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 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 Structure and Dynamics of Proteins and Peptides Revealed by Two dimensional Infrared Spectroscopy written by Huong Tran Kratochvil and published by . This book was released on 2016 with total page 231 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

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 Dynamics in Peptides and Proteins Using Two Dimensional Infrared Spectroscopy written by Ayanjeet Ghosh and published by . This book was released on 2012 with total page 285 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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 Two Dimensional Optical Spectroscopy written by Minhaeng Cho and published by CRC Press. This book was released on 2009-06-16 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: Two-Dimensional Optical Spectroscopy discusses the principles and applications of newly emerging two-dimensional vibrational and optical spectroscopy techniques. It provides a detailed account of basic theory required for an understanding of two-dimensional vibrational and electronic spectroscopy. It also bridges the gap between the formal developm

Download or read book Protein Dynamics by Two dimensional Infrared Spectroscopy written by Goran Tumbic and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins function as ensembles of interconverting structures. The motions span from picosecond bond rotations to millisecond and longer subunit displacements. Characterization of functional dynamics on all spatial and temporal scales remains challenging experimentally. Two-dimensional IR spectroscopy (2D IR) is maturing as a powerful approach for investigating proteins and their dynamics. This document outlines the advantages of IR spectroscopy, describes 2D IR and the information it provides, and introduces vibrational groups for protein analysis. Following this introduction, example studies are presented that illustrate the power and versatility of 2D IR for characterizing protein dynamics. The thesis concludes with a brief discussion of the outlook for biomolecular 2D IR.

Download or read book Revealing the Structure and Dynamics of Small molecule Solutions and Proteins Using Theoretical Vibrational Spectroscopy written by and published by . This book was released on 2014 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Due to the sensitivity of vibrational chromophores to their local environments, linear and ultrafast vibrational spectroscopy have proven to be very useful techniques for studying the structure and dynamics of condensed phases. Because spectroscopic techniques encode information related to the time-dependent configuration of an entire system into spectra resolved over at most a few dimensions, however, it is very difficult to interpret vibrational line shapes in a detailed and unambiguous manner. One approach to surmounting this difficulty is to calculate vibrational line shapes from molecular dynamics (MD) simulations by employing vibrational response theory and spectroscopic maps. (The maps relate observables in classical MD simulations to quantum spectroscopic quantities.) Once validated by comparison of experimental and theoretical line shapes, MD simulations can be used as an unequivocal basis for the interpretation of vibrational spectra. Here, we employ this approach in order to gain insight into small-molecule solutions and proteins. After sketching the theoretical formalism underlying the calculations of vibrational spectra (Chapter 2), vibrational spectroscopic analysis of the urea/water (Chapter 3) and cyanide/water (Chapter 4) solutions is presented. Analysis of linear infrared (IR) line shapes provides information concerning the local solvation structure of these molecules, while analysis of two-dimensional IR and anisotropy decay yields insight into frequency and rotational dynamics. The remainder of this work concerns the vibrational spectroscopy of the amide I (mostly CO-stretch) band of proteins. After presenting additional theoretical formalism and maps for protein spectroscopy (Chapter 5), the maps are evaluated by examining IR spectra for a single conformation of an alpha-helical model peptide in the gas phase (Chapter 6). These methods are then applied to evaluate the 2D IR spectra of two important biological systems: polyglutamine (Chapter 7) and the potassium ion channel KcsA (Chapter 8). Notably, these studies employ isotope-labeling techniques to isolate the vibrational response of a subset of amide I modes in a non-perturbative fashion. Finally, extensions to the theory are presented to enable the computation of amide I vibrational sum-frequency generation spectra (Chapter 9), which are expected to be sensitive to the structures of interfacial proteins.

Download or read book Recent Progress in Computational Sciences and Engineering 2 vols written by Theodore Simos and published by CRC Press. This book was released on 2019-05-07 with total page 1600 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume brings together selected contributed papers presented at the International Conference of Computational Methods in Science and Engineering (ICCMSE 2006), held in Chania, Greece, October 2006. The conference aims to bring together computational scientists from several disciplines in order to share methods and ideas. The ICCMSE is unique in its kind. It regroups original contributions from all fields of the traditional Sciences, Mathematics, Physics, Chemistry, Biology, Medicine and all branches of Engineering. It would be perhaps more appropriate to define the ICCMSE as a conference on computational science and its applications to science and engineering. Topics of general interest are: Computational Mathematics, Theoretical Physics and Theoretical Chemistry. Computational Engineering and Mechanics, Computational Biology and Medicine, Computational Geosciences and Meteorology, Computational Economics and Finance, Scientific Computation. High Performance Computing, Parallel and Distributed Computing, Visualization, Problem Solving Environments, Numerical Algorithms, Modelling and Simulation of Complex System, Web-based Simulation and Computing, Grid-based Simulation and Computing, Fuzzy Logic, Hybrid Computational Methods, Data Mining, Information Retrieval and Virtual Reality, Reliable Computing, Image Processing, Computational Science and Education etc. More than 800 extended abstracts have been submitted for consideration for presentation in ICCMSE 2005. From these 500 have been selected after international peer review by at least two independent reviewers.

Download or read book Biological and Biomedical Infrared Spectroscopy written by A. Barth and published by IOS Press. This book was released on 2009-09-02 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 characterisation 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 ultrafast speeds. The main focus is on the mid-infrared region, since the great majority of studies are carried out in this region but there is increasing use of the near infrared for biomedical applications and a chapter is devoted to this part of the spectrum. Major advances in theoretical analysis have also enabled better interpretation of the infrared spectra of biological molecules and these are covered. The editors, Professor Andreas Barth of Stockholm University, Stockholm, Sweden and Dr Parvez I. Haris of De Montfort University, Leicester, U.K., who both have extensive research experience in biological infrared spectroscopy per se and in its use in the solution of biophysical problems, have felt it timely therefore to bring together this book. The book is intended for use both by research scientists already active in the use of biological infrared spectroscopy and for those coming new to the technique. Graduate students will also find it useful as an introduction to the technique.

Download or read book Coherent Vibrational Dynamics written by Guglielmo Lanzani and published by CRC Press. This book was released on 2007-11-29 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: Remarkable developments in the spectroscopy field regarding ultrashort pulse generation have led to the possibility of producing light pulses ranging from 50 to5 fs and frequency tunable from the near infrared to the ultraviolet range. Such pulses enable us to follow the coupling of vibrational motion to the electronic transitions in molecules and

Download or read book Concepts and Methods of 2D Infrared Spectroscopy written by Peter Hamm and published by Cambridge University Press. This book was released on 2011-02-24 with total page 297 pages. Available in PDF, EPUB and Kindle. Book excerpt: 2D infrared (IR) spectroscopy is a cutting-edge technique, with applications in subjects as diverse as the energy sciences, biophysics and physical chemistry. This book introduces the essential concepts of 2D IR spectroscopy step-by-step to build an intuitive and in-depth understanding of the method. This unique book introduces the mathematical formalism in a simple manner, examines the design considerations for implementing the methods in the laboratory, and contains working computer code to simulate 2D IR spectra and exercises to illustrate involved concepts. Readers will learn how to accurately interpret 2D IR spectra, design their own spectrometer and invent their own pulse sequences. It is an excellent starting point for graduate students and researchers new to this exciting field. Computer codes and answers to the exercises can be downloaded from the authors' website, available at www.cambridge.org/9781107000056.

Download or read book Self assembling Biomaterials written by Helena S. Azevedo and published by Woodhead Publishing. This book was released on 2018-04-17 with total page 614 pages. Available in PDF, EPUB and Kindle. Book excerpt: Self-assembling biomaterials: molecular design, characterization and application in biology and medicine provides a comprehensive coverage on an emerging area of biomaterials science, spanning from conceptual designs to advanced characterization tools and applications of self-assembling biomaterials, and compiling the recent developments in the field. Molecular self-assembly, the autonomous organization of molecules, is ubiquitous in living organisms and intrinsic to biological structures and function. Not surprisingly, the exciting field of engineering artificial self-assembling biomaterials often finds inspiration in Biology. More important, materials that self-assemble speak the language of life and can be designed to seamlessly integrate with the biological environment, offering unique engineering opportunities in bionanotechnology. The book is divided in five parts, comprising design of molecular building blocks for self-assembly; exclusive features of self-assembling biomaterials; specific methods and techniques to predict, investigate and characterize self-assembly and formed assemblies; different approaches for controlling self-assembly across multiple length scales and the nano/micro/macroscopic properties of biomaterials; diverse range of applications in biomedicine, including drug delivery, theranostics, cell culture and tissue regeneration. Written by researchers working in self-assembling biomaterials, it addresses a specific need within the Biomaterials scientific community. - Explores both theoretical and practical aspects of self-assembly in biomaterials - Includes a dedicated section on characterization techniques, specific for self-assembling biomaterials - Examines the use of dynamic self-assembling biomaterials

Download or read book Unfolded Proteins written by Trevor P. Creamer and published by Nova Publishers. This book was released on 2008 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: The word revolution has a number of definitions (The American Heritage Dictionary, 2006). The one most pertinent to this series and volume is 'a sudden or momentous change in a situation'. Recent years have seen an unprecedented explosion of interest in unfolded proteins in all of their various forms. Coupled with this increase in interest we have seen momentous changes in the way unfolded proteins are viewed. Two particular paradigms have come under close scrutiny: unfolded proteins are disordered random coils devoid of persistent structure, and protein function first requires protein structure. The first of these is currently a hotly debated subject. The second paradigm we can safely claim has been overturned. There is a second definition of revolution that is quite relevant to a significant portion of the work reviewed herein, in particular those chapters dealing with local and persistent structure in unfolded proteins. That definition is 'a turning or rotational motion about an axis' (The American Heritage Dictionary, 2006). About four decades ago, Charles Tanford (1968) demonstrated that highly denatured proteins possess hydrodynamic properties consistent with Paul Flory's random coil (Flory, 1969). Given that the Flory random coil definition included the stipulation that conformers making up the denatured state ensemble would differ in energy by just a few kT, there has been the assumption that denatured states must therefore be completely random in nature with no persistent structure or biases towards particular conformers. Notably however, Tanford did note the random coil-like hydrodynamic data he obtained did not necessarily rule out the presence of structure in denatured proteins (Tanford, 1968). Around the same time, Sam Krimm and M. Lois Tiffany noted that the CD spectra they obtained for proteins in the presence of high concentration of chemical denaturants had similarities to spectra obtained for homopolymers of proline, lysine, and glutamic acid in water (Tiffany and Krimm, 1968a, 1968b, 1973, 1974). Homopolymers of these residues were known to adopt the left-handed polyproline II conformation, leading Tiffany and Krimm to hypothesise that highly denatured proteins possess significant polyproline II helix content. Of these two views, that espousing the lack of structure in denatured proteins became more widely adopted and was, over time, adopted as a central paradigm in protein folding. As several of the chapters in this volume note, a Tiffany and Krimm-like view appears to be, to some extent, the more correct one. The level to which it is correct is still unknown, although it is clear that the polyproline II helical conformation is not the only, perhaps not even the most common, persistent conformation present in unfolded proteins. Thus we have come through a full circle or revolution. (from the preface)

Download or read book Journal written by American Chemical Society and published by . This book was released on 2004 with total page 800 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Trends and Perspectives in Modern Computational Science written by George Maroulis and published by CRC Press. This book was released on 2006-10-27 with total page 606 pages. Available in PDF, EPUB and Kindle. Book excerpt: Contains a collection of the lectures of the invited speakers presented at the International Conference of Computational methods in Science and Engineering (ICCMSE 2006), held in Chania, Greece, October 2006. This book presents developments of Computational Science pertinent to Physics, Chemistry, Biology, Medicine, Mathematics and Engineering.