Measuring Protein Dynamics with Diverse Methods of Fluorescence Spectroscopy PDF Download
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Author: Alexandra Albanese
Publisher:
ISBN:
Category :
Languages : en
Pages : 262
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Book Description
Author: Alexandra Albanese
Publisher:
ISBN:
Category :
Languages : en
Pages : 262
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Book Description
Author: Ke-li Han
Publisher: Springer Science & Business Media
ISBN: 3319029703
Category : Medical
Languages : en
Pages : 488
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Book Description
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.
Author: Weihong Qiu
Publisher:
ISBN:
Category : Femtochemistry
Languages : en
Pages : 180
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Book Description
Abstract: Protein hydration dynamics is essential for many biological functions. However, understanding protein hydration dynamics has been technically challenged by the time and spatial resolution. This dissertation thus is a systematic investigation of protein hydration dynamics by integrating ultrafast fluorescence spectroscopy with the site-directed mutagenesis method. Using single tryptophan as the local optical probe, we first studied the site-specific solvation dynamics in various different conformations of the prototype peptide melittin and protein human serum albumin; both studies showed a strong correlation between local solvation dynamics and peptide/protein conformation transitions, and the critical role of hydration water in the structural integrity of the peptide/protein. To clarify the molecular interpretation of the solvation dynamics from time-resolved fluorescence studies, we also examined the local solvation dynamics at the surface of protein Staphylococcus nuclease using site-directed mutations; we replaced the local charged residues in close proximity to the tryptophan probe one at a time with an uncharged residue and did not observe significant change in the measured solvation dynamics, thus confirming that solvation correlation functions mainly measure the water dynamics in the protein hydration layer; the solvation dynamics is typically biexponential with the fast time constant resulting from local water relaxation in the hydration layer while the slow time from hydration water network rearrangement tightly coupled with protein fluctuations. To better understand the molecular mechanism of tryptophan fluorescence behaviors in proteins, we then surveyed the tryptophan fluorescence in more than 40 proteins with the femtosecond fluorescence method and molecular dynamics simulations. We were able to identify the carbonyl- and sulfur-containing residues as able quenching groups of tryptophan fluorescence within 100-ps; the former includes glutamine and glutamate residues while the later disulfide bond and cysteine residues. We studied the protein dynamics in human thioredoxin and were able to distinguish four time-overlapping dynamical processes at its active-site and determined their respective time scales; these results elucidated the temporal evolution of hydration water motions, electron transfer reactions and local protein fluctuations at the active site of human thioredoxin, and illustrated continuously synergistic dynamics of biological functions over wide time scales. Building on our understanding of hydration dynamics in isolated proteins or protein mimics, we are applying protein hydration dynamics as a tool to address more biologically relevant questions. Preliminary results are summarized in the final chapter for our efforts to unveil the molecular mechanism of molecular recognition in calmodulin using femtosecond-resolved fluorescence spectroscopy.
Author: Valentin Dunsing
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
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 ...
Author: Alexander P. Demchenko
Publisher: Springer Science & Business Media
ISBN: 3642708471
Category : Science
Languages : en
Pages : 323
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Book Description
The aim of this book is to give a comprehensive description of the basic methods used in the ultraviolet spectroscopy of proteins, to discuss new trends and development of these methods, and to analyze their different applications in the study of various aspects of protein structure and dynamics. Ultraviolet spectroscopy is one of the oldest and most popular methods in the field of biochemistry and molecular biophysics. At present, it is difficult to imagine the biochemical laboratory without a recording spectrophotometer or spectrofluorimeter. There are several hundreds of publications directly devoted to protein ultraviolet spectroscopy and in a great number of studies UV spectroscopic methods are used for the structural analysis of different proteins. Meanwhile a unified description of the theoretical basis of the methods, experimental techniques, data analysis, and generalization of results obtained in solving the specific problems of protein structure are lacking. There are three reasons for which a monograph on ultraviolet spectroscopy is needed today. Firstly, there has been significant growth in facilities of experimental technique, its precision, and versatility associated with computer data analysts. This new technique is available to a wide circle of scientists engaged in the field of protein research. Most of them are not spectroscopists and, thus, there is a need for a conceivable and precise source of information on how to use this method and what kind of data it should provide.
Author: Radek Šachl
Publisher: Springer Nature
ISBN: 3031303628
Category : Science
Languages : en
Pages : 532
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Book Description
This book provides the reader with an updated comprehensive view of the rapidly developing and fascinating field of fluorescence spectroscopy and microscopy. In recent years, fluorescence spectroscopy and microscopy have experienced rapid technological development, which has enabled the detection and monitoring of single molecules with high spatial and temporal resolution. Thanks to these developments, fluorescence has become an even more popular method in physical, biological and related fields. This book guides the reader through both basic and advanced fluorescence spectroscopy and microscopy approaches with a focus on their applications in membrane and protein biophysics. Each of the four parts: A - Fluorescence Spectroscopy, B - Fluorescence Microscopy, C - Applications of Fluorescence Spectroscopy and Microscopy to biological membranes and D - Applications of Fluorescence Spectroscopy to protein studies are written by experts within the field. The book is intended for both complete beginners who want to quickly orient themselves in the large number of existing fluorescent methods, as well as for advanced readers who are interested in particular methods and their proper use.
Author: Joseph R. Lakowicz
Publisher: Springer Science & Business Media
ISBN: 146157658X
Category : Science
Languages : en
Pages : 487
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Book Description
Fluorescence methods are being used increasingly in biochemical, medical, and chemical research. This is because of the inherent sensitivity of this technique. and the favorable time scale of the phenomenon of fluorescence. 8 Fluorescence emission occurs about 10- sec (10 nsec) after light absorp tion. During this period of time a wide range of molecular processes can occur, and these can effect the spectral characteristics of the fluorescent compound. This combination of sensitivity and a favorable time scale allows fluorescence methods to be generally useful for studies of proteins and membranes and their interactions with other macromolecules. This book describes the fundamental aspects of fluorescence. and the biochemical applications of this methodology. Each chapter starts with the -theoreticalbasis of each phenomenon of fluorescence, followed by examples which illustrate the use of the phenomenon in the study of biochemical problems. The book contains numerous figures. It is felt that such graphical presentations contribute to pleasurable reading and increased understand ing. Separate chapters are devoted to fluorescence polarization, lifetimes, quenching, energy transfer, solvent effects, and excited state reactions. To enhance the usefulness of this work as a textbook, problems are included which illustrate the concepts described in each chapter. Furthermore, a separate chapter is devoted to the instrumentation used in fluorescence spectroscopy. This chapter will be especially valuable for those perform ing or contemplating fluorescence measurements. Such measurements are easily compromised by failure to consider a number of simple principles.
Author: T.S.L Radhika
Publisher: CRC Press
ISBN: 1466588136
Category : Mathematics
Languages : en
Pages : 584
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Book Description
Approximate Analytical Methods for Solving Ordinary Differential Equations (ODEs) is the first book to present all of the available approximate methods for solving ODEs, eliminating the need to wade through multiple books and articles. It covers both well-established techniques and recently developed procedures, including the classical series solution method, diverse perturbation methods, pioneering asymptotic methods, and the latest homotopy methods. The book is suitable not only for mathematicians and engineers but also for biologists, physicists, and economists. It gives a complete description of the methods without going deep into rigorous mathematical aspects. Detailed examples illustrate the application of the methods to solve real-world problems. The authors introduce the classical power series method for solving differential equations before moving on to asymptotic methods. They next show how perturbation methods are used to understand physical phenomena whose mathematical formulation involves a perturbation parameter and explain how the multiple-scale technique solves problems whose solution cannot be completely described on a single timescale. They then describe the Wentzel, Kramers, and Brillown (WKB) method that helps solve both problems that oscillate rapidly and problems that have a sudden change in the behavior of the solution function at a point in the interval. The book concludes with recent nonperturbation methods that provide solutions to a much wider class of problems and recent analytical methods based on the concept of homotopy of topology.
Author:
Publisher: Academic Press
ISBN: 0080923348
Category : Science
Languages : en
Pages : 403
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Book Description
Fluorescence spectroscopy is a type of electromagnetic spectroscopy, using a beam of light, which analyzes fluorescence from a sample. Given its extremely high sensitivity and selectivity, it is an important investigational tool in many areas including material sciences, analytical sciences, and across a broad range of chemical, biochemical and medical research. It has become an essential investigational technique allowing detailed, real-time observation of the structure and dynamics of intact biological systems. The pharmaceutical industry uses it heavily and it has become a dominating technique in biochemistry and molecular genetics. - Keeps MIE buyers and online subscribers up-to-date with the latest research with this highly used technique - Provides tried and tested techniques which eliminate searching through many different sources
Author: Hanns-Christian Mahler
Publisher: John Wiley & Sons
ISBN: 0470497181
Category : Medical
Languages : en
Pages : 480
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Book Description
This book describes how to address the analysis of aggregates and particles in protein pharmaceuticals, provides a comprehensive overview of current methods and integrated approaches used to quantify and characterize aggregates and particles, and discusses regulatory requirements. Analytical methods covered in the book include separation, light scattering, microscopy, and spectroscopy.
