Thermal Unfolding Dynamics of Proteins Probed by Nonlinear Infrared Spectroscopy PDF Download
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Author: Hoi Sung Chung
Publisher:
ISBN:
Category :
Languages : en
Pages : 231
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Book Description
This thesis presents spectroscopic approaches to study the thermal unfolding dynamics of proteins. The spectroscopic tool is nonlinear infrared (IR) spectroscopy of the protein amide I band. Among various nonlinear IR techniques, two-dimensional infrared (2D IR) spectroscopy, which is an IR analogue of 2D NMR, is the most informative. A 2D IR spectrum is obtained from a double Fourier transform of the heterodyned third-order nonlinear signal, which is generated by three consecutive interactions between femtosecond IR pulses and the vibrations of the system. This technique is sensitive to the presence of P-sheet structure in proteins through the formation of cross peaks between the two characteristic vibrational modes of 0-sheets. In this work, 2D IR spectroscopy is used to measure equilibrium thermal unfolding of ribonuclease A and ubiquitin. For transient unfolding studies, the temperature of the solution is rapidly raised by a nanosecond temperature jump (T-jump) laser, which is followed by probing structural changes of proteins with dispersed vibrational echo (DVE) spectroscopy or 2D IR spectroscopy.
Author: Hoi Sung Chung
Publisher:
ISBN:
Category :
Languages : en
Pages : 231
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Book Description
This thesis presents spectroscopic approaches to study the thermal unfolding dynamics of proteins. The spectroscopic tool is nonlinear infrared (IR) spectroscopy of the protein amide I band. Among various nonlinear IR techniques, two-dimensional infrared (2D IR) spectroscopy, which is an IR analogue of 2D NMR, is the most informative. A 2D IR spectrum is obtained from a double Fourier transform of the heterodyned third-order nonlinear signal, which is generated by three consecutive interactions between femtosecond IR pulses and the vibrations of the system. This technique is sensitive to the presence of P-sheet structure in proteins through the formation of cross peaks between the two characteristic vibrational modes of 0-sheets. In this work, 2D IR spectroscopy is used to measure equilibrium thermal unfolding of ribonuclease A and ubiquitin. For transient unfolding studies, the temperature of the solution is rapidly raised by a nanosecond temperature jump (T-jump) laser, which is followed by probing structural changes of proteins with dispersed vibrational echo (DVE) spectroscopy or 2D IR spectroscopy.
Author: Heinz Fabian
Publisher: Springer Science & Business Media
ISBN: 3642222307
Category : Science
Languages : en
Pages : 257
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Book Description
Infrared spectroscopy is a new and innovative technology to study protein folding/misfolding events in the broad arsenal of techniques conventionally used in this field. The progress in understanding protein folding and misfolding is primarily due to the development of biophysical methods which permit to probe conformational changes with high kinetic and structural resolution. The most commonly used approaches rely on rapid mixing methods to initiate the folding event via a sudden change in solvent conditions. Traditionally, techniques such as fluorescence, circular dichroism or visible absorption are applied to probe the process. In contrast to these techniques, infrared spectroscopy came into play only very recently, and the progress made in this field up to date which now permits to probe folding events over the time scale from picoseconds to minutes has not yet been discussed in a book. The aim of this book is to provide an overview of the developments as seen by some of the main contributors to the field. The chapters are not intended to give exhaustive reviews of the literature but, instead to illustrate examples demonstrating the sort of information, which infrared techniques can provide and how this information can be extracted from the experimental data. By discussing the strengths and limitations of the infrared approaches for the investigation of folding and misfolding mechanisms this book helps the reader to evaluate whether a particular system is appropriate for studies by infrared spectroscopy and which specific advantages the techniques offer to solve specific problems.
![Observing the Unfolding Transition of [beta]-hairpin Peptides with Nonlinear Infrared Spectroscopy PDF](https://books.google.com/books/content/images/frontcover/iFSVPgAACAAJ?fife=w80-h100)
Author: Adam Wilcox Smith
Publisher:
ISBN:
Category :
Languages : en
Pages : 283
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Book Description
The biological function of a protein is in large measure determined by its three-dimensional structure. To date, however, the transition of the protein between the native and non-native conformations is not well-understood. Part of the difficulty is the large conformational space available to a poly-peptide chain, and a general lack of experimental probes that can access local structural information on the time scale of the transition. Single domain peptides are excellent model systems that reduce the size and complexity of the problem, while maintaining the essential physical interactions. In this thesis, P-hairpin peptides are used as model systems for studying P-sheet secondary structure. Hairpin folding has been studied for a number of years, but there is still debate in the literature about the relative importance of the cross-strand hydrogen bonds, tertiary side chain contacts, and p-turn in the folding pathway. In addition, the denatured state is very poorly understood, which complicates any attempt to describe the folding pathway. In this work, amide I vibrational spectroscopy is used to resolve the secondary structure of P-hairpin peptides during thermal denaturation. Spectroscopic modeling is presented to describe the amide I band of 0-hairpins and relate it to structural features. Three spectroscopic methods are used to probe the amide I band: Fourier transform infrared (FTIR) spectroscopy, two-dimensional infrared (2D IR) spectroscopy, and dispersed vibrational echo (DVE) spectroscopy. 2D IR and DVE spectroscopy are 3rd order-nonlinear methods that interrogate the system with a series of ultrafast (100 fs) laser pulses. 2D IR spectra reveal vibrational couplings and measure spectral dynamics on a picosecond time scale.
Author: Ilya Joseph Finkelstein
Publisher:
ISBN:
Category :
Languages : en
Pages : 366
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Book Description
Author: Paul Stevenson (Ph. D.)
