folding-unfolding conformational fluctuation dynamics of calmodulin (CaM) at thermodynamic equilibrium conditions by using single-molecule fluorescence resonance energy transfer (FRET) spectroscopy. We studied protein folding dynamics under simulated biological conditions to gain a deep, mechanistic understanding of this important biological process. We have identified multiple folding transition pathways and characterized the underlying energy landscape of the single-molecule protein conformational fluctuation trajectories. Our results suggest that the folding dynamics of CaM molecules involves a complex multiple-pathway multiple-state energy landscape, rather than an energy landscape of two-state dynamical process. Our probing single-molecule FRET fluctuation experiments demonstrate a new approach of studying spontaneous protein folding-unfolding conformational dynamics at the equilibrium that features recording long time single-molecule conformational fluctuation trajectories. This technique yields rich statistical and dynamical information far beyond traditional ensemble-averaged measurements. We characterize the conformational dynamics of single CaM interacting with C28W. The single CaM molecules are partially unfolded by GdmCl, and the folded and unfolded CaM molecules are approximately equally populated. Under this condition, the majority of the single protein CaM undergoes spontaneous folding-unfolding conformational fluctuations. Using single molecule FRET spectroscopy, we study each of the single protein’s conformational dynamics inthe presence of C28W-CaM interactions. The results show an interesting folding-upon-binding dynamic process, and a conformational selection mechanism is further confirmed. The effect of molecular crowding on protein folding process is a key issue in the understanding of protein folding dynamics in living cells. Due to the complexity and interplay between various interactions existing in an equally favored environment of protein folding and unfolding conformational dynamics, such simple reduced entropic enhancement model do not suffice in describing protein folding conformational dynamics. We observe, at higher concentration of crowding reagent Ficoll 70, single protein molecules spontaneously denature into unfolded proteins which involves a combined process of polymer-polymer interaction, entropic effects and solvation thermodynamics and dynamics. Such heterogeneous unfolding process can serve as a first step to a mechanistic understanding of living cell disease as a result of molecular crowding effect, protein aggregates and fibril formation.
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 Probing and Manipulating Protein Conformation Changes by Time-Resolved Single-Molecule Spectroscopy and Site-Specific Ultramicroscopy by :
Download or read book Probing and Manipulating Protein Conformation Changes by Time-Resolved Single-Molecule Spectroscopy and Site-Specific Ultramicroscopy written by and published by . This book was released on 2008 with total page 9 pages. Available in PDF, EPUB and Kindle. Book excerpt: This project was to develop and demonstrate a novel single-molecule spectroscopy and imaging technique to support the DARPA program on Control of Protein Conformations. The goal of our project is to advance, integrate, and apply cutting-edge atomic force microscopy (AFM) and single-molecule imaging techniques to control and analyze the protein conformational changes and according activity changes through AFM force manipulation and fluorescence resonant energy transfer (FRET) measurements as a function of local site geometry and molecular structure. In this project, we have focused our demonstration and study on controlling protein conformations to manipulate the enzyme reactivity, affinity, and selectivity. Our approach has been to use AFM tip to control protein conformational states and to apply single-molecule FRET imaging to measure the protein enzyme activity in real time. Our progress towards the demonstration of the new technology has provided an unprecedented advancement on a high spatially (nanometers) and temporally (micro's to seconds) resolved single-molecule spectroscopy of optically and mechanically controlling single-molecule protein conformational changes and activities.
Book Synopsis Observing Protein Dynamics and Conformational Changes by Ensemble and Single-molecule Fluorescence Spectroscopy by : So Yeon Kim
Download or read book Observing Protein Dynamics and Conformational Changes by Ensemble and Single-molecule Fluorescence Spectroscopy written by So Yeon Kim and published by . This book was released on 2008 with total page 420 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Measuring Conformational Dynamics of Biological Molecules with Single-molecule Tracking and Fluorescence Correlation Spectroscopy by : Charles Limouse
Download or read book Measuring Conformational Dynamics of Biological Molecules with Single-molecule Tracking and Fluorescence Correlation Spectroscopy written by Charles Limouse and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The past two decades have seen great advances in single-molecule techniques capable of probing biomolecular systems with spatial resolution down to the nanometer level. However few techniques are specifically designed to measure larger scale organization between a few tens and a few hundreds of nanometers, especially when other figures of merit are considered, such as high time-resolution or the possibility to do measurements in bulk and without immobilization. Such features would be particularly useful in the study of molecular structures like chromatin or other nucleoprotein complexes, that exhibit organizational details and dynamics across a broad range of time and length scales. I present how the combination of fluorescence correlation spectroscopy (FCS) and single molecule tracking can be used to measure the conformational dynamics of molecules that diffuse freely in solution, at the scale of a few tens of nanometers. I discuss some aspects of the instrumentation as well as the parameters that define the spatial and temporal resolution. I describe other advantages of the technique such as the possibility to bypass a common difficulty associated with fluorescence correlation measurements and obtain a signal that is not convolved with the blinking dynamics of the fluorescent probe itself. Finally I present an experimental proof-of-principle where tracking-FCS was applied to measure the end-to-end Brownian dynamics of short DNA fragments in the semilflexible regime.
