Download or read book Methods in Protein Structure and Stability Analysis Vibrational spectroscopy written by Vladimir N. Uversky and published by Nova Publishers. This book was released on 2007 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein research is a frontier field in science. Proteins are widely distributed in plants and animals and are the principal constituents of the protoplasm of all cells, and consist essentially of combinations of a-amino acids in peptide linkages. Twenty different amino acids are commonly found in proteins, and serve as enzymes, structural elements, hormones, immunoglobulins, etc., and are involved throughout the body, and in photosynthesis. This book gathers new leading-edge research from throughout the world in this exciting and exploding field of research.
Download or read book Vibrational Spectroscopy in Protein Research written by Yukihiro Ozaki and published by Academic Press. This book was released on 2020-05-19 with total page 609 pages. Available in PDF, EPUB and Kindle. Book excerpt: Vibrational Spectroscopy in Protein Research offers a thorough discussion of vibrational spectroscopy in protein research, providing researchers with clear, practical guidance on methods employed, areas of application, and modes of analysis. With chapter contributions from international leaders in the field, the book addresses basic principles of vibrational spectroscopy in protein research, instrumentation and technologies available, sampling methods, quantitative analysis, origin of group frequencies, and qualitative interpretation. In addition to discussing vibrational spectroscopy for the analysis of purified proteins, chapter authors also examine its use in studying complex protein systems, including protein aggregates, fibrous proteins, membrane proteins and protein assemblies. Emphasis throughout the book is placed on applications in human tissue, cell development, and disease analysis, with chapters dedicated to studies of molecular changes that occur during disease progression, as well as identifying changes in tissues and cells in disease studies. - Provides thorough guidance in implementing cutting-edge vibrational spectroscopic methods from international leaders in the field - Emphasizes in vivo, in situ and non-invasive analysis of proteins in biomedical and life science research more broadly - Contains chapters that address vibrational spectroscopy for the study of simple purified proteins and protein aggregates, fibrous proteins, membrane proteins and protein assemblies
Download or read book Vibrational Spectroscopy in Life Science written by Friedrich Siebert and published by John Wiley & Sons. This book was released on 2008-07-15 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: The authors describe basic theoretical concepts of vibrational spectroscopy, address instrumental aspects and experimental procedures, and discuss experimental and theoretical methods for interpreting vibrational spectra. It is shown how vibrational spectroscopy provides information on general aspects of proteins, such as structure, dynamics, and protein folding. In addition, the authors use selected examples to demonstrate the application of Raman and IR spectroscopy to specific biological systems, such as metalloproteins, and photoreceptors. Throughout, references to extensive mathematical and physical aspects, involved biochemical features, and aspects of molecular biology are set in boxes for easier reading. Ideal for undergraduate as well as graduate students of biology, biochemistry, chemistry, and physics looking for a compact introduction to this field.
Download or read book Methods in Protein Structure and Stability Analysis Conformational stability size shape and surface of protein molecules written by Vladimir N. Uversky and published by Nova Publishers. This book was released on 2007 with total page 414 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein research is a frontier field in science. Proteins are widely distributed in plants and animals and are the principal constituents of the protoplasm of all cells, and consist essentially of combinations of a-amino acids in peptide linkages. Twenty different amino acids are commonly found in proteins, and serve as enzymes, structural elements, hormones, immunoglobulins, etc., and are involved throughout the body, and in photosynthesis. This book gathers new leading-edge research from throughout the world in this exciting and exploding field of research.
Download or read book Theoretical Vibrational Spectroscopy of Proteins written by and published by . This book was released on 2012 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Theoretical Vibrational Spectroscopy of Proteins Lu Wang Under the supervision of Professor James L. Skinner At the University of Wisconsin-Madison Vibrational spectroscopy, such as linear and two-dimensional infrared (IR) spectroscopy, is widely utilized to study the structure and dynamics of peptides and proteins. Interpretation of the experiment, or a direct assignment of the complex experimental spectra to the underlying protein structure, can be difficult. Molecular dynamics (MD) simulations offer a complementary approach to provide high-resolution structural and temporal information of proteins, although they are limited by factors such as force field accuracy and are not directly comparable to spectroscopic experiments. We have developed vibrational frequency maps for proteins that generate instantaneous site frequencies directly from MD simulations. We combine the frequency maps with established nearest-neighbor frequency shift and coupling schemes and a mixed quantum/classical framework to form a theoretical strategy for calculating protein linear and 2D IR spectra in the amide I region. This theoretical method provides a means to bridge spectroscopic experiments and molecular simulations, which allows a critical assessment of MD simulations by comparison to experiment, and enables the interpretation of experimental spectra at the molecular level. In this dissertation, we present the development of the vibrational frequency maps and provide the theoretical protocol that allows the calculation of protein vibrational spectra directly from MD simulations. We validate the theoretical method by applying it to peptides with various secondary structures in aqueous solution, and apply it to a few biologically relevant problems. For instance, we have studied the thermal unfolding transition of the villin headpiece subdomain (HP36) using IR spectra calculations. We follow the unfolding process of HP36 by monitoring its spectral changes as a function of temperature. With the help of isotope labeling, we are able to capture the feature that helix 2 of HP36 loses its secondary structure before global unfolding occurs, in agreement with experiment. In collaboration with the Zanni group and the de Pablo group at University of Wisconsin, we have also carried out studies on IAPP, a peptide closely related to type 2 diabetes. By combining theoretical modeling with extensive computer simulations and spectroscopic experiments, we have investigated the structure and dynamics of IAPP in aqueous solution, in the fibril form and in the vicinity of lipid membranes.
Download or read book Vibrational Spectroscopy in Diagnosis and Screening written by Feride Severcan and published by IOS Press. This book was released on 2012 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years there has been a tremendous growth in the use of vibrational spectroscopic methods for diagnosis and screening. These applications range from diagnosis of disease states in humans, such as cancer, to rapid identification and screening of microorganisms. The growth in such types of studies has been possible thanks to advances in instrumentation and associated computational and mathematical tools for data processing and analysis. This volume of Advances in Biomedical Spectroscopy contains chapters from leading experts who discuss the latest advances in the application of Fourier transform infrared (FTIR), Near infrared (NIR), Terahertz and Raman spectroscopy for diagnosis and screening in fields ranging from medicine, dentistry, forensics and aquatic science. Many of the chapters provide information on sample preparation, data acquisition and data interpretation that would be particularly valuable for new users of these techniques including established scientists and graduate students in both academia and industry.
Download or read book Ultrafast Infrared Vibrational Spectroscopy written by Michael D. Fayer and published by CRC Press. This book was released on 2013-03-04 with total page 491 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 such interactions evolve on very fast time scales, but also in some instances on very slow time scales. Ultrafast Infrared Vibrational Spectroscopy is an advanced overview of the field of ultrafast infrared vibrational spectroscopy based on the scientific research of the leading figures in the field. The book discusses experimental and theoretical topics reflecting the latest accomplishments and understanding of ultrafast infrared vibrational spectroscopy. Each chapter provides background, details of methods, and explication of a topic of current research interest. Experimental and theoretical studies cover topics as diverse as the dynamics of water and the dynamics and structure of biological molecules. Methods covered include vibrational echo chemical exchange spectroscopy, IR-Raman spectroscopy, time resolved sum frequency generation, and 2D IR spectroscopy. Edited by a recognized leader in the field and with contributions from top researchers, including experimentalists and theoreticians, this book presents the latest research methods and results. It will serve as an excellent resource for those new to the field, experts in the field, and individuals who want to gain an understanding of particular methods and research topics.
Download or read book Applications of Vibrational Spectroscopy in Food Science 2 Volume Set written by Eunice Li-Chan and published by John Wiley & Sons. This book was released on 2010-11-01 with total page 753 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bringing several disparate aspects of food science and analysis together in one place, Applications of Vibrational Spectroscopy to Food Science provides a comprehensive, state-of the-art text presenting the fundamentals of the methodology, as well as underlying current areas of research in food science analysis. All of the major spectroscopic techniques are also covered – showing how each one can be used beneficially and in a complementary approach for certain applications. Case studies illustrate the many applications in vibrational spectroscopy to the analysis of foodstuffs.
Download or read book Biological and Biomedical Infrared Spectroscopy written by Andreas Barth and published by IOS Press. This book was released on 2009 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although infrared spectroscopy has been applied with success to the study of important biological and biomedical processes for many years, key advances in this vibrant technique have led to its increasing use, ranging from characterization of individual macromolecules (DNA, RNA, lipids, proteins) to human tissues, cells and their components. Infrared spectroscopy thus has a significant role to play in the analysis of the vast number of genes and proteins being identified by the various genomic sequencing projects. Whilst this book gives an overview of the field, it highlights more recent developments, such as the use of bright synchrotron radiation for recording infrared spectra, the development of two-dimensional infrared spectroscopy and the ability to record infrared spectra at ultra fast speeds.
Download or read book Membrane Spectroscopy written by E. Grell and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: The last 10 years have seen an enormous growth in our understanding of the molecular organisation of biological membranes. Experimental methods have been devised to meas ure the translational and rotational mobility of lipids and proteins, thereby furnishing a quantitative basis for the concept of membrane fluidity. Likewise, the asymmetry of bi layer membranes as evidenced by the asymmetric insertion of proteins and lipids has been put on firm experimental ground. At higher molecular resolution it has been possible to provide a detailed pi2ture of the molecular conformation and dynamics of lipids and, to some extent, even of small peptides embedded in a bilayer matrix. Many of these achieve ments would not have been possible without the application of modem spectroscopic methods. Since these techniques are scattered in a variety of specialized textbooks the present monograph attempts to describe the key spectroscopic methods employed in present-day membrane research at an intermediate level. There is no question that the elusive detailed structure of the biological membrane demands a multiplicity of experi mental approaches and that no single spectroscopic method can cover the full range of physical phenomena encountered in a membrane. Much confusion in the literature has arisen by undue generalizations without considering the frequency range or other limi tations of the methods employed. It is to be hoped that the present monograph with its comprehensive description of most modem spectroscopic techniques, will contribute to- .
Download or read book Simulations of Two dimensional Vibrational Spectroscopy of Proteins and Peptides written by Nicholas K. Preketes and published by . This book was released on 2013 with total page 152 pages. Available in PDF, EPUB and Kindle. Book excerpt: Simulations of two-dimensional infrared (2DIR) spectroscopy of several proteins are presented. Applications of 2DIR spectroscopy to protein folding, protein aggregation, and photosensing are reported. We demonstrate that 2DIR spectroscopy is an excellent probe of protein structure and dynamics. Our simulations predict future experiments as well as provide detailed explanations of previous experiments. We also present simulations of the related two-dimensional ultraviolet and two-dimensional stimulated resonance Raman spectroscopies, which are shown to provide complementary information to 2DIR spectroscopy. This thesis can be viewed as a guide for the design and analysis of future two-dimensional optical measurements on proteins.
Download or read book Vibrational Spectroscopy in Diagnosis and Screening written by IOS Press (Firm) and published by IOS Press. This book was released on 2012-06-15 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years there has been a tremendous growth in the use of vibrational spectroscopic methods for diagnosis and screening. These applications range from diagnosis of disease states in humans, such as cancer, to rapid identification and screening of microorganisms. The growth in such types of studies has been possible thanks to advances in instrumentation and associated computational and mathematical tools for data processing and analysis. This volume of Advances in Biomedical Spectroscopy contains chapters from leading experts who discuss the latest advances in the application of Fourier transform infrared (FTIR), Near infrared (NIR), Terahertz and Raman spectroscopy for diagnosis and screening in fields ranging from medicine, dentistry, forensics and aquatic science. Many of the chapters provide information on sample preparation, data acquisition and data interpretation that would be particularly valuable for new users of these techniques including established scientists and graduate students in both academia and industry.
Download or read book Modern Vibrational Spectroscopy and Micro Spectroscopy written by Max Diem and published by John Wiley & Sons. This book was released on 2015-06-30 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern Vibrational Spectroscopy and Micro-Spectroscopy: Theory, Instrumentation and Biomedical Applications unites the theory and background of conventional vibrational spectroscopy with the principles of microspectroscopy. It starts with basic theory as it applies to small molecules and then expands it to include the large biomolecules which are the main topic of the book with an emphasis on practical experiments, results analysis and medical and diagnostic applications. This book is unique in that it addresses both the parent spectroscopy and the microspectroscopic aspects in one volume. Part I covers the basic theory, principles and instrumentation of classical vibrational, infrared and Raman spectroscopy. It is aimed at researchers with a background in chemistry and physics, and is presented at the level suitable for first year graduate students. The latter half of Part I is devoted to more novel subjects in vibrational spectroscopy, such as resonance and non-linear Raman effects, vibrational optical activity, time resolved spectroscopy and computational methods. Thus, Part 1 represents a short course into modern vibrational spectroscopy. Part II is devoted in its entirety to applications of vibrational spectroscopic techniques to biophysical and bio-structural research, and the more recent extension of vibrational spectroscopy to microscopic data acquisition. Vibrational microscopy (or microspectroscopy) has opened entirely new avenues toward applications in the biomedical sciences, and has created new research fields collectively referred to as Spectral Cytopathology (SCP) and Spectral Histopathology (SHP). In order to fully exploit the information contained in the micro-spectral datasets, methods of multivariate analysis need to be employed. These methods, along with representative results of both SCP and SHP are presented and discussed in detail in Part II.
Download or read book Protein NMR Spectroscopy written by Lu-Yun Lian and published by John Wiley & Sons. This book was released on 2011-06-09 with total page 345 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nuclear Magnetic Resonance (NMR) spectroscopy, a physical phenomenon based upon the magnetic properties of certain atomic nuclei, has found a wide range of applications in life sciences over recent decades. This up-to-date volume covers NMR techniques and their application to proteins, with a focus on practical details. Providing newcomers to NMR with practical guidance to carry out successful experiments with proteins and analyze the resulting spectra, those familiar with the chemical applications of NMR will also find it useful in understanding the special requirements of protein NMR.
Download or read book Physical Methods to Characterize Pharmaceutical Proteins written by James N. Herron and published by Springer Science & Business Media. This book was released on 2013-11-21 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are still gaining importance in the pharmaceutical world, where they are used to improve our arsenal of therapeutic drugs and vaccines and as diagnostic tools. Proteins are different from "traditional" low-molecular-weight drugs. As a group, they exhibit a number of biopharmaceutical and formulation problems. These problems have drawn considerable interest from both industrial and aca demic environments, forcing pharmaceutical scientists to explore a domain previ ously examined only by peptide and protein chemists. Biopharmaceutical aspects of proteins, e.g., low oral bioavailability, have been extensively investigated. Although all possible conventional routes of ad ministration have been examined for proteins, no real, generally applicable alter native to parenteral administration in order to achieve systemic effects has yet been discovered. Several of these biopharmaceutical options have been discussed in Volume 4 of this series, Biological Barriers to Protein Delivery. Proteins are composed of many amino acids, several of which are notorious for their chemical instability. Rational design of formulations that optimize the native structure and/or bioactivity of a protein is therefore of great importance when long shelf life is required, as it is for pharmaceutical products. This issue has also been examined in two prior volumes of this series: Volume 2: Stability of Protein Pharmaceuticals (Part A) and Volume 5: Stability and Characterization of Protein and Peptide Drugs.
Download or read book Study of Chemically Modified Food Proteins by Vibrational Spectroscopy written by Hing-Wan Wong and published by . This book was released on 2017-01-27 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation, "Study of Chemically Modified Food Proteins by Vibrational Spectroscopy" by Hing-wan, Wong, 王慶雲, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Abstract of thesis entitled STUDY OF CHEMICALLY MODIFIED FOOD PROTEINS BY VIBRATIONAL SPECTROSCOPY Submitted by Wong Hing Wan for the degree of Doctor of Philosophy at The University of Hong Kong in August 2006 The Raman and Fourier-transform infrared (FTIR) vibrational spectroscopic methods were used to study chemically modified food proteins. Four chemical modification methods: acid deamidation, tryptophan-amidation, sulfitolysis, and trypsin-hydrolysis, and several widely-used food protein products: soy protein isolates (SPI), spray-dried egg white powders (EW), whey protein isolates (WPI), gluten, and casein were selected for study. Raman and FTIR spectra of the chemically modified proteins showed characteristic -1 marker bands. A new Raman C=O stretch vibration band at 1780 cm was observed in deamidated proteins, and was attributed to the γ-carboxyl groups of aspartic and -1 glutamic acids. Similarly, a phenyl stretch vibration at 1552 cm (Raman) was found in - -1 amidated proteins, a -S-SO (thiosulfate) stretch vibration at 1028 cm (in both Raman and FTIR) was found in disulfide bond cleaved samples, and a C=O stretch vibration at -1 -1 1732 cm (Raman) and 1746 cm (FTIR) was observed in trypsin-hydrolyzed proteins. The intensity of these marker bands was found to increase with increases in the level of chemical modification. Calibration curves were constructed by plotting the ratio of the -1 intensity of a particular marker band to the intensity of a Raman 1003 cm -1 phenylalanine stretching band or a FTIR 2116 cm ferricyanide stretching band (used as internal standards) against the extent of modification determined by conventional wet chemistry methods. Linear fits were obtained with correlation coefficients (r) >0.98 and > 0.94 for the Raman and FTIR calibration curves, respectively, indicating strong linear relationships between the marker band intensities and the levels of modification for all the modified protein products. Advantages of the newly developed Raman and FTIR methods over wet chemistry methods are simple and rapid sample preparation, fast determination, and utilization of relatively safe chemicals. Hence, Raman and FTIR spectroscopy have the potential to be further developed for quality control in the food processing industry. The effects of chemical modifications on the conformation and molecular structure of food proteins were studied by vibrational spectroscopy, supplemented by circular dichroism spectroscopy and laser light scattering. Deamidation increased the negative charges in the proteins, resulting in pronounced conformational changes including exposure of hydrophobic residues, increases in disordered conformations and formation of aggregated molecules with compact structures. Amidation also led to increases in disordered structures, possibly due to the attachment of bulky non-polar tryptophan residues. Sulfitolysis breaks up disulfide bonds in proteins, leading to increases in random coil structures and disaggregation of molecules. Hydrolyzed proteins showed marked spectral changes in the amide I and C-H bending vibrations, and progressive increases in random coil structures with concomitant decreases in ordered secondary structure components, suggesting protein denaturation due to cleavage of the peptide bonds. The present study demonstrates the wide application of Raman and FTIR
Download or read book Protein Folding and Misfolding written by Heinz Fabian and published by Springer Science & Business Media. This book was released on 2011-09-18 with total page 257 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