Publisher:
ISBN:
Category :
Languages : en
Pages : 307
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Book Description
Proteins are the machinery of the cell, performing functions essential for life. Proteins do not operate in isolation, however. Their function is intimately coupled to their environment; changes in this environment modulate the behavior of the protein. One of the most striking examples of protein-environment coupling is the interaction between membrane proteins and membranes. These interactions govern some of the most fundamental processes in biology, yet the origins of protein-membrane coupling are not well understood. Infrared (IR) spectroscopy offers a route to non-invasively probing these interactions. However, despite sustained interest in the problem over many decades, only limited progress has been made using IR spectroscopy to study protein-membrane interactions. One of the main reasons for this is the density of information encoded into a small frequency range - many hundreds of oscillators may contribute to a signal which spans a
Author: Heinz Fabian
Publisher: Springer
ISBN: 9783642222313
Category : Science
Languages : en
Pages : 244
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Book Description
Infrared spectroscopy is a new and innovative technology to study protein folding/misfolding events in the broad arsenal of techniques conventionally used in this field. The progress in understanding protein folding and misfolding is primarily due to the development of biophysical methods which permit to probe conformational changes with high kinetic and structural resolution. The most commonly used approaches rely on rapid mixing methods to initiate the folding event via a sudden change in solvent conditions. Traditionally, techniques such as fluorescence, circular dichroism or visible absorption are applied to probe the process. In contrast to these techniques, infrared spectroscopy came into play only very recently, and the progress made in this field up to date which now permits to probe folding events over the time scale from picoseconds to minutes has not yet been discussed in a book. The aim of this book is to provide an overview of the developments as seen by some of the main contributors to the field. The chapters are not intended to give exhaustive reviews of the literature but, instead to illustrate examples demonstrating the sort of information, which infrared techniques can provide and how this information can be extracted from the experimental data. By discussing the strengths and limitations of the infrared approaches for the investigation of folding and misfolding mechanisms this book helps the reader to evaluate whether a particular system is appropriate for studies by infrared spectroscopy and which specific advantages the techniques offer to solve specific problems.
Author: Huong Tran Kratochvil
Publisher:
ISBN:
Category :
Languages : en
Pages : 231
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Book Description
Understanding the structure and dynamics of proteins is essential to understanding their roles and functions in these physiological processes. In this thesis, I describe the implementation of an ultrafast nonlinear spectroscopic technique, two-dimensional infrared (2D IR) spectroscopy to probe the structure and dynamics of ion channels and amyloid fibers. Regarding ion channels, I describe the combination of semisynthesis, 2D IR spectroscopy and molecular dynamic (MD) simulations in addressing the longstanding question of ion permeation through the selectivity filter of a potassium ion channel. I show that ions and water alternate through the filter and that these ions cannot occupy adjacent binding sites. Furthermore, 2D IR experiments revealed a flipped state that is predicted by MD simulations but not observed in x-ray crystallography. In another aspect of this work, we show that the collapsed state of the filter is structurally different in low K+ and low pH. Moreover, our work also reveals how the large conformational motions of the protein are coupled to structural changes in the selectivity filter, as evidenced by a change in the ion occupancy. In a second research direction, I developed an optical technique to quantify photoactivatable fluorophores with fluorescence microscopy. This technique allows for the quantification of a limitless number of fluorophores, and corrects for stochastic events such as fluorescence intermittency. This work can be extended to the study of amyloids, where determining the number of proteins in a prefibrillar aggregates is necessary for understanding their roles in amyloid related diseases. Finally, using 2D IR spectroscopy we describe the effect of common solvents on the anharmonicity of small molecule chromophores. The data indicates that the carbonyl anharmonicity, and, subsequently, the Stark tuning rate, is an intrinsic property of the carbonyl vibrational probes, which have important implications on the interpretation of carbonyl vibrational frequency shifts in the condensed phase.
Author:
Publisher:
ISBN:
Category : Dissertations, Academic
Languages : en
Pages : 800
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Book Description
Author: Michael D. Fayer
Publisher: CRC Press
ISBN: 1466510145
Category : Science
Languages : en
Pages : 475
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Book Description
The advent of laser-based sources of ultrafast infrared pulses has extended the study of very fast molecular dynamics to the observation of processes manifested through their effects on the vibrations of molecules. In addition, non-linear infrared spectroscopic techniques make it possible to examine intra- and intermolecular interactions and how su
Author: Takayoshi Kobayashi
Publisher: Springer Science & Business Media
ISBN: 3540272135
Category : Science
Languages : en
Pages : 914
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Book Description
This volume is a collection of papers presented at the Fourteenth International Conference on Ultrafast Phenomena held in Niigata, Japan from July 25-30, 2004. The Ultrafast Phenomena Conferences are held every two years and provide a forum for discussion of the latest results in ultrafast optics and their applications in science and engineering. A total of more than 300 papers were presented, reporting the forefront of research in ultrashort pulse generation and characterization, including new techniques for shortening the duration of laser pulses, for stabilizing their absolute phase, and for improving tenability over broad wavelength ranges, output powers and peak intensities. Ultrafast spectroscopies, particularly time-resolved X-ray and electron diffraction and two-dimensional spectroscopy, continue to give new insights into fundamental processes in physics, chemistry and biology. Control and optimization of the outcome of ultrafast processes represent another important field of research. There are an increasing number of applications of ultrafast methodology in material diagnostics and processing, microscopy and medical imaging. The enthusiasm of the participants, the involvement of many students, the high quality of the papers in both oral and poster sessions made the conference very successful. Many people and organizations made invaluable contributions. The members of the international program committee reviewed the submissions and organized the program. The staff of the Optical Society of America deserves special thanks for making the meeting arrangements and running the meeting smoothly.