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 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 Spectroscopy Studies of Protein Conformational Dynamics in DNA Damage Recognition and Cell Signaling by : Sunidhi Jaiswal
Download or read book Single-molecule Spectroscopy Studies of Protein Conformational Dynamics in DNA Damage Recognition and Cell Signaling written by Sunidhi Jaiswal and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-molecule fluorescence spectroscopy has been developed as a powerful technique that provides details of protein-protein and protein-DNA interactions, enzyme reactions, and conformational dynamics. It is highly informative to study protein's conformational dynamics during their activity or under the enzymatic condition to understand their function. The real-time monitoring of the enzyme's active site conformational dynamics and simultaneously activity is informative towards understanding the mechanism of action. Studying how conformational fluctuation dynamics play role in protein or enzyme activity can shed light on the field of enzymology. Particularly in this dissertation, we have employed FoÌrster Resonance Energy Transfer (FRET) as a powerful tool to study the conformational dynamics of Calmodulin (CaM) during its interaction with an autoinhibitory domain (C28W peptide) of the Plasma Membrane Calcium ATPase (PMCA). FRET between donor dye-labeled N-domain of the calmodulin interacting with acceptor dye-labeled peptide reports the real-time conformational dynamics of this interaction which is essential for PMCA activation. Interestingly, by using a unique statistical method, the results provide a mechanistic understanding of CaM signaling interaction and activation of the Ca-ATPase through multiple-state binding to the C28W. The new single-molecule spectroscopic analyses demonstrated in this work can be applied for broad studies of protein functional conformation fluctuation and protein-protein interaction dynamics. In another study, the conformational dynamics of recognition proteins are studied to understand the mechanism of identification of DNA damage by two recognition proteins, Replication Protein A (RPA) and Xeroderma Pigmentosum Protein A (XPA). We use single-molecule fluorescence fluctuation measurements of a dye, labeled at a damaged position on DNA, to understand the interaction of the damage site with RPA14 and XPA. Our results suggest that interactive conformational dynamics of RPA14 with damaged DNA are inhomogeneous due to its low affinity for DNA, whereas binding of XPA with the already formed DNA- RPA14 complex may increase the specificity of damage recognition by controlling the conformational fluctuation dynamics of the complex. Further, we studied the activation of calmodulin by applying compressive force using the AFM technique. Significantly, we found that the picoNewton level compressive force can turn a calcium-free CaM molecule into an active binding form just like the calcium-activated CaM.
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 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 Quantitative Biology by : Michael E. Wall
Download or read book Quantitative Biology written by Michael E. Wall and published by CRC Press. This book was released on 2012-08-25 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantitative methods are revolutionizing modern molecular and cellular biology. Groundbreaking technical advances are fueling the rapid expansion in our ability to observe, as seen in multidisciplinary studies that integrate theory, computation, experimental assays, and the control of microenvironments. Integrating new experimental and theoretical
Book Synopsis Intrinsically Disordered Proteins Studied by NMR Spectroscopy by : Isabella C. Felli
Download or read book Intrinsically Disordered Proteins Studied by NMR Spectroscopy written by Isabella C. Felli and published by Springer. This book was released on 2015-09-19 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses the paradigm-shifting phenomenon of intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered domains and functional IDP regions (IDPRs). The properties of IDPs and IDPRs are highly complementary to those deriving from the presence of a unique and well-defined three-dimensional fold. Ignored for a long time in high-resolution studies of proteins, intrinsic protein disorder is now recognized as one of the key features for a large variety of cellular functions, where structural flexibility presents a functional advantage in terms of binding plasticity and promiscuity and this volume explores this exciting new research. Recent progress in the field has radically changed our perspective to study IDPs through NMR: increasingly complex IDPs can now be characterized, a wide range of observables can be determined reporting on the structural and dynamic properties, computational methods to describe the structure and dynamics are in continuous development and IDPs can be studied in environments as complex as whole cells. This volume communicates the new exciting possibilities offered by NMR and presents open questions to foster further developments. Intrinsically Disordered Proteins Studied by NMR Spectroscopy provides a snapshot to researchers entering the field as well as providing a current overview for more experienced scientists in related areas.
Book Synopsis Conformational Dynamics of Proteins by Fluorescence Fluctuation Spectroscopy by : Robel Birru Yirdaw
Download or read book Conformational Dynamics of Proteins by Fluorescence Fluctuation Spectroscopy written by Robel Birru Yirdaw and published by . This book was released on 2012 with total page 151 pages. Available in PDF, EPUB and Kindle. Book excerpt:
