Structure and Dynamics of the Membrane Protein Bacteriorodopsin Studies by Mass Spectrometry

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ISBN 13 :
Total Pages : 400 pages
Book Rating : 4.:/5 (16 download)

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Book Synopsis Structure and Dynamics of the Membrane Protein Bacteriorodopsin Studies by Mass Spectrometry by : Yan Pan

Download or read book Structure and Dynamics of the Membrane Protein Bacteriorodopsin Studies by Mass Spectrometry written by Yan Pan and published by . This book was released on 2011 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: Membrane proteins continue to represent a major challenge for most analytical techniques. Using bacteriorhodopsin (BR) as model system, this work aims to develop mass spectrometry (MS)-based approaches for exploring the structure, dynamics and folding of membrane proteins. As the first step, BR in its native lipid environment was exposed to hydroxyl radicals, which were produced by laser photolysis of hydrogen peroxide. It was found that the resulting methionine (Met) labeling pattern was consistent with the known BR structure. This finding demonstrates that laser-induced oxidative Met labeling can provide structural information on membrane proteins. In subsequent experiments, the effects of different denaturing agents (heat, acid, and SDS) on the BR conformation were investigated. It was demonstrated that each of these non-native conditions results in unique structural features that give rise to characteristic Met labeling patterns. These results highlight the ability of laser-induced oxidative labeling to detect conformational changes of membrane proteins. Obtaining better insights into the structural properties of SDS-denatured BR is particularly important because this form of protein is widely used as starting point for folding studies. Combining oxidative labeling with site-directed mutagenesis and fluorescence measurements, this work yielded a detailed structural model of SDS-denatured BR. Subsequently, pulsed oxidative labeling coupled with rapid mixing and MS was used to characterize short-lived intermediates that become populated during BR refolding. The combination of pulsed oxidative labeling and stopped-flow spectroscopy provided key structural insights into the kinetic mechanism by which the SDS-denatured protein inserts and folds into the lipid bilayer. Complementary to oxidative labeling, hydrogen/deuterium exchange (HDX) MS was employed to examine the structure and dynamics of BR under various physiochemical conditions. Structural features of different detergent/lipid-bound BR samples were characterized by their HDX kinetics. Comparative HDX experiments of BR were carried out in the dark (resting state) and under illumination where the induced retinal isomerization mediates proton transport (functioning state). Isotope exchange was found to be much faster during light exposure than in the dark. This observation reveals that structural dynamics of the protein scaffold are "accelerated" by motions of the retinal reflecting a direct coupling between protein dynamics and function.

Membrane Proteins in Aqueous Solutions

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Publisher : Springer
ISBN 13 : 3319731483
Total Pages : 724 pages
Book Rating : 4.3/5 (197 download)

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Book Synopsis Membrane Proteins in Aqueous Solutions by : Jean-Luc Popot

Download or read book Membrane Proteins in Aqueous Solutions written by Jean-Luc Popot and published by Springer. This book was released on 2018-06-08 with total page 724 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the first to be entirely devoted to the challenging art of handling membrane proteins out of their natural environment, a key process in biological and pharmaceutical research, but one plagued with difficulties and pitfalls. Written by one of the foremost experts in the field, Membrane Proteins in Aqueous Solutions is accessible to any member of a membrane biology laboratory. After presenting the structure, functions, dynamics, synthesis, natural environment and lipid interactions of membrane proteins, the author discusses the principles of extracting them with detergents, the mechanisms of detergent-induced destabilization, countermeasures, and recent progress in developing detergents with weaker denaturing properties. Non-conventional alternatives to detergents, including bicelles, nanodiscs, amphipathic peptides, fluorinated surfactants and amphipols, are described, and their relative advantages and drawbacks are compared. The synthesis and solution properties of the various types of amphipols are presented, as well as the formation and properties of membrane protein/amphipol complexes and the transfer of amphipol-trapped proteins to detergents, nanodiscs, lipidic mesophases, or living cells. The final chapters of the book deal with applications: membrane protein in vitro folding and cell-free expression, solution studies, NMR, crystallography, electron microscopy, mass spectrometry, amphipol-mediated immobilization of membrane proteins, and biomedical applications. Important features of the book include introductory sections describing foundations as well as the state-of-the-art for each of the biophysical techniques discussed, and topical tables which organize a widely dispersed literature. Boxes and annexes throughout the book explain technical aspects, and twelve detailed experimental protocols, ranging from in vitro folding of membrane proteins to single-particle electron cryomicroscopy, have been contributed by and commented on by experienced users. Membrane Proteins in Aqueous Solutions offers a concise, accessible introduction to membrane protein biochemistry and biophysics, as well as comprehensive coverage of the properties and uses of conventional and non-conventional surfactants. It will be useful both in basic and applied research laboratories and as a teaching aid for students, instructors, researchers, and professionals within the field.

