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Author: Publisher: ISBN: Category : Languages : en Pages : 134
Book Description
Terahertz (THz) generation and detection techniques have been developed widely and improved in the last few decades. THz techniques have been applied to many fields, such as medical support (THz imaging for breast cancer and skin cancer), security devices, material studies and astronomy. In our group, we utilize THz time domain spectroscopy (1-67 cm -1, 30 GHz-2 THz, 0.1-8 meV) to study both intramolecular interaction and intermolecular interaction, such as the flexibility changes due to the electron transfer of cytochrome c and ligand binding of lysozyme and tri-N-acetyl-D-glucosamine. My work is focused on the electron transfer of cytochrome c and the hydration and temperature effects on cytochrome c. In the studies of cytochrome c, I investigated the THz dielectric response of cytochrome c as a function of oxidation, hydration and temperature in order to elucidate the underlying structural mechanisms involved in the electron transfer of cytochrome c. The THz dielectric response of cytochrome c dramatically increases with oxidation, implying either a significant global softening of the potential and/or a significant increase in polarizability with oxidation. Hydration dependence measurements show that a difference in the equilibrium water content with oxidation does not explain the change in THz response. The temperature dependence of both ferri- and ferro-cytochrome c THz dielectric response also cannot elucidate this large increase with oxidation. The results of these different THz dielectric measurements of cytochrome c strongly suggest that the flexibility increases as a function of oxidation state. The experimental results were compared to the normal mode calculations. These calculations were performed to determine what impact electron transfer and hydration have on the harmonic response of cytochrome c. The calculated normal mode density from CHARMM shows similar frequency dependence at low frequencies for all hydrations. The hydration dependence of the calculated absorption intensities are in approximate agreement with the measured THz absorbance, except at low hydrations and at low frequencies. The breakdown in agreement may be due to all waters, including crystal waters, being treated with the simplified TIP3 water force field. In the study of ligand binding, a method for rapid determination of protein ligand binding on solution phase samples using terahertz dielectric spectroscopy is demonstrated. Measurements were performed using terahertz time domain spectroscopy on aqueous solutions below the liquid-solid transition for water. Small ligand binding sensitivity was demonstrated using tri-acetylgluosamine and hen egg white lysozyme with a decrease in dielectric response with binding. The magnitude of the change increases with frequency.
Author: Publisher: ISBN: Category : Languages : en Pages : 134
Book Description
Terahertz (THz) generation and detection techniques have been developed widely and improved in the last few decades. THz techniques have been applied to many fields, such as medical support (THz imaging for breast cancer and skin cancer), security devices, material studies and astronomy. In our group, we utilize THz time domain spectroscopy (1-67 cm -1, 30 GHz-2 THz, 0.1-8 meV) to study both intramolecular interaction and intermolecular interaction, such as the flexibility changes due to the electron transfer of cytochrome c and ligand binding of lysozyme and tri-N-acetyl-D-glucosamine. My work is focused on the electron transfer of cytochrome c and the hydration and temperature effects on cytochrome c. In the studies of cytochrome c, I investigated the THz dielectric response of cytochrome c as a function of oxidation, hydration and temperature in order to elucidate the underlying structural mechanisms involved in the electron transfer of cytochrome c. The THz dielectric response of cytochrome c dramatically increases with oxidation, implying either a significant global softening of the potential and/or a significant increase in polarizability with oxidation. Hydration dependence measurements show that a difference in the equilibrium water content with oxidation does not explain the change in THz response. The temperature dependence of both ferri- and ferro-cytochrome c THz dielectric response also cannot elucidate this large increase with oxidation. The results of these different THz dielectric measurements of cytochrome c strongly suggest that the flexibility increases as a function of oxidation state. The experimental results were compared to the normal mode calculations. These calculations were performed to determine what impact electron transfer and hydration have on the harmonic response of cytochrome c. The calculated normal mode density from CHARMM shows similar frequency dependence at low frequencies for all hydrations. The hydration dependence of the calculated absorption intensities are in approximate agreement with the measured THz absorbance, except at low hydrations and at low frequencies. The breakdown in agreement may be due to all waters, including crystal waters, being treated with the simplified TIP3 water force field. In the study of ligand binding, a method for rapid determination of protein ligand binding on solution phase samples using terahertz dielectric spectroscopy is demonstrated. Measurements were performed using terahertz time domain spectroscopy on aqueous solutions below the liquid-solid transition for water. Small ligand binding sensitivity was demonstrated using tri-acetylgluosamine and hen egg white lysozyme with a decrease in dielectric response with binding. The magnitude of the change increases with frequency.
Author: Publisher: ISBN: Category : Languages : en Pages : 206
Book Description
The primary goal of this dissertation was to elucidate and quantify the physical basis of protein flexibility at terahertz (THz) frequencies in two distinct systems: lysozyme and Photoactive Yellow Protein (PYP). To this end, I have probed these systems using the technique of Terahertz Time-Domain Spectroscopy (THz-TDS) in order to determine how the flexibility changes as a function of various conditions, such as changes in hydration, temperature, conformation and ligand binding. Measurements on lysozyme films as a function of ligand binding suggest a decrease in flexibility with binding. A procedure for making uniform protein films was established. Hydration dependent measurements on lysozyme films reveal a transition in the flexibility at the point where the first hydration shell is filled. Analysis of the dielectric response showed that the response cannot be solely attributed to relaxational effects, but one must include at least one resonant contribution. Temperature dependent measurements on lysozyme solutions show that the so-called dynamical transition for proteins is present in the terahertz dielectric response. Arrhenius plots of the imaginary part of the permittivity yield the activation energy for the system and this is shown to be dependent on frequency. Non-linear Arrhenius plots are obtained in some cases, perhaps indicating a different origin for the class of motions responsible for the transition. The final part of this dissertation concerns measurements made on PYP. A hydration transition was observed in the THz dielectric response as a function of hydration in PYP films, similar to that observed in the lysozyme films. This transition coincides with the point where the conformational equilibrium of the protein itself changes, as verified via UV/VIS spectroscopic measurements. These data are discussed in terms of an activated process. The THz response was also studied as a function of conformational state occupation between two photointermediate states. Static measurements indicated loss of flexibility in the photo-excited state. This is consistent with loss of tertiary structure that is also associated with this particular photointermediate. Time-resolved measurements were also performed, though the results from these measurements did not indicate any such change. This apparent contradiction could not be resolved and can be attributed to sample degradation or heating effects.
Author: David M. Leitner Publisher: CRC Press ISBN: 1420087045 Category : Science Languages : en Pages : 450
Book Description
Computational modeling can provide a wealth of insight into how energy flow in proteins mediates protein function. Computational methods can also address fundamental questions related to molecular signaling and energy flow in proteins. Proteins: Energy, Heat and Signal Flow presents state-of-the-art computational strategies for studying energy redi
Author: Paul Agris Publisher: Elsevier ISBN: 0323144128 Category : Science Languages : en Pages : 641
Book Description
Biomolecular Structure and Function covers the proceedings of the 1977 ?Cellular Function and Molecular Structure: Biophysical Approaches to Biological Problems? symposium. It summarizes the application of several biophysical techniques to molecular research in biology. This book starts by describing the use of deuterium-labeled lipids, as monitors of the degree of organization of membrane lipids. It also describes the use of carbon-13-labeled lipids, as indicators of molecular mobility. It explains the lipid-protein interactions involving two integral membrane proteins, mitochondrial cytochrome oxidase and calcium-dependent ATPase of muscle sarcoplasmic reticulum. The book goes on to present NMR studies on the organization and conformation of phospholipids, chloroplast membranes, and erythrocyte membranes. It also presents the ESR study of spectrin-phospholipid associations. It discusses the use of fluorescence probes, electrokinetics, neutron diffraction and ion theory studies of phospholipid-protein association, hormone disease, and senescence effects on prokaryotic and eukaryotic cells. Moreover, this book presents the experiments and phosphorus-31 NMR methodology to simultaneously monitor the intracellular pH and phosphate metabolism in a beating heart, functioning kidney, or an intact living microorganism. This book then describes physical probing of intracellular fluidity and structural changes attending tissue or cell cycles. It also relates relatively narrow lines in the hydrogen-1 NMR spectrum of the extremely viscous complex of the muscle protein troponin and highly polymerized tropomyosin. Structure-function studies of fibrous proteins, such as collagen, actin, and myosin, and active site analysis of enzymes are also presented. Finally, a wide variety of methodologies and technologies is exemplified. This includes proton, carbon, fluorine, phosphorus, and lithium NMR spectroscopy; spin labeling and EPR spectroscopy; chemical studies; light scattering and fluorescence; and electron microscopy.
Author: Valerica Raicu Publisher: OUP Oxford ISBN: 0191510041 Category : Science Languages : en Pages : 451
Book Description
The study of dielectric properties of biological systems and their components is important not only for fundamental scientific knowledge but also for its applications in medicine, biology, and biotechnology. The associated technique - known as dielectric spectroscopy - has enabled researchers to quickly and accurately acquire time- or frequency-spectra of permittivity and conductivity and permitted the derivation and testing of realistic electrical models for cells and organelles. This text covers the theoretical basis and practical aspects of the study of dielectric properties of biological systems, such as water, electrolyte and polyelectrolytes, solutions of biological macromolecules, cells suspensions and cellular systems. The authors' combined efforts provide a comprehensive and cohesive book that takes advantage of the expertise of multiple scientists involved in cutting-edge research in the specific sub-fields of bio-dielectric spectroscopy while maintaining its self-consistency through numerous discussions. The first six chapters cover theoretical, methodological and experimental aspects of relaxation and dispersion in biological dielectrics at molecular, cellular and cellular aggregate level. Applications are presented in the following chapters which are organized in the order of increased complexity, beginning with pure water, amino acids and proteins, continuing with vesicles and simple cells such as erythrocytes, and then with more complex, organelle-containing cells and cellular aggregates. Due to its broad coverage, the text could be used as a reference book by researchers, and as a textbook for upper-level undergraduate classes and graduate classes in (bio) physics, medical physics, quantitative biology, and engineering.
Author: Ruth M. Lynden-Bell Publisher: CRC Press ISBN: 1439803579 Category : Medical Languages : en Pages : 398
Book Description
Reflecting a rich technical and interdisciplinary exchange of ideas, Water and Life: The Unique Properties of H20 focuses on the properties of water and its interaction with life. The book develops a variety of approaches that help to illuminate ways in which to address deeper questions with respect to the nature of the universe and our place withi
Author: Richard R. Sinden Publisher: Elsevier ISBN: 0080571735 Category : Science Languages : en Pages : 423
Book Description
DNA Structure and Function, a timely and comprehensive resource, is intended for any student or scientist interested in DNA structure and its biological implications. The book provides a simple yet comprehensive introduction to nearly all aspects of DNA structure. It also explains current ideas on the biological significance of classic and alternative DNA conformations. Suitable for graduate courses on DNA structure and nucleic acids, the text is also excellent supplemental reading for courses in general biochemistry, molecular biology, and genetics. - Explains basic DNA Structure and function clearly and simply - Contains up-to-date coverage of cruciforms, Z-DNA, triplex DNA, and other DNA conformations - Discusses DNA-protein interactions, chromosomal organization, and biological implications of structure - Highlights key experiments and ideas within boxed sections - Illustrated with 150 diagrams and figures that convey structural and experimental concepts
Author: D Saeedkia Publisher: Elsevier ISBN: 0857096494 Category : Technology & Engineering Languages : en Pages : 684
Book Description
The recent development of easy-to-use sources and detectors of terahertz radiation has enabled growth in applications of terahertz (Thz) imaging and sensing. This vastly adaptable technology offers great potential across a wide range of areas, and the Handbook of terahertz technology for imaging, sensing and communications explores the fundamental principles, important developments and key applications emerging in this exciting field.Part one provides an authoritative introduction to the fundamentals of terahertz technology for imaging, sensing and communications. The generation, detection and emission of waves are discussed alongside fundamental aspects of surface plasmon polaritons, terahertz near-field imaging and sensing, room temperature terahertz detectors and terahertz wireless communications. Part two goes on to discuss recent progress and such novel techniques in terahertz technology as terahertz bio-sensing, array imagers, and resonant field enhancement of terahertz waves. Fiber-coupled time-domain spectroscopy systems (THz-TDS), terahertz photomixer systems, terahertz nanotechnology, frequency metrology and semiconductor material development for terahertz applications are all reviewed. Finally, applications of terahertz technology are explored in part three, including applications in tomographic imaging and material spectroscopy, art conservation, and the aerospace, wood products, semiconductor and pharmaceutical industries.With its distinguished editor and international team of expert contributors, the Handbook of terahertz technology for imaging, sensing and communications is an authoritative guide to the field for laser engineers, manufacturers of sensing devices and imaging equipment, security companies, the military, professionals working in process monitoring, and academics interested in this field. - Examines techniques for the generation and detection of terahertz waves - Discusses material development for terahertz applications - Explores applications in tomographic imaging, art conservation and the pharmaceutical and aerospace industries
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Author: David M. Leitner
Author: Biman Bagchi
Author: Paul Agris
Author: Valerica Raicu
Author: Ruth M. Lynden-Bell
Author: Richard R. Sinden
Author: D Saeedkia