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Extending Two Dimensional Infrared Spectroscopy To Study Dna Structure With Native And Non Native Infrared Probes
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Book Synopsis Extending Two-dimensional Infrared Spectroscopy to Study DNA Structure with Native and Non-native Infrared Probes by : Amber T. Krummel
Download or read book Extending Two-dimensional Infrared Spectroscopy to Study DNA Structure with Native and Non-native Infrared Probes written by Amber T. Krummel and published by . This book was released on 2007 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Studies of the Structure and Ultrafast Dynamics of DNA Using 2D-IR Spectroscopy by : Gordon Hithell
Download or read book Studies of the Structure and Ultrafast Dynamics of DNA Using 2D-IR Spectroscopy written by Gordon Hithell and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this thesis, two-dimensional infrared spectroscopy (2D-IR) spectroscopy is used to study changes in structure and dynamics in deoxyribonucleic acid (DNA) containing only Adenine-Thymine (AT) base pairs. The aims of the studies in this thesis are to demonstrate the ability of 2D-IR spectroscopy to extract unique dynamic information, not accessible via established experimental methods from nucleic acid systems, as it has for protein- and peptide-based systems. The underlying theory of both linear and nonlinear 2D-IR spectroscopies is described in the initial Chapter, following this the details of the types of information already obtained using these methods from DNA in the current literature is presented.
Book Synopsis Temperature-jump 2D IR Spectroscopy to Study Protein Conformational Dynamics by : Kevin Chapman Jones
Download or read book Temperature-jump 2D IR Spectroscopy to Study Protein Conformational Dynamics written by Kevin Chapman Jones and published by . This book was released on 2012 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: Temperature-jump (T-jump) two-dimensional infrared spectroscopy (2D IR) is developed, characterized, and applied to the study of protein folding and association. In solution, protein conformational changes span a wide range of timescale from nanoseconds to minutes. Ultrafast 2D IR spectroscopy measures time-dependent structural changes within the protein ensemble by probing the frequency changes associated with amide I backbone vibrations. Combining 2D IR with a perturbing laser-induced T-jump enables the study of conformational dynamics from 5 ns to 50 ms. To access a finer time-sampling of the conformational evolution, a one-dimensional variant of 2D IR, heterodyne-detected dispersed vibrational echo spectroscopy (HDVE), is implemented. The framework for interpreting transient HDVE and 2D IR spectra is developed, and we propose a method to remove the linear absorption distortions along both frequency axes. We first present the T-jump 2D IR spectra of a dipeptide to reveal the general amide I baseline response expected in the absence of conformational change. To facilitate the analysis of T-jump data, singular value decomposition (SVD) is employed for reducing noise, identifying the number of distinguishable states, and separating spectral changes based on shared timescales. Finally, T-jump 2D IR spectroscopy is applied to study the unfolding of ubiquitin, disordering of the 12-residue p-hairpin peptide trpzip2 (TZ2), and the dissociation of insulin dimers to monomers. Experimental results for ubiquitin highlight the importance of linear absorption corrections for interpretation of the data. In response to the T-jump, 2D IR results indicate p-sheet structure melts in ubiquitin with a small amplitude (~10 gs) and large amplitude (17 ms) response. Isotope-labeling T-jump experiments on TZ2 allow for the proposal of a free energy surface in which transitions from a native and misfolded state proceed through a disordered hub-like state with a 1-2 gs timescale. Multiple timescales are observed in the T-jump induced dissociation of insulin. Based on their spectral features and concentration dependence, the insulin timescales can be assigned to dissociation, disordering, and oligomerization processes. With these applications, we demonstrate the capability of T-jump 2D IR spectroscopy to reveal detailed molecular dynamics.
Book Synopsis Using Infrared Spectroscopy to Uncover Structure in Biomolecular Assemblies Related to Disease by : David A. Price
Download or read book Using Infrared Spectroscopy to Uncover Structure in Biomolecular Assemblies Related to Disease written by David A. Price and published by . This book was released on 2020 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: The functional and pathogenic roles of biomolecules are often coupled to the self-association of their basic units into oligomers and aggregates whose structural details are difficult to distinguish because of their insoluble and heterogenous nature. This work focuses on DNA G-quadruplex motifs and amyloid peptides whose oligomers and aggregates are associated with numerous biological roles and human diseases. Infrared (IR) spectroscopy is a powerful tool which probes vibrational transitions whose signatures report on their arrangement within molecules. Advances in two-dimensional infrared (2D IR) spectroscopy have allowed structural characterization in increasingly complex biomolecules that are not amenable to traditional high-resolution techniques. However, careful consideration of the physical phenomena that lead to IR spectra are necessary to make accurate assignments. In the first portion of this work, using FTIR and 2D IR, we determine spectral markers that can differentiate size, metal ion coordination, and topology in DNA G-quadruplex motifs. IR studies aided by isotope labeling define the physical origin of these markers and allow for the construction of a structural landscape in parallel DNA G-quadruplex motifs. It is also shown that 2D IR and isotope editing probes site-specific structural changes in G-quadruplex motifs that can differentiate ion identity and location based on spectral shifts. In the latter portion of this work, we use a combination of spectroscopy and imaging techniques to show that a peptide derived from the human pro-apoptotic protein BAX forms amyloid aggregates whose structure is dependent on the presence of model membranes. Combined, the work in this thesis allows for the formulation of multiple hypotheses based on IR structural assignments regarding disease states and functional mechanisms of these systems.
Book Synopsis Encyclopedia of Biophysics by : Gordon Roberts
Download or read book Encyclopedia of Biophysics written by Gordon Roberts and published by Springer. This book was released on 2012-10-08 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Encyclopedia of Biophysics is envisioned both as an easily accessible source of information and as an introductory guide to the scientific literature. It includes entries describing both Techniques and Systems. In the Techniques entries, each of the wide range of methods which fall under the heading of Biophysics are explained in detail, together with the value and the limitations of the information each provides. Techniques covered range from diffraction (X-ray, electron and neutron) through a wide range of spectroscopic methods (X-ray, optical, EPR, NMR) to imaging (from electron microscopy to live cell imaging and MRI), as well as computational and simulation approaches. In the Systems entries, biophysical approaches to specific biological systems or problems – from protein and nucleic acid structure to membranes, ion channels and receptors – are described. These sections, which place emphasis on the integration of the different techniques, therefore provide an inroad into Biophysics from a biological more than from a technique-oriented physical/chemical perspective. Thus the Encyclopedia is intended to provide a resource both for biophysicists interested in methods beyond those used in their immediate sub-discipline and for those readers who are approaching biophysics from either a physical or biological background.
Book Synopsis Ultrafast Two-dimensional Infrared Spectroscopy of Hydrogen-bonded Base Pairs and Hydrated DNA by : Ming Yang
Download or read book Ultrafast Two-dimensional Infrared Spectroscopy of Hydrogen-bonded Base Pairs and Hydrated DNA written by Ming Yang and published by . This book was released on 2012 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Index Medicus written by and published by . This book was released on 2004 with total page 2388 pages. Available in PDF, EPUB and Kindle. Book excerpt: Vols. for 1963- include as pt. 2 of the Jan. issue: Medical subject headings.
Book Synopsis Electron-vibration-vibration Two-dimensional Infrared Spectroscopy as a Structural Probe of Interactions in Proteins and DNA. by : Hugh Richard Sowley
Download or read book Electron-vibration-vibration Two-dimensional Infrared Spectroscopy as a Structural Probe of Interactions in Proteins and DNA. written by Hugh Richard Sowley and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Modern Techniques of Spectroscopy by : Dheeraj Kumar Singh
Download or read book Modern Techniques of Spectroscopy written by Dheeraj Kumar Singh and published by Springer Nature. This book was released on 2021-04-01 with total page 663 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book highlights recent developments in the field of spectroscopy by providing the readers with an updated and high-level of overview. The focus of this book is on the introduction to concepts of modern spectroscopic techniques, recent technological innovations in this field, and current examples of applications to molecules and materials relevant for academia and industry. The book will be beneficial to researchers from various branches of science and technology, and is intended to point them to modern techniques, which might be useful for their specific problems. Spectroscopic techniques, that are discussed include, UV-Visible absorption spectroscopy, XPS, Raman spectroscopy, SERS, TERS, CARS, IR absorption spectroscopy, SFG, LIBS, Quantum cascade laser (QCL) spectroscopy, fluorescence spectroscopy, ellipsometry, cavity-enhanced absorption spectroscopy, such as cavity ring-down spectroscopy (CRDS) and evanescent wave-CRDS both in gas and condensed phases, time-resolved spectroscopy etc. Applications introduced in the different chapters demonstrates the usefulness of the spectroscopic techniques for the characterization of fundamental properties of molecules, e.g. in connection with environmental impact, bio-activity, or usefulness for pharmaceutical drugs, and materials important e.g. for nano-science, nuclear chemistry, or bio-applications. The book presents how spectroscopic techniques can help to better understand substances, which have also great impact on questions of social and economic relevance (environment, alternative energy, etc.).
Book Synopsis Probing Molecular Structure with Two-dimensional Infrared Spectroscopy by : Daniel Ryan DeNeve
Download or read book Probing Molecular Structure with Two-dimensional Infrared Spectroscopy written by Daniel Ryan DeNeve and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Cumulated Index Medicus written by and published by . This book was released on 2000 with total page 1840 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis 2d Infrared Spectroscopy for the Study of Membrane-bound Proteins and Peptides by : Erin Rose Birdsall
Download or read book 2d Infrared Spectroscopy for the Study of Membrane-bound Proteins and Peptides written by Erin Rose Birdsall and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins and peptides associated with cell membranes play a vital role in cell signaling and cell health. From ion channels that allow cells to transduce electrical signals to antibiotic peptides that break open cell membranes, membrane-associated and membrane-bound proteins are of interest due to their importance. However, due to the nature of lipid membranes, the ion channels and other membrane proteins have historically been more challenging to study since they cannot be simply in aqueous solution like soluble proteins. Increased knowledge of protein expression and purification in the last few decades has made membrane-associated and membrane-bound proteins and peptides more readily studied, however, there is still much to learn about the basic function of these macromolecules. For example, one of the most fundamental processes is ion channel conduction. In potassium channels, potassium ions flow at nearly the diffusion limit with exquisite selectivity when the channel is open. The previously established mechanism for ion transduction has been recently called into question. Two-dimensional infrared spectroscopy is an excellent method to study membrane-bound proteins and peptides because of its structural sensitivity, inherent time resolution, and ability to be modeled from structural and computational results. In this dissertation, methods with which to study potassium channels, as well as other membrane-bound peptides are developed, along with strategies to study surfaces, including working with proteins bound in a single lipid bilayer. First, a voltage and pH-sensitive antimicrobial peptide is studied using surface-enhanced 2D IR spectroscopy and an applied voltage. Since the peptide is in a bilayer tethered to a surface, the sample is no longer isotropic and relative intensities of spectral peaks allowed for the extraction of insertion angles upon a change in pH and a change in voltage. Insertion angles were determined through modeling the spectra based on the peptide structure and helical coupling values. Next, progress to studying the selectivity filter of two potassium channels is outlined, including experiment looking at an ester label in the selectivity filter. The ester label causes a water pocket in the ion channel to collapse and changes the binding sites for ions in the selectivity filter. Using waiting time analysis, the dynamics of the labeled residue can be measured. Finally advances to polarization controls to distinguish bulk and surface signals is theoretically developed to create a surface specific spectroscopy. Finally, a chapter is included to disseminate the work presented in this dissertation to the public.
Book Synopsis Developing 2D IR Spectroscopy as a Quantitative Probe for Protein Structure by :
Download or read book Developing 2D IR Spectroscopy as a Quantitative Probe for Protein Structure written by and published by . This book was released on 2012 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Biological Water by : Gertz I. Likhtenshtein
Download or read book Biological Water written by Gertz I. Likhtenshtein and published by Springer Nature. This book was released on 2021-10-21 with total page 523 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book embraces all physiochemical aspects of the structure and molecular dynamics of water, focusing on its role in biological objects, e.g. living cells and tissue, and in the formation of functionally active structures of biological molecules and their ensembles. Water is the single most abundant chemical found in all living things. It offers a detailed look into the latest modern physical methods for studying the molecular structure and dynamics of the water and provides a critical analysis of the existing literature data on the properties of water in biological objects. Water as a chemical reagent and as a medium for the formation of conditions for enzymatic catalysis is a core focus of this book. Although well suited for active researchers, the book as a whole, as well as each chapter on its own, can be used as fundamental reference material for graduate and undergraduate students throughout chemistry, physics, biophysics and biomedicine.
Book Synopsis Dissertation Abstracts International by :
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2009 with total page 810 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Two-dimensional Infrared Spectroscopy for Protein Analysis by :
Download or read book Two-dimensional Infrared Spectroscopy for Protein Analysis written by and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Near-Infrared Spectroscopy by : Yukihiro Ozaki
Download or read book Near-Infrared Spectroscopy written by Yukihiro Ozaki and published by Springer Nature. This book was released on 2020-11-13 with total page 593 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides knowledge of the basic theory, spectral analysis methods, chemometrics, instrumentation, and applications of near-infrared (NIR) spectroscopy—not as a handbook but rather as a sourcebook of NIR spectroscopy. Thus, some emphasis is placed on the description of basic knowledge that is important in learning and using NIR spectroscopy. The book also deals with applications for a variety of research fields that are very useful for a wide range of readers from graduate students to scientists and engineers in both academia and industry. For readers who are novices in NIR spectroscopy, this book provides a good introduction, and for those who already are familiar with the field it affords an excellent means of strengthening their knowledge about NIR spectroscopy and keeping abreast of recent developments.