Membrane Biophysics

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Publisher : Springer
ISBN 13 : 9811068232
Total Pages : 425 pages
Book Rating : 4.8/5 (11 download)

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Book Synopsis Membrane Biophysics by : Hongda Wang

Download or read book Membrane Biophysics written by Hongda Wang and published by Springer. This book was released on 2017-11-21 with total page 425 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book highlights recent advances in and diverse techniques for exploring the plasma membrane’s structure and function. It starts with two chapters reviewing the history of membrane research and listing recent advances regarding membrane structure, such as the semi-mosaic model for red blood cell membranes and the protein layer-lipid-protein island model for nucleated tissue cell membranes. It subsequently focuses on the localization and interactions of membrane components, dynamic processes of membrane transport and transmembrane signal transduction. Classic and cutting-edge techniques (e.g. high-resolution atomic force microscopy and super-resolution fluorescence microscopy) used in biophysics and chemistry are presented in a very comprehensive manner, making them useful and accessible to both researchers in the field and novices studying cell membranes. This book provides readers a deeper understanding of the plasma membrane’s organization at the single molecule level and opens a new way to reveal the relationship between the membrane’s structure and functions, making it essential reading for researchers in various fields.

Biophysical Analysis of Membrane Proteins

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Publisher : John Wiley & Sons
ISBN 13 : 3527621237
Total Pages : 368 pages
Book Rating : 4.5/5 (276 download)

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Book Synopsis Biophysical Analysis of Membrane Proteins by : Eva Pebay-Peyroula

Download or read book Biophysical Analysis of Membrane Proteins written by Eva Pebay-Peyroula and published by John Wiley & Sons. This book was released on 2008-06-25 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: Meeting the need for a book on developing and using new methods to investigate membrane proteins, this is the first of its kind to present the full range of novel techniques in one resource. Top researchers from around the world focus on the physical principles exploited in the different techniques, and provide examples of how these can bring about important new insights. Following an introduction, further sections discuss structural approaches, molecular interaction and large assemblies, dynamics and spectroscopies, finishing off with an exploration of structure-function relationships in whole cells.

Study of Bacteriorhodopsin in a Controlled Lipid Environment

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Publisher : Springer
ISBN 13 : 9811312389
Total Pages : 151 pages
Book Rating : 4.8/5 (113 download)

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Book Synopsis Study of Bacteriorhodopsin in a Controlled Lipid Environment by : Vivien Yeh

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 151 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.

Advances in Protein Molecular and Structural Biology Methods

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Publisher : Academic Press
ISBN 13 : 0323902650
Total Pages : 716 pages
Book Rating : 4.3/5 (239 download)

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Book Synopsis Advances in Protein Molecular and Structural Biology Methods by : Timir Tripathi

Download or read book Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. - Presents a thorough overview of the latest and emerging methods and technologies for protein study - Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy - Includes computational and machine learning methods - Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins

Characterization of Integral Membrane Proteins Using Mass Spectrometry

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Publisher :
ISBN 13 :
Total Pages : 520 pages
Book Rating : 4.:/5 (467 download)

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Book Synopsis Characterization of Integral Membrane Proteins Using Mass Spectrometry by : David Robert Barnidge

Download or read book Characterization of Integral Membrane Proteins Using Mass Spectrometry written by David Robert Barnidge and published by . This book was released on 1998 with total page 520 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Membrane Protein Structure and Dynamics

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Publisher : Humana Press
ISBN 13 : 9781627030243
Total Pages : 357 pages
Book Rating : 4.0/5 (32 download)

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Book Synopsis Membrane Protein Structure and Dynamics by : Nagarajan Vaidehi

