Download or read book Solution and Solid state NMR of Membrane bound Proteins and Peptides written by Alessandro Mascioni and published by . This book was released on 2003 with total page 670 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Membrane Protein Structure Determination written by Jean-Jacques Lacapère and published by Methods in Molecular Biology. This book was released on 2010-08-06 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: Membrane proteins, representing nearly 40% of all proteins, are key components of cells involved in many cellular processes, yet only a small number of their structures have been determined. Membrane Protein Structure Determination: Methods and Protocols presents many detailed techniques for membrane protein structure determination used today by bringing together contributions from top experts in the field. Divided into five convenient sections, the book covers various strategies to purify membrane proteins, approaches to get three dimensional crystals and solve the structure by x-ray diffraction, possibilities to gain structural information for a membrane protein using electron microscopy observations, recent advances in nuclear magnetic resonance (NMR), and molecular modelling strategies that can be used either to get membrane protein structures or to move from atomic structure to a dynamic understanding of a molecular functioning mechanism. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and easy to use, Membrane Protein Structure Determination: Methods and Protocols serves as an ideal reference for scientists seeking to further our knowledge of these vital and versatile proteins as well as our overall understanding of the complicated world of cell biology.
Download or read book Modern Techniques in Protein NMR written by N. Rama Krishna and published by Springer Science & Business Media. This book was released on 2006-03-16 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 16 marks the beginning of a special topic series devoted to modern techniques in protein NMR, under the Biological Magnetic Resonance series. This volume is being followed by Volume 17 with the subtitle Structure Computation and Dynamics in Protein NMR. Volumes 16 and 17 present some of the recent, significant advances in biomolecular NMR field with emphasis on developments during the last five years. We are honored to have brought together in these volumes some of the world’s foremost experts who have provided broad leadership in advancing this field. Volume 16 contains advances in two broad categories: the first, Large Proteins, Complexes, and Membrane Proteins, and second, Pulse Methods. Volume 17, which will follow covers major advances in Computational Methods, and Structure and Dynamics. In the opening chapter of Volume 16, Marius Clore and Angela Gronenborn give a brief review of NMR strategies including the use of long range restraints in the structure determination of large proteins and protein complexes. In the next two chapters, Lewis Kay and Ron Venters and their collaborators describe state-of-t- art advances in the study of perdeuterated large proteins. They are followed by Stanley Opella and co-workers who present recent developments in the study of membrane proteins. (A related topic dealing with magnetic field induced residual dipolar couplings in proteins will appear in the section on Structure and Dynamics in Volume 17).
Download or read book Investigations of Membrane Protein Dynamics Using Solid State NMR written by Daryl Good and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins populate ensembles of conformations at ambient temperature. Protein dynamics result from transitions between conformational states and occur over a broad range of time scales. Although dynamics play important roles in protein function, understanding how the proteins' interactions with the surrounding environment, e.g., with solvent, lipids and other proteins, affect the energetics of internal motions is a major challenge. In this Thesis, we focus on the analysis of motions in membrane proteins. They reside in a highly anisotropic environment of a lipid bilayer, and are not easily studied by commonly used techniques, such as x-ray crystallography, electron microscopy, or solution NMR. We use a novel technique of solid-state NMR (SSNMR) spectroscopy to investigate internal motions in two alpha-helical transmembrane microbial rhodopsins. First, we combine multidimensional SSNMR relaxation and order parameter measurements to characterize conformational dynamics of Anabaena Sensory Rhodopsin (ASR), a light sensing protein. We demonstrate that both fast picosecond and slow nanosecond motions occur in ASR; the amplitudes of the slower motions are small in the well-structured TM regions and increase towards the cytoplasmic ends of helices and the interhelical loop regions. Larger amplitudes of nanosecond motions on the cytoplasmic side of the TM helices correlates with the location of the binding sites where ASR is likely to undergo large conformational changes during the binding/unbinding of a soluble transducer. Second, we measure SSNMR bulk relaxation rates over the temperature range from 104 K - 289 K in the light-driven proton pump green proteorhodopsin (GPR). Using model-free analysis, we directly determine the activation energies of the local backbone and sidechain fluctuations as well as of the sidechain rotations and collective backbone and side chain motions. We relate these motions to the dynamics of the solvent and the lipids, thus highlighting the influence of the surrounding environment on membrane protein dynamics. From a structural perspective, ASR and GPR share their alpha-helical bundle architecture with other membrane proteins and in particular, with G-protein coupled receptors. Understanding the nature of motions in ASR and GPR provides a general framework to understanding the factors determining stability and motions in other membrane proteins.
Download or read book Peptide Lipid Interactions written by Sidney A. Simon and published by Academic Press. This book was released on 2002-11-13 with total page 606 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains a comprehensive overview of peptide-lipid interactions by leading researchers. The first part covers theoretical concepts, experimental considerations, and thermodynamics. The second part presents new results obtained through site-directed EPR, electron microscopy, NMR, isothermal calorimetry, and fluorescence quenching. The final part covers problems of biological interest, including signal transduction, membrane transport, fusion, and adhesion. Key Features * world-renowned experts * state-of-the-art experimental methods * monolayers, bilayers, biological membranes * theoretical aspects and computer simulations * rafts * synaptic transmission * membrane fusion * signal transduction
Download or read book Phospholipids Handbook written by Gregor Cevc and published by CRC Press. This book was released on 1993-08-02 with total page 1162 pages. Available in PDF, EPUB and Kindle. Book excerpt: Employing a multidisciplinary approach to phospholipid research, this work catalogues the current knowledge of this class of molecules and details the general, chemical, physical and structural properties of phospholipid monolayers and bilayers. Phospholipid applications are also covered.
Download or read book Membrane active Peptides written by Miguel A. R. B. Castanho and published by Internat'l University Line. This book was released on 2010 with total page 675 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Structure and Dynamics of Membrane Proteins from Solid state NMR written by Myungwoon Lee and published by . This book was released on 2018 with total page 241 pages. Available in PDF, EPUB and Kindle. Book excerpt: Solid-state nuclear magnetic resonance (SSNMR) spectroscopy is an essential tool to elucidate the structure, dynamics, and function of biomolecules. This thesis mainly focuses on the structure determination of the hydrophobic domains for fusion proteins which are involved in membrane fusion between the cell membrane and viral envelope. Although extensive structural studies have been conducted on the soluble ectodomain by crystallography, the structural topologies of the hydrophobic TMD of the fusion proteins have been poorly understood. Here, we introduced SSNMR to investigate the secondary structure and oligomeric states of the TMD of two fusion proteins, PIV5 F and HIV gp41. For the PIV5 TMD, the membrane dependent secondary structure was determined by measuring the chemical shifts: predominant a-helical conformation in the POPC/cholesterol membrane shifts to the [Beta]-strand in the POPE membrane. Using 19F spin diffusion experiments on the fluorinated TMD, we have determined that the TMD forms a trimeric helical bundle. For the HIV gp4l MPER-TMD, we found the presence of a turn between the MPER helix and the TMD helix by measuring intramolecular distances and probing the lipid-peptide and water-peptide interactions. Intermolecular 19F- 19F distances of the fluorinated peptides indicate that the MPER-TMD is a trimeric. In addition to membrane fusion proteins, we have studied the oligomeric structure and the zinc-bound coordination geometry of a de novo designed amyloid fibril that catalyzes ester hydrolysis. By measuring the intermolecular contacts, we determined that peptides form parallel-in- register P-sheets and further assemble into stacked bilayers in an antiparallel orientation. The zinc binding sites were confirmed by the chemical shifts perturbation of histidines with zinc and the specific zinc-bound geometry was identified by measuring intra-residue distances of histidines. We also investigated the effects of cryoprotectants on the spectral resolution of lipid membranes and membrane peptides at low temperature. 13C and 1H MAS spectra of various cryoprotected membranes showed that DMSO provides the best resolution enhancement with the best ice formation retardation at low temperature and DLPE lipid exhibits the excellent resolution.
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 Solid state Nuclear Magnetic Resonance Structural Studies of the HIV 1 Fusion Peptide in the Membrane Environment written by Jun Yang and published by . This book was released on 2003 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Antimicrobial Peptides written by Katsumi Matsuzaki and published by Springer. This book was released on 2019-04-12 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of antimicrobial peptides (AMPs), their mechanisms of antimicrobial action, other activities, and various problems that must still be overcome regarding their clinical application. Divided into four major parts, the book begins with a general overview of AMPs (Part I), and subsequently discusses the various mechanisms of antimicrobial action and methods for researching them (Part 2). It then addresses a range of activities other than antimicrobial action, such as cell penetration, antisepsis, anticancer, and immunomodulatory activities (Part 3), and explores the prospects of clinical application from various standpoints such as the selective toxicity, design, and discovery of AMPs (Part 4). A huge number of AMPs have been discovered in plants, insects, and vertebrates including humans, and constitute host defense systems against invading pathogenic microorganisms. Consequently, many attempts have been made to utilize AMPs as antibiotics. AMPs could help to solve the urgent problem of drug-resistant bacteria, and are also promising with regard to sepsis and cancer therapy. Gathering a wealth of information, this book will be a bible for all those seeking to develop antibiotics, anti-sepsis, or anticancer agents based on AMPs.
Download or read book Introduction to Protein Structure Prediction written by Huzefa Rangwala and published by John Wiley & Sons. This book was released on 2011-03-16 with total page 611 pages. Available in PDF, EPUB and Kindle. Book excerpt: A look at the methods and algorithms used to predict protein structure A thorough knowledge of the function and structure of proteins is critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this reference sheds light on the methods used for protein structure prediction and reveals the key applications of modeled structures. This indispensable book covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. With this resource, readers will find an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction and they will acquire unique insight into the future applications of the modeled protein structures. The book begins with a thorough introduction to the protein structure prediction problem and is divided into four themes: a background on structure prediction, the prediction of structural elements, tertiary structure prediction, and functional insights. Within those four sections, the following topics are covered: Databases and resources that are commonly used for protein structure prediction The structure prediction flagship assessment (CASP) and the protein structure initiative (PSI) Definitions of recurring substructures and the computational approaches used for solving sequence problems Difficulties with contact map prediction and how sophisticated machine learning methods can solve those problems Structure prediction methods that rely on homology modeling, threading, and fragment assembly Hybrid methods that achieve high-resolution protein structures Parts of the protein structure that may be conserved and used to interact with other biomolecules How the loop prediction problem can be used for refinement of the modeled structures The computational model that detects the differences between protein structure and its modeled mutant Whether working in the field of bioinformatics or molecular biology research or taking courses in protein modeling, readers will find the content in this book invaluable.
Download or read book Solid state NMR Studies of Membrane Proteins and Membrane Protein Complexes written by Lindsay J. Sperling and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Membrane proteins help control nearly every process in the cell, which is why approximately 50% of pharmaceuticals currently on the market target membrane proteins. Knowledge of structure-function relationships of these proteins could be leveraged to produce more efficient drugs. However, the traits that make membrane proteins so interesting also make them difficult targets for traditional structure elucidation techniques. X-ray crystallography relies on the use of single crystals, production of which are elusive for membrane proteins due to their inherent dynamic loops and stretches of hydrophobic residues, which contribute to aggregation and/or loss of function without the presence of a lipid environment. Solution NMR experiences difficulty dealing with slow molecular tumbling due to the large sizes of membrane proteins. Conversely, solid-state NMR (SSNMR) has no inherent size limitation and does not require the use of crystals, which presents SSNMR with the unique capability to study membrane proteins in native environments at atomic-resolution. However, this technique is still a relatively new tool for solving structures of biomolecules. Here, we begin to develop strategies for solid-state NMR de novo structure determination. We provide a 0́−divide-and-conquer0́+ investigation of an E. coli 41 kDa membrane protein complex, DsbA/DsbB. We begin by completing chemical shift assignments, the first step in structure determination in NMR studies, of the 21 kDa protein DsbA to optimize sensitivity and resolution of data collection and analysis of large systems. We then use this study to drive forward structural examination of the disulfide bond forming system DsbA/DsbB. Finally, SSNMR techniques are used to study a 144 kDa cytochrome bo3 ubiquinol oxidase demonstrating the power of this technique to investigate large membrane complexes in native environments.
Download or read book Synthesis Enhanced Fusogenicity and Solid State NMR Measurements of Oligomeric HIV 1 Fusion Peptide Constructs written by Rong Yang and published by . This book was released on 2005 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Study of Bacteriorhodopsin in a Controlled Lipid Environment written by Vivien Yeh and published by Springer. This book was released on 2018-10-26 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on the study of how the properties of nanodiscs, such as lipid composition and size, influence the function of the embedding integral membrane protein, bacteriorhodopsin. The author performed systematic studies to show that the lipid composition and the charge of the hydrophobic head and the structure of hydrophilic tails affect the photocycle pathway of bacteriorhodopsin, which is closely associated with its proton-pumping activity. Furthermore, the author demonstrated a highly efficient method for extracting membrane proteins directly from the biological membrane, preserving protein conformation, function and essential native lipids. This book demonstrates optimization and sample preparation, and presents practical methods of preparing membrane protein-embedded nanodisc samples for biophysical studies, which benefit structural and functional studies in the field of membrane protein characterization, both.
Download or read book Structural Biology of Membrane Proteins written by Reinhard Grisshammer and published by Royal Society of Chemistry. This book was released on 2007-10-31 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last few years there have been many exciting and innovative developments in the field of membrane protein structure and this trend is set to continue. Structural Biology of Membrane Proteins is a new monograph covering a wide range of topics with contributions from leading experts in the field. The book is split into three sections: the first discusses topics such as expression, purification and crystallisation; the second covers characterisation techniques and the final section looks at new protein structures. The book will hence have wide appeal to researchers working in and around the field and provide an up-to-date reference source. Introductory sections to each topic are accompanied by more detailed discussions for the more experienced biochemist. Detailed descriptions of experimental methods are included to demonstrate practical approaches to membrane protein structure projects. The book also offers an up-to-date reference source in addition to descriptions of new and emerging developments, including state-of-the-art techniques for solving membrane protein structures. Structural Biology of Membrane Proteins encompasses both basic introductions and detailed descriptions of themes and should appeal to a wide range of biochemical scientists, both experienced and beginner.
