Download or read book Single Molecular Spectroscopy and Atomic Force Manipulation of Protein Conformation and Dynamics written by Jin Cao and published by . This book was released on 2014 with total page 122 pages. Available in PDF, EPUB and Kindle. Book excerpt: The present thesis describes the study of protein conformation dynamics probed by single molecule techniques. Protein structural dynamic have been studied for many years. Interesting topics such as protein folding/unfolding, protein denature, and protein-protein interactions had been widely studied. Scientists are still interested in questions like: what exact forces contribute to the stability of protein secondary and tertiary structure; why different protein has different function based on their structure. Single molecular spectroscopy has the advantage to observe inhomogeneous behavior of protein molecule compared to ensemble measurement. The typical approach of single molecular spectroscopy is to record one single molecule at a time and repeat this process at one or multiple molecules that are chemically identical. Then use statistics way to analyze these data. The binding dynamics of CaM-C28W complex was studied using single molecule FRET experiment. The statistics results indicate the inhomogeneous nature of the process and the evidence of a slower process gauging the binding dynamics has been claimed. Furthermore, the responding mechanical dynamics of CaM molecule under AFM tip manipulation has been investigated by AFM-FRET correlated measurement. The repeated "collapsing" pattern in the force curve leads us to deeper study on the process. The nature of the process and the dynamics of the underlying conformation change have also been detailed described. Lastly, a similar AFM manipulation experiment has been performed on EGFR dimer complex that has more biological potential in terms of dimer formation and aggregation dynamics. In order to fit the nature of the molecule, we used two identical dyes to label either monomer. Instead of single molecule FRET, photo-stamping measurement has been used to build an AFM-optical correlated measurement. The statistics results shows the presents of multiple intermediate states. With the help of known crystal structure and the knowledge of EGFR dimer complex, we managed to find clue from our correlated results and assign possible conformation of each intermediate states. A possible conjugated state upon collapsing has been claimed.
Download or read book Molecular Manipulation with Atomic Force Microscopy written by Anne-Sophie Duwez and published by CRC Press. This book was released on 2011-12-07 with total page 285 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the invention of scanning probe techniques in the early 1980s, scientists can now play with single atoms, single molecules, and even single bonds. Force, dynamics, and function can now be probed at the single-molecule level. Molecular Manipulation with Atomic Force Microscopy (AFM) presents a series of topics that discuss concepts and methodol
Download or read book Single molecule Force Manipulation and Nanoscopic Imaging of Protein Structure dynamics function Relationship written by Susovan Roy Chowdhury and published by . This book was released on 2021 with total page 141 pages. Available in PDF, EPUB and Kindle. Book excerpt: The anisotropic nature of the force fluctuation inside cells makes it very biologically relevant to study the dynamics of the structure-function relationship of protein molecules under force. The ability to manipulate individual molecules under near-physiological conditions makes the Atomic force microscope a very widely used technique. Force applied by AFM can be either compressive force or pulling force. Here in the thesis, we have explored the compressive force response of the protein molecules and the impact of the compressive force using AFM.The abrupt ruptures of protein native structures under compressive force were demonstrated by single-molecule AFM-FRET spectroscopic nanoscopy. The simultaneous measurement of the force curve and the FRET efficiency showed a temporal correlation between the compressive force drop and the FRET efficiency drop which indicated a spontaneous and abrupt rupture of the protein native tertiary structure.Furthermore, a similar compressive force experiment was done on targeted calmodulin molecules to characterize two different forms of CaM, the Ca2+-ligated activated form, and the Ca2+ free non-activated form (Apo-Calmodulin). A sudden and spontaneous rupture of Apo-CaM molecules was observed under the compressive force applied by an AFM tip, though no such events were recorded in the case of the Ca2+-ligated form.To further prove that this kind of compressive force rupture of Apo-CaM can trigger new chemistry inside the cell, a similar experiment was carried out where we observed compressive force rupture of apo-CaM molecules and successive binding of C28W peptide to the ruptured protein, a typical protein signaling activity that only a Ca2+-activated CaM has. This observation demonstrates that both chemical activation and force activation can play a vital role in biology, such as cell-signaling protein dynamics and function.Lastly, we further explored the entangled protein state formed following the events of the multiple and simultaneous tau protein ruptures under crowding. Crowded proteins simultaneously rupture and then spontaneously refold to an entangled folding state, different from either folded or unfolded states of the tau protein, which can be a plausible pathway for the tau protein aggregation that is related to several neurodegenerative diseases like Alzheimer's disease and Parkinson's disease.
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.
Download or read book Handbook of Molecular Force Spectroscopy written by Aleksandr Noy and published by Springer Science & Business Media. This book was released on 2007-12-03 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: Researchers in academia and industry who are interested in techniques for measuring intermolecular forces will find this an essential text. It presents a review of modern force spectroscopy, including fundamentals of intermolecular forces, technical aspects of the force measurements, and practical applications. The handbook begins with a review of the fundamental physics of loading single and multiple chemical bonds on the nanometer scale. It contains a discussion of thermodynamic and kinetic models of binding forces and dissipation effects in nanoscale molecular contacts, covers practical aspects of modern single-molecule level techniques, and concludes with applications of force spectroscopy to chemical and biological processes. Computer modeling of force spectroscopy experiments is also addressed.
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.
Download or read book Handbook of Single Molecule Biophysics written by Peter Hinterdorfer and published by Springer Science & Business Media. This book was released on 2009-12-24 with total page 634 pages. Available in PDF, EPUB and Kindle. Book excerpt: This handbook describes experimental techniques to monitor and manipulate individual biomolecules, including fluorescence detection, atomic force microscopy, and optical and magnetic trapping. It includes single-molecule studies of physical properties of biomolecules such as folding, polymer physics of protein and DNA, enzymology and biochemistry, single molecules in the membrane, and single-molecule techniques in living cells.
Download or read book Atomic Force Microscopy in Liquid written by Arturo M. Baró and published by John Wiley & Sons. This book was released on 2012-08-01 with total page 385 pages. Available in PDF, EPUB and Kindle. Book excerpt: About 40 % of current atomic force microscopy (AFM) research is performed in liquids, making liquid-based AFM a rapidly growing and important tool for the study of biological materials. This book focuses on the underlying principles and experimental aspects of AFM under liquid, with an easy-to-follow organization intended for new AFM scientists. The book also serves as an up-to-date review of new AFM techniques developed especially for biological samples. Aimed at physicists, materials scientists, biologists, analytical chemists, and medicinal chemists. An ideal reference book for libraries. From the contents: Part I: General Atomic Force Microscopy * AFM: Basic Concepts * Carbon Nanotube Tips in Atomic Force Microscopy with * Applications to Imaging in Liquid * Force Spectroscopy * Atomic Force Microscopy in Liquid * Fundamentals of AFM Cantilever Dynamics in Liquid * Environments * Single-Molecule Force Spectroscopy * High-Speed AFM for Observing Dynamic Processes in Liquid * Integration of AFM with Optical Microscopy Techniques Part II: Biological Applications * DNA and Protein-DNA Complexes * Single-Molecule Force Microscopy of Cellular Sensors * AFM-Based Single-Cell Force Spectroscopy * Nano-Surgical Manipulation of Living Cells with the AFM
Download or read book Molecular Manipulation with Atomic Force Microscopy written by Anne-Sophie Duwez and published by CRC Press. This book was released on 2011-12-07 with total page 291 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the invention of scanning probe techniques in the early 1980s, scientists can now play with single atoms, single molecules, and even single bonds. Force, dynamics, and function can now be probed at the single-molecule level. Molecular Manipulation with Atomic Force Microscopy (AFM) presents a series of topics that discuss concepts and methodologies used to manipulate and study single (bio)molecules with AFM. The first part is dedicated to the pulling of single molecules with force spectroscopy to investigate molecular interactions, mechanics, and mechanochemical processes, and the second part to the manipulation, repositioning, and targeted delivery of single molecules on substrates. Single molecule manipulation is an exciting area of research which made important breakthroughs in nanoscience and which could find potential applications in a diverse range of disciplines, including chemistry, biology, physics, material and polymer science, and engineering. New and experienced AFM researchers looking for applications beyond imaging will find a wealth of information in this informative volume.
Download or read book Theory and Evaluation of Single molecule Signals written by Eli Barkai and published by World Scientific. This book was released on 2008 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews recently developed theoretical and numerical approaches to deal with optical and mechanical signals from individual molecules. The character of data generated by single molecules, and more generally by single nano-objects, qualitatively differs from those obtained in conventional experiments on large ensembles of molecules. Fluctuations, randomness and irreproducibility are central to single-molecule measurements, and the specific methods required to extract reliable and statistically relevant information from them are presented here. With contributions mainly from participants of the ?Theory, Modeling and Evaluation of Single-Molecule Measurements? workshop held in Leiden, the Netherlands, on April 16-20, 2007, this book is an authoritative compendium on the subject.
Download or read book Protein Conformation written by Derek J. Chadwick and published by John Wiley & Sons. This book was released on 2008-04-30 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: How the amino acid sequence of a protein determines its three-dimensional structure is a major problem in biology and chemistry. Leading experts in the fields of NMR spectroscopy, X-ray crystallography, protein engineering and molecular modeling offer provocative insights into current views on the protein folding problem and various aspects for future progress.
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 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.
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.
Download or read book Single Molecule Biology written by Alexander E. Knight and published by Academic Press. This book was released on 2009-02-26 with total page 369 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single molecule techniques, including single molecule fluorescence, optical tweezers, and scanning probe microscopy, allow for the manipulation and measurement of single biological molecules within a live cell or in culture. These approaches, amongst the most exciting tools available in biology today, offer powerful new ways to elucidate biological function, both in terms of revealing mechanisms of action on a molecular level as well as tracking the behaviour of molecules in living cells. This book provides the first complete and authoritative treatment of this rapidly emerging field, explicitly from a biological perspective.The contents are organized by biological system or molecule. Each chapter discusses insights that have been revealed about their mechanism, structure or function by single molecule techniques. Among the topics covered are enzymes, motor proteins, membrane channels, DNA, ribozymes, cytoskeletal proteins, and other key molecules of current interest. An introduction by the editor provides a concise review of key principles and an historical overview. The last section discusses applications in molecular diagnostics and drug discovery. Organized by biological system or molecule Each chapter discusses insights into mechanism of action, structure, and function Covers enzymes, motor proteins, membrane channels, DNA, ribozymes, etc Includes an introduction to key principles and an historical overview Discusses applications in molecular diagnostics and drug discovery Provides an expert's perspective on future development
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:
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.