Download or read book Membrane Protein Structure and Dynamics written by Nagarajan Vaidehi and published by Humana Press. This book was released on 2012-09-14 with total page 357 pages. Available in PDF, EPUB and Kindle. Book excerpt: Membrane proteins play key roles in numerous cellular processes, in particular mediating cell-to-cell communication and signaling events that lead to a multitude of biological effects. Membrane proteins have also been implicated in many critical diseases such as atherosclerosis, hypertension, diabetes and cancer. In Membrane Protein Structure Predictions Methods: Methods and Protocols, expert researcher in the field detail the advances in both experimental and computational approaches of the structure, dynamics and interactions of membrane proteins dividing the volume into two sections. The first section details the procedures used for measurements of structure and dynamics of membrane proteins. While the second section contains a survey of the computational methods that have played a critical role in membrane protein structure prediction as well as in providing atomic level insight into the mechanism of the dynamics of membrane receptors. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Membrane Protein Structure Predicitons: Methods and Protocols seeks to aid scientists in the further study of membrane protein structure and function.

Probing the Dynamics of Antibodies and Membrane Proteins by Structural Mass Spectrometry

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ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (131 download)

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Book Synopsis Probing the Dynamics of Antibodies and Membrane Proteins by Structural Mass Spectrometry by : Kjetil Hansen

Download or read book Probing the Dynamics of Antibodies and Membrane Proteins by Structural Mass Spectrometry written by Kjetil Hansen and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Protein Structure Analysis

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Publisher : Springer Science & Business Media
ISBN 13 : 9783540615002
Total Pages : 340 pages
Book Rating : 4.6/5 (15 download)

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Book Synopsis Protein Structure Analysis by : Roza Maria Kamp

Download or read book Protein Structure Analysis written by Roza Maria Kamp and published by Springer Science & Business Media. This book was released on 1997 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Protein Structure Analysis - Preparation and Characterization" is a compilation of practical approaches to the structural analysis of proteins and peptides. Here, about 20 authors describe and comment on techniques for sensitive protein purification and analysis. These methods are used worldwide in biochemical and biotechnical research currently being carried out in pharmaceu tical and biomedical laboratories or protein sequencing facilities. The chapters have been written by scientists with extensive ex perience in these fields, and the practical parts are well documen ted so that the reader should be able to easily reproduce the described techniques. The methods compiled in this book were demonstrated in student courses and in the EMBO Practical Course on "Microsequence Analysis of Proteins" held in Berlin September 10-15, 1995. The topics also derived from a FEBS Workshop, held in Halkidiki, Thessaloniki, Greece, in April, 1995. Most of the authors participated in these courses as lecturers and tutors and made these courses extremely lively and successful. Since polypeptides greatly vary depending on their specific structure and function, strategies for their structural analysis must for the most part be adapted to each individual protein. Therefore, advantages and limitations of the experimen tal approaches are discussed here critically, so that the reader becomes familiar with problems that might be encountered.

Membrane Protein Structure

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Publisher : Springer
ISBN 13 : 1461475155
Total Pages : 403 pages
Book Rating : 4.4/5 (614 download)

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Book Synopsis Membrane Protein Structure by : Stephen H White

Download or read book Membrane Protein Structure written by Stephen H White and published by Springer. This book was released on 2013-05-27 with total page 403 pages. Available in PDF, EPUB and Kindle. Book excerpt: Studies of receptors, ion channels, and other membrane proteins require a solid understanding of the structural principles of these important biomolecules. Membrane protein structure is, however, a very challenging field. The structures of only three types of transmembrane proteins have been determined to moderate or high resolution during the last two decades, a period during which the amino acid sequences of hundreds, if not thousands, of membrane proteins have been reported. As a result, the creation of structural models to serve as guides for studies of receptors, channels, and other membrane proteins has become crucially important. This book has been assembled in order to share the experiences and findings of expert researchers in protein structure and structure-prediction methods as well as membrane biophysics and lipid physical chemistry, whose work establishes the basis for the development of suitable model structures. The reviews presented here emphasize fundamental ideas and provide an entry to the diverse and complex literature. The four major sections deal with the general nature of the membrane protein structure problem, biochemical and molecular biological approaches to protein topology, direct structural methods, and model and physicochemical approaches. The work will be of interest to physiologists, cellular and molecular biologists, biophysicists, and biochemists working on the function of membrane proteins such as receptors, ion channels, and transporters, as well as senior graduate students and independent investigators.

The Biochