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Biomolecule Conformational Dynamics Studies Using Two Beam Fluorescence Fluctuation Spectroscopy
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Book Synopsis Biomolecule Conformational Dynamics Studies Using Two-beam Fluorescence Fluctuation Spectroscopy by : Jaemyeong Jung
Download or read book Biomolecule Conformational Dynamics Studies Using Two-beam Fluorescence Fluctuation Spectroscopy written by Jaemyeong Jung and published by . This book was released on 2005 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Biophysics and Poisson Process Approach to Statistical Mechanics by : Susanta K Sarkar
Download or read book Single Molecule Biophysics and Poisson Process Approach to Statistical Mechanics written by Susanta K Sarkar and published by Morgan & Claypool Publishers. This book was released on 2016-04-01 with total page 64 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is an overview of single molecule physics, the study of both equilibrium and non-equilibrium properties at the single molecule level. It begins with an introduction to this fascinating science and includes a chapter on how to build the most popular instrument for single molecule biophysics, the total internal reflection fluorescence (TIRF) microscope. It concludes with the Poisson process approach to statistical mechanics, explaining how to relate the process to diverse areas and see how data analysis and error bars are integral parts of science.
Book Synopsis Structure, Dynamics and Function of Biomolecules by : Anders Ehrenberg
Download or read book Structure, Dynamics and Function of Biomolecules written by Anders Ehrenberg and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a collection of papers presented and discussed at the first EBSA workshop held at Saltsj6baden outside stockholm in Sweden, July 6-10, 1986. The common theme of these papers is dynamics of biomolecules, and how the dynamics depends on the molecular structure and organi zation, and connects to and determines the biological function. This is a rapidly expanding field of research which combines many different aspects of molecular bio physics. Much material is new and presented for the first time. Even if the work so far has been of the kind that is usually called basic research, practical applications are clearly indicated in some articles, and are waiting around the corner in several other cases. At the workshop only one third of the time was used for the formal presentations and two thirds for discussion. To this should also be added discussions during the poster sessions. During these lively and unrecorded discussions fresh viewpoints emerged and new ideas were created. Ad mittedly, our knowledge at present is only fragmentary but when pieces of the puzzle are brought together at a workshop or in a publication of this kind more extended and sometimes unexpected contours and shapes become vi sible. It is our hope that this rapid publication of camera-ready manuscripts will transfer some of the spi rit at the workshop to the reader, and in his or her institute or laboratory initiate further discussions, bring forward more ideas and start new experimental ap roaches.
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 Fluorescent Biomolecules by : David M. Jameson
Download or read book Fluorescent Biomolecules written by David M. Jameson and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 459 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is based on an international symposium held during September 9-12, 1986 in Bocca di Magra, Italy. The intent of the organizers was to bring together expert practitioners of fluorescence spectroscopy, particularly as applied to biological systems, to assess recent developments in the field and discuss future directions. At the same time the meeting was intended to honor the singular and outstanding scientific career of Gregorio Weber on the occasion of his seventieth birthday. Gregorio Weber is truly the pioneer in the application of fluores cence methods to biochemistry and biophysics. A complete list of his scientific contributions to fluorescence and to protein biochemistry is beyond the scope of this preface. Suffice it to say that since his initial landmark articles on fluorescence, published in the late 1940's and early 1950's, Gregorio Weber has continued to make seminal contribu tions to both the theory and practice of fluorescence and, contrary to many who might be tempted to rest on their laurels, he shows no signs of slackening his pace. In addition to his more obvious tangible contributions to the scientific field, Gregorio Weber has made equally valuable contributions of another type. Specifically, he has had the most profound impact, both profeSSionally and personally, on generations of young scientists.
Book Synopsis Dissertation Abstracts International by :
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2008 with total page 850 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 Fluorescence Fluctuation Spectroscopy Techniques to Quantify Molecular Interactions and Dynamics in Complex Biological Systems by : Valentin Dunsing
Download or read book Fluorescence Fluctuation Spectroscopy Techniques to Quantify Molecular Interactions and Dynamics in Complex Biological Systems written by Valentin Dunsing and published by . This book was released on 2020* with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Living cells rely on transport and interaction of biomolecules to perform their diverse functions. A powerful toolbox to study these highly dynamic processes in the native environment is provided by fluorescence fluctuation spectroscopy (FFS) techniques. In more detail, FFS takes advantage of the inherent dynamics present in biological systems, such as diffusion, to infer molecular parameters from fluctuations of the signal emitted by an ensemble of fluorescently tagged molecules. In particular, two parameters are accessible: the concentration of molecules and their transit times through the observation volume. In addition, molecular interactions can be measured by analyzing the average signal emitted per molecule - the molecular brightness - and the cross-correlation of signals detected from differently tagged species. In the present work, several FFS techniques were implemented and applied in different biological contexts. In particular, scanning fluorescence correlation spectroscopy (sFCS) was performed to measure protein dynamics ...
Book Synopsis Measurement of Molecular Conformations and Dynamics Using Single Molecule Fluorescence Techniques by : Huimin Chen
Download or read book Measurement of Molecular Conformations and Dynamics Using Single Molecule Fluorescence Techniques written by Huimin Chen and published by . This book was released on 2012 with total page 122 pages. Available in PDF, EPUB and Kindle. Book excerpt: The use of fluorescence spectroscopy to study biological problems has gained popularity over the past few decades. Beyond a spatial understanding provided by microscopy, fluorescence techniques like Fluorescence Correlation Spectroscopy (FCS) and fluorescence lifetime spectroscopy can also elucidate the important temporal dynamics of molecular conformations. We have applied FCS to study the conformational fluctuations in a model protein apomyoglobin. By pushing the technical limitations of FCS, we were able to observe conformational dynamics spanning two orders of magnitude in time (10[-]6 to 10[-]3 seconds). We found that the amplitude of fluctuations changes as the molecule becomes unfolded, with principal shifts of amplitudes and timescales occurring at the transition across the molten globule state. We also measured the diffusion of apomyoglobin, confirming theoretical predictions of less compaction of the molecule upon acid denaturation. We were able to observe the fluctuations in apomyoglobin using FCS due to the quenching of an N-terminal labeled Alexa488 fluorophore by contact with various amino acids. We showed that quenching can occur with up to four amino acids. We investigated the mechanisms of quenching using a combination of fluorescence intensity and lifetime measurements. We showed that quenching takes place through a combination of static and dynamic mechanisms. Our results demonstrate that care needs to be taken when making quan- titative measurements of fluorescently labeled proteins. Coupling single molecule functionality to fluorescence techniques allows researchers to discern subpopulations within ensembles. We used single molecule Förster Resonance Energy Transfer (smFRET) to measure the end-to-end distances in single stranded nucleic acids as a probe of the flexibility. We also measured the radius of gyration using small angle X-ray scattering, and extracted parameters of polymer properties that fit the data from both techniques. We observed clear differences between our model single stranded DNA (ssDNA) and RNA (ssRNA). We also observed a difference between the screening efficiency of monovalent and divalent cations. By characterizing the intrinsic differences in nucleic acids and its dependence on the ionic strength, we hope to improve our understanding of the mechanisms of RNA folding and the role of ions in the process.
Book Synopsis Biomolecules' Conformational Changes Studied by Simulations and Enhanced Sampling by : Yui Tik (Andrew) Pang
Download or read book Biomolecules' Conformational Changes Studied by Simulations and Enhanced Sampling written by Yui Tik (Andrew) Pang and published by Springer. This book was released on 2024-10-17 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis illuminates the critical roles biomolecules, from small molecules to proteins, play in cellular functionality, particularly highlighting their conformational changes in response to environmental cues or binding events—a cornerstone concept in drug design as well as the manifestations of disease. It explores the conformational flexibility of small molecules and proteins, essential for predicting drug interactions and understanding biological processes. Through advanced molecular dynamics simulations and enhanced sampling techniques, this research offers unprecedented insights into the structural dynamics of three distinct biomolecular systems: the capsid assembly modulator AT130, the passenger domain of pertactin, and the SARS-CoV-2 spike protein. Each system represents a unique facet of biological complexity, underscoring the thesis's contribution to our understanding of biomolecular behavior across various scales. Furthermore, the thesis advances the field by updating the Force Field Toolkit for improved simulation accuracy. This work not only showcases the adaptability and importance of simulation techniques in modern biological research but also paves the way for novel therapeutic strategies by deepening our understanding of biomolecular dynamics.
Book Synopsis Fluorescence Correlation Spectroscopy by : R. Rigler
Download or read book Fluorescence Correlation Spectroscopy written by R. Rigler and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 503 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first book-length treatment of both the theoretical background to fluorescence correlation spectroscopy (FCS) and a variety of applications in various fields of science. The high spatial and temporal resolution of FCS has made it a powerful tool for the analysis of molecular interactions and kinetics, transport properties due to thermal motion, and flow. It contains an essential contribution from Nobel Prize winner M. Eigen, who is credited with inventing FCS.
Book Synopsis Conformational Fluctuations of Biomolecules Studied Using Molecular Dynamics and Enhanced Sampling by : Geoffrey M. Gray
Download or read book Conformational Fluctuations of Biomolecules Studied Using Molecular Dynamics and Enhanced Sampling written by Geoffrey M. Gray and published by . This book was released on 2018 with total page 261 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA sequences exist in a prebent conformation compared to nongcognate sequence. This results in a lower deformation energy for the binding of a cognate sequence. Simulations of the C-terminal domain of Cdc37 (chapter 3) in which Y298 was unphosphorylated, phosphorylated and mutated to a phosphomimetic residue, revealed the importance of conformational fluctuations in the regulation of the Hsp90 chaperone cycle. Both the phosphomimetic and phosphorylated systems resulted in the loss of native like contacts and hydrogen bonding for that residue. This resulted in an unfolding of α1 helix and an exposure of an SH2-binding domain. This domain is important for the recognition of client chaperones. Contrastingly, while α1
Book Synopsis Fast Dynamics of Aqueous Biological Molecules Investigated with 2D IR Spectroscopy by : Jean K. Chung
Download or read book Fast Dynamics of Aqueous Biological Molecules Investigated with 2D IR Spectroscopy written by Jean K. Chung and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are dynamic structures that are in constant fluctuations, and their ability to undergo structural changes is critical to their function. However, their fastest dynamics in thermal equilibrium have remained largely unexplored. In this work, studies that examine the dynamics of aqueous proteins using two-dimensional infrared echo spectroscopy (2D IR) are presented. In particular, investigations of fast fluctuations in proteins and peptides within the context of structural changes upon denaturation are discussed. 2D IR is a nonlinear optical spectroscopic technique that can measure ultrafast dynamics of complex molecules in the picoseconds regime, timescales ~6-10 orders of magnitude faster than nuclear magnetic resonance. In addition, the relatively low energy mid-IR laser pulses used in this study probe the relevant nuclear degrees of freedom without significantly perturbing the protein structure or dynamics. Brief descriptions of the experimental setup and methods, as well as analysis and interpretation, are given.
Book Synopsis Using Molecular Simulations and Statistical Models to Understand Biomolecular Conformational Dynamics by : Yunhui Ge
Download or read book Using Molecular Simulations and Statistical Models to Understand Biomolecular Conformational Dynamics written by Yunhui Ge and published by . This book was released on 2020 with total page 246 pages. Available in PDF, EPUB and Kindle. Book excerpt: Conformational dynamics are important to the function of biological molecules. While many experimental techniques (e.g. X-ray crystallography and NMR spectroscopy) have been developed for providing the structure of functional conformations, it is exceptionally challenging to understand conformational dynamics from experimental characterization. Molecular dynamics (MD) simulations is a powerful tool for probing conformational dynamics. The timescale resolution of MD simulations enables people to investigate intermediate conformations and transition pathways in atomic detail. Recent advancements in computer hardware have increased the timescales accessible to MD simulations. Meanwhile, more accurate and specific force fields have been developed to accurately model a variety biological system of different sizes. My graduate research has been focused on using MD simulations to study the conformational dynamics of proteins. Markov State Model (MSM) based approaches are extensively applied to investigate a variety of folding and/or binding mechanisms in atomic detail. Another focus of my work has been developing a Bayesian inference-based approach called BICePs to reconcile experimental measurements with simulation data to determine conformational ensembles and to validate force fields.
Book Synopsis Fluorescence Spectroscopic Studies of Protein Conformational Dynamics by : Phillip Gunther Kroehn
Download or read book Fluorescence Spectroscopic Studies of Protein Conformational Dynamics written by Phillip Gunther Kroehn and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Research Awards Index written by and published by . This book was released on 1982 with total page 1212 pages. Available in PDF, EPUB and Kindle. Book excerpt:
