Download or read book Studies of Structure Hydration and Dynamics of Biological Macromolecules by Use of NMR Spectroscopy written by and published by . This book was released on 2007 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nuclear magnetic resonance (NMR) has emerged as a powerful tool for studying biological macromolecules in aqueous solution. This dissertation describes the efforts to study the structure, hydration and dynamics of biological macromolecules by solution state NMR spectroscopy. There are three projects covered by the dissertation: (i) polypeptide hydration studied by NMR in supercooled water; (ii) structure determination of protein AQ-1857 by NMR spectroscopy and (iii) base flipping mechanism of M. Hha I DNA methyltransferase. Chapter 1 gives brief introduction of NMR applications in biological sciences. Chapter 2 describes the first investigation of polypeptide hydration in supercooled water at temperatures down to -18, which allowed identification of the zero crossing points of intermolecular NOEs between hydration water protons and peptide protons. The experimental results were then fitted to spatial motional models to calculate the translational diffusion coefficients of different hydration water molecules. Chapter 3 presents data collection, spectral analysis and structure calculation of the NESGC target protein AQ-1857, pursued in the context of high-throughput structure determination efforts for structural genomics. Chapter 4, the centerpiece of this dissertation, describes the tremendous efforts in investigating the base flipping mechanism of M. Hha I DNA methyltransferase, including enzymatic synthesis of a partially 13 C, 15 N labeled cognate DNA duplex and the NMR studies on the MTase-DNA complexes. The ample NMR information from chemical shifts, line widths and peak intensities, and imino proton exchange rates provided new insights for understanding the base flipping process.
Download or read book NMR in Structural Biology written by Kurt Wthrich and published by World Scientific. This book was released on 1995 with total page 770 pages. Available in PDF, EPUB and Kindle. Book excerpt: The volume presents a survey of the research by Kurt Wthrich and his associates during the period 1965 to 1994. A selection of reprints of original papers on the use of NMR spectroscopy in structural biology is supplemented with an introduction, which outlines the foundations and the historical development of the use of NMR spectroscopy for the determination of three-dimensional structures of biological macromolecules in solution. The original papers are presented in groups highlighting protein structure determination by NMR, studies of dynamic properties and hydration of biological macromolecules, and practical applications of the NMR methodology in fields such as enzymology, transcriptional regulation, immunosuppression and protein folding.
Download or read book Biological NMR Spectroscopy written by John L. Markley and published by Oxford University Press. This book was released on 1997-01-30 with total page 375 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a critical assessment of progress on the use of nuclear magnetic resonance spectroscopy to determine the structure of proteins, including brief reviews of the history of the field along with coverage of current clinical and in vivo applications. The book, in honor of Oleg Jardetsky, one of the pioneers of the field, is edited by two of the most highly respected investigators using NMR, and features contributions by most of the leading workers in the field. It will be valued as a landmark publication that presents the state-of-the-art perspectives regarding one of today's most important technologies.
Download or read book Dynamics Structure and Function of Biological Macromolecules written by Oleg Jardetzky and published by IOS Press. This book was released on 2001 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: A collection of articles looking at modern structural biology, summarizing the applications of physical methods - such as x-ray diffraction, high resolution nuclear magnetic resonance and molecular dynamics - to the study of protein structure and dynamics. There is a review of contemporary thoughts within the field, looking at the mechanisms of alloateric transitions and allosteric control, the transmission of information within protein structures and the role of dynamics in determining the specificity of protein - ligand interactions. There is also a look at future innovations.
Download or read book Fundamentals of Protein NMR Spectroscopy written by Gordon S. Rule and published by Springer Science & Business Media. This book was released on 2006-02-16 with total page 543 pages. Available in PDF, EPUB and Kindle. Book excerpt: NMR spectroscopy has proven to be a powerful technique to study the structure and dynamics of biological macromolecules. Fundamentals of Protein NMR Spectroscopy is a comprehensive textbook that guides the reader from a basic understanding of the phenomenological properties of magnetic resonance to the application and interpretation of modern multi-dimensional NMR experiments on 15N/13C-labeled proteins. Beginning with elementary quantum mechanics, a set of practical rules is presented and used to describe many commonly employed multi-dimensional, multi-nuclear NMR pulse sequences. A modular analysis of NMR pulse sequence building blocks also provides a basis for understanding and developing novel pulse programs. This text not only covers topics from chemical shift assignment to protein structure refinement, as well as the analysis of protein dynamics and chemical kinetics, but also provides a practical guide to many aspects of modern spectrometer hardware, sample preparation, experimental set-up, and data processing. End of chapter exercises are included to emphasize important concepts. Fundamentals of Protein NMR Spectroscopy not only offer students a systematic, in-depth, understanding of modern NMR spectroscopy and its application to biomolecular systems, but will also be a useful reference for the experienced investigator.
Download or read book Biological NMR written by and published by Academic Press. This book was released on 2019-01-10 with total page 544 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological NMR, Part B, the latest release in the Methods of Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of topics, including Protein methyl labeling, Membrane protein expression – yeast, Protein aromatic labeling, His-tag/Metal contamination, Bicelles, nanodiscs & micelles MP host, PTM – phosphorylation, PTM – lipidation, Screening platform for receptor-ligand discovery, Solution Spectroscopy, Large protein strategies, NUS data collection/analysis, F19 incl. hydration, ODNP - hydration, Reverse micelle - Hydration, Solid State Spectroscopy, SS NMR membrane proteins, SS NMR soluble/aggregate proteins, SS DNP - general, SS NMR nucleic acids, and much more. Authoritative contributors Protocols for state-of-the-art advances Timeliness
Download or read book Dynamics and the Problem of Recognition in Biological Macromolecules written by Oleg Jardetzky and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: From within complex structures of organisms and cells down to the molecular level, biological processes all involve movement. Muscular fibers slide on each other to activate the muscle, as polymerases do along nucleic acids for replicating and transcribing the genetic material. Cells move and organize themselves into organs by recognizing each other through macromolecular surface-specific interactions. These recognition processes involve the mu tual adaptation of structures that rely on their flexibility. All sorts of conformational changes occur in proteins involved in through-membrane signal transmission, showing another aspect of the flexibility of these macromolecules. The movement and flexibility are inscribed in the polymeric nature of essential biological macromolecules such as proteins and nucleic acids. For instance, the well-defined structures formed by the long protein chain are held together by weak noncovalent interac tions that design a complex potential well in which the protein floats, permanently fluctuating between several micro- or macroconformations in a wide range of frequencies and ampli tudes. The inherent mobility of biomolecular edifices may be crucial to the adaptation of their structures to particular functions. Progress in methods for investigating macromolecular structures and dynamics make this hypothesis not only attractive but more and more testable.
Download or read book Structure Computation and Dynamics in Protein NMR written by N. Rama Krishna and published by Springer Science & Business Media. This book was released on 2006-05-09 with total page 565 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 17 is the second in a special topic series devoted to modern techniques in protein NMR, under the Biological Magnetic Resonance series. Volume 16, with the subtitle Modern Techniques in Protein NMR , is the first in this series. These two volumes present some of the recent, significant advances in the biomolecular NMR field with emphasis on developments during the last five years. We are honored to have brought together in these volume some of the world s foremost experts who have provided broad leadership in advancing this field. Volume 16 contains - vances in two broad categories: I. Large Proteins, Complexes, and Membrane Proteins and II. Pulse Methods. Volume 17 contains major advances in: I. Com- tational Methods and II. Structure and Dynamics. The opening chapter of volume 17 starts with a consideration of some important aspects of modeling from spectroscopic and diffraction data by Wilfred van Gunsteren and his colleagues. The next two chapters deal with combined automated assignments and protein structure determination, an area of intense research in many laboratories since the traditional manual methods are often inadequate or laborious in handling large volumes of NMR data on large proteins. First, Werner Braun and his associates describe their experience with the NOAH/DIAMOD protocol developed in their laboratory.
Download or read book NMR of Large 25 KDa Proteins and Protein Complexes written by Gerhard Wider and published by . This book was released on 1998 with total page 93 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Nuclear magnetic Resonance in biochemistry written by Thomas James and published by Elsevier. This book was released on 2012-12-02 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nuclear Magnetic Resonance in Biochemistry: Principles and Applications focuses on the principles and applications of nuclear magnetic resonance (NMR) in biochemistry. Topics covered include experimental methods in NMR; the mechanisms of NMR relaxation; chemical and paramagnetic shifts; spin-spin splitting; the use of NMR in investigations of biopolymers and biomolecular interactions; and molecular dynamics in biological and biochemical systems. This text is comprised of eight chapters; the first of which gives an overview of NMR spectroscopy and its use in studies of biological systems. The next two chapters discuss the theoretical basis for NMR applications in biochemistry, with emphasis on Bloch equations, quantum mechanics, correlation function and correlation time, double resonance, and chemical exchange. The reader is then introduced to the basis for chemical shifts and spin-spin splitting, along with several examples of the use of these NMR parameters in studies of small molecule interactions and structure. The experimental apparatus and procedures employed in NMR studies, Fourier transform NMR, and NMR spectral parameters of small molecules interacting with macromolecules are also considered. The book highlights the information obtainable from the spectra of biopolymers, and then concludes with a chapter on NMR investigations of the state of motion of lipids in membranes and model membranes; water in macromolecular and cellular systems; and sodium ion in biological tissue. This book is intended primarily for chemists, biochemists, biophysicists, and molecular biologists, as well as graduate students.
Download or read book Water and Biological Macromolecules written by Westhof and published by CRC Press. This book was released on 1993-08-16 with total page 492 pages. Available in PDF, EPUB and Kindle. Book excerpt: Water and Biological Macromolecules presents an excellent description of the structural aspects of water molecules around biological macromolecules. Topics discussed include the properties of water in solid and liquid states; proteins, nucleic acids, polysaccharides, and lipids; and theoretical approaches for understanding the macroscopic observations and integrating microscopic descriptions. The nature and roles of hydration forces in macromolecular complexation and cell-cell interactions are explained, in addition to phenomena such as entropy-enthalpy compensation and the thermodynamic treatment of water bridging. Water and Biological Macromolecules will be a valuable reference for biophysicists, biochemists, and macromolecular biologists.
Download or read book Protein NMR written by Lawrence Berliner and published by Springer. This book was released on 2015-08-24 with total page 193 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers new techniques in protein NMR, from basic principles to state-of-the-art research. It covers a spectrum of topics ranging from a “toolbox” for how sequence-specific resonance assignments can be obtained using a suite of 2D and 3D NMR experiments and tips on how overlap problems can be overcome. Further topics include the novel applications of Overhauser dynamic nuclear polarization methods (DNP), assessing protein structure, and aspects of solid-state NMR of macroscopically aligned membrane proteins. This book is an ideal resource for students and researchers in the fields of biochemistry, chemistry, and pharmacology and NMR physics. Comprehensive and intuitively structured, this book examines protein NMR and new novel applications that include the latest technological advances. This book also has the features of: • A selection of various applications and cutting-edge advances, such as novel applications of Overhauser dynamic nuclear polarization methods (DNP) and a suite of 2D and 3D NMR experiments and tips on how overlap problems can be overcome • A pedagogical approach to the methodology • Engaging the reader and student with a clear, yet critical presentation of the applications
Download or read book Conformation of Biological Molecules written by G. Govil and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: The determination of the three-dimensional structure of a biological molecule is the starting point in the understanding of molecular mechanisms involved in its complex biochemical reactions. The molecular architecture of multimolecular systems such as membranes and chromosomes provides the key to the fascinating field of molecular biology. Stereochemical details of biological macromolecules and their interactions with pharmacological agents form the basis for drug design. Naturally, the study of the structure and function of biological molecules has aroused tremendous interest and investigations in this area are being carried out in a large number of laboratories. The techniques used for this purpose include both experimental methods (X-ray and neutron diffraction measurements, study of NMR, ESR, vibrational and electronic spectra, ORD, CD and dipole moment measurements, biochemical modifications etc. ) and the oretical methods (quantum mechanical and classical potential energy calculations, Monte Carlo simulations and molecular graphics). F or several years now, X-ray diffraction [1] has served as our only source of infor mation on the three-dimensional arrangements of atoms in biopolymers. Fiber-diffrac tion of DNA led to the proposal of the DNA double helix. Fibers of long~hain polymers show ordering in the direction of the fibre-axis but not in the transverse plane. Accurate estimates of the dimensions of helical structures can be made using techniques on the basis of which models of biopolymers can be constructed.
Download or read book Fifth International Conference on the Spectroscopy of Biological Molecules written by T. Theophanides and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt: The series of Conferences on the Spectroscopy of Biological Molecules aims to stimulate research and development in this area of Science. The relationship between the structure and the biological activity of such materials as proteins, lipids, and nucleic acids is fundamental. The 5th European Conference on the Spectroscopy of Biological Molecules (ECSBM) is held at the Hotel Poseidon Club, Loutraki, Greece, on 5-10 September 1993. The scientific contents are remained the same as in the past conferences. Emphasis is given to vibrational spectroscopy, mainly infrared and Raman applied to the study of structure and dynamics of proteins, nucleic acids, porphyrins, carbohydrates, membranes, etc. Most of the contributions describe molecular dynamics and excitation processes, in particular the electronic-vibrational excitations, which are studied by Fr-Raman, Fourier Transform Infrared (Fr-IR) coupled often with microscopy and chromatography. Contributions also include Fr-Raman and FT-IR instrumentation and new developments in this area, and applications in Biology and Medicine. Furthermore, there is a plenary lecture in Mass Spectrometry and its applications in biomedical analysis, and a session devoted to Nuclear Magnetic Resonance (NMR) and its application in the study of biological molecules. Several contributions are devoted to other methods, such as CD, optical absorption, fluorescence and molecular graphics simulations. This volume of ECSBM contains shon articles by the invited and contributed lectures as well as from the Poster presentations from many European and non-European countries.
Download or read book NMR of Proteins and Small Biomolecules written by Guang Zhu and published by Springer Science & Business Media. This book was released on 2012-03-28 with total page 255 pages. Available in PDF, EPUB and Kindle. Book excerpt: Application of NMR and Molecular Docking in Structure-Based Drug Discovery, by Jaime L. Stark and Robert Powers NMR as a Unique Tool in Assessment and Complex Determination of Weak Protein-Protein Interactions, by Olga Vinogradova and Jun Qin The Use of Residual Dipolar Coupling in Studying Proteins by NMR, by Kang Chen und Nico Tjandra NMR Studies of Metalloproteins, by Hongyan Li and Hongzhe Sun Recent Developments in 15N NMR Relaxation Studies that Probe Protein Backbone Dynamics, by Rieko Ishima Contemporary Methods in Structure Determination of Membrane Proteins by Solution NMR, by Tabussom Qureshi and Natalie K. Goto Protein Structure Determination by Solid-State NMR, by Xin Zhao Dynamic Nuclear Polarization: New Methodology and Applications, by Kong Hung Sze, Qinglin Wu, Ho Sum Tse and Guang Zhu
Download or read book NMR Applications in Biopolymers written by John W. Finley and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 512 pages. Available in PDF, EPUB and Kindle. Book excerpt: Elucidating the structures of biopolymers as they exist in nature has long been a goal of biochemists and biologists. Understanding how these substances interact with themselves, other solutes, and solvents can provide useful insights into many areas of biochemistry, agriculture, food science and medicine. Knowledge of the structure of a protein or complex carbohydrate in its native form provides guidelines for the chemical or genetic modifications often desired to optimize these compounds to specific needs and applications. For example, in the pharmaceutical industry, structure-function relationships involving biopolymers are studied rou tinely as a means to design new drugs and improve their efficacies. The tools to conduct structure investigations of biopolymers at the molecular level are limited in number. Historically X-ray crystallography has been the most attractive method to conduct studies of this type. How ever, X-ray methods can only be applied to highly ordered, crystalline materials, thus obviating studies of solution dynamics that are often critical to attaining a global understanding of biopolymer behavior. In recent years, nuclear magnetic resonance (NMR) spectroscopy has evolved to become a powerful tool to probe the structures of biopolymers in solution and in the solid state. NMR provides a means to study the dynamics of polymers in solution, and to examine the effects of solute, solvent and' other factors~n polymer behavior. With the development of 2D and 3D forms of NMR spectroscopy, it is now possible to assess the solution conforma tions of small proteins, oligonucleotides and oligosaccharides.
Download or read book Structure and Dynamics of Biological Macromolecules Using NMR Spectroscopy written by Ye Tian and published by . This book was released on 2010 with total page 147 pages. Available in PDF, EPUB and Kindle. Book excerpt: Another practice of NMR in my work is using 31 P Dynamic NMR to characterize the backbone conformation and dynamics in DNA Dickerson Dodecamer. The results confirm solid-state 2 H-NMR experiments showing that the C3pG4 and C9pG10 steps experience unique dynamics. And cytosine methylation has significant impact on the local dynamics. The results also show that 31 P Dynamic NMR is an efficient way to extract DNA backbone dynamic information, and provide detail knowledge to study DNA-protein interactions.
