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Single Molecule Spectroscopy And Imaging Studies Of Protein Folding Unfolding Conformational Dynamics
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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 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 Molecular Spectroscopy and Atomic Force Manipulation of Protein Conformation and Dynamics by : Jin Cao
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.
Book Synopsis Protein Folding, Misfolding and Aggregation by : Victor Muñoz
Download or read book Protein Folding, Misfolding and Aggregation written by Victor Muñoz and published by Royal Society of Chemistry. This book was released on 2008-06-24 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein folding and aggregation is the process by which newly synthesized proteins fold into the specific three-dimensional structures defining their biologically active states. It has always been a major focus of research in biochemistry and has often been seen as the unsolved second part of the genetic code. In the last 10 years we have witnessed a quantum leap in the research in this exciting area. Computational methods have improved to the extent of making possible to simulate the complete folding process of small proteins and the early stages of protein aggregation. Experimental methods have evolved to permit resolving fast processes of folding reactions and visualizing single molecules during folding. The findings from these novel experiments and detailed computer simulations have confirmed the main predictions of analytical theory of protein folding. In summary, protein folding research has finally acquired the status of a truly quantitative science, paving the way for more exciting developments in the near future. This unique book covers all the modern approaches and the many advances experienced in the field during the last 10 years. There is also much emphasis on computational methods and studies of protein aggregation which have really flourished in the last decade. It includes chapters in the areas that have witnessed major developments and are written by top experts including:computer simulations of folding, fast folding, single molecule spectroscopy, protein design, aggregation studies (both computational and experimental). Readers will obtain a unique perspective of the problems faced in the biophysical study of protein conformational behaviour in aqueous solution and how these problems are being solved with a multidisciplinary approach that combines theory, experiment and computer simulations. Protein Folding, Misfolding and Aggregation Classical Themes and Novel Approaches is essential reading for graduate students actively involved in protein folding research, other scientists interested in the recent progress of the field and instructors revamping the protein folding section of their biochemistry and biophysics courses.
Book Synopsis Protein Folding Protocols by : Yawen Bai
Download or read book Protein Folding Protocols written by Yawen Bai and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covering experiment and theory, bioinformatics approaches, and state-of-the-art simulation protocols for better sampling of the conformational space, this volume describes a broad range of techniques to study, predict, and analyze the protein folding process. Protein Folding Protocols also provides sample approaches toward the prediction of protein structure starting from the amino acid sequence, in the absence of overall homologous sequences.
Book Synopsis Protein Conformation by : Derek J. Chadwick
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.
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 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 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 Protein Folding by : Cláudio M. Gomes
Download or read book Protein Folding written by Cláudio M. Gomes and published by Springer. This book was released on 2019-02-25 with total page 63 pages. Available in PDF, EPUB and Kindle. Book excerpt: This snapshot volume is designed to provide a smooth entry into the field of protein folding. Presented in a concise manner, each section introduces key concepts while providing a brief overview of the relevant literature. Outlook subsections will pinpoint specific aspects related to emerging methodologies, concepts and trends.
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 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 Protein Folding Dynamics and Stability by : Prakash Saudagar
Download or read book Protein Folding Dynamics and Stability written by Prakash Saudagar and published by Springer Nature. This book was released on 2023-05-27 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes recent important advancements in protein folding dynamics and stability research, as well as explaining fundamentals and examining potential methodological approaches in protein science. In vitro, in silico, and in vivo method based research of how the stability and folding of proteins help regulate the cellular dynamics and impact cell function that are crucial in explaining various physiological and pathological processes. This book offers a comprehensive coverage on various techniques and related recent developments in the experimental and computational methods of protein folding, dynamics, and stability studies. The book is also structured in such a way as to summarize the latest developments in the fiddle and key concepts to ensure that readers can understand advanced concepts as well as the fundamental big picture. And most of all, fresh insights are provided into the convergence of protein science and technology. Protein Folding Dynamics and Stability is an ideal guide to the field that will be of value for all levels of researchers and advanced graduate students with training in biochemical laboratory research.
Book Synopsis Single Molecules and Nanotechnology by : Rudolf Rigler
Download or read book Single Molecules and Nanotechnology written by Rudolf Rigler and published by Springer Science & Business Media. This book was released on 2007-12-07 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on recent advances in the rapidly evolving field of single molecule research. These advances are of importance for the investigation of biopolymers and cellular biochemical reactions, and are essential to the development of quantitative biology. Written by leading experts in the field, the articles cover a broad range of topics, including quantum photonics of organic dyes and inorganic nanoparticles and monitoring of single molecule (enzymatic) reactions.
Book Synopsis Protein Folding by : Grace E. Orellana
Download or read book Protein Folding written by Grace E. Orellana and published by American Chemical Society. This book was released on 2024-05-08 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: Life as we know it would not exist if proteins did not fold into functional three-dimensional structures, where α-helices, loops, and β-sheets act together to form active sites that drive a myriad of biochemical reactions in the cell. The failure of this process is linked to the pathology of various diseases, such as neurodegenerative disorders like Alzheimer’s, genetic conditions (like cystic fibrosis), and cancer. It is no wonder that close to $2 billion in worldwide research funding has been devoted over the last five years (2019–2025) to helping scientists understand the molecular details of protein folding, how it can fail in ways that promote disease in humans, and clinical paths to treat or prevent diseases linked to protein misfolding. This primer is prerequisite reading to the literature on this important topic for readers new to the field. Chapter one provides exposure to the three-dimensional structure of proteins; readers will learn how to identify secondary structures, protein motifs, and domains involved in biological function. Chapter two introduces methodologies to determine the three-dimensional structure of proteins; readers will learn modern techniques to determine the secondary structure composition and the orientation of atoms in three-dimensional space. By providing exposure to how the physical environment (i.e., chemical denaturants, pH, pressure, and temperature) controls protein denaturation, readers will learn how such information can be used to study the biophysical characteristics of proteins through various probes and methodologies.
Book Synopsis Handbook of Single-Molecule Biophysics by : Peter Hinterdorfer
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.
Book Synopsis Handbook of Fluorescence Spectroscopy and Imaging by : Markus Sauer
Download or read book Handbook of Fluorescence Spectroscopy and Imaging written by Markus Sauer and published by John Wiley & Sons. This book was released on 2010-12-23 with total page 425 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing much-needed information on fluorescence spectroscopy and microscopy, this ready reference covers detection techniques, data registration, and the use of spectroscopic tools, as well as new techniques for improving the resolution of optical microscopy below the resolution gap. Starting with the basic principles, the book goes on to treat fluorophores and labeling, single-molecule fluorescence spectroscopy and enzymatics, as well as excited state energy transfer, and super-resolution fluorescence imaging. Examples show how each technique can help in obtaining detailed and refined information from individual molecular systems.
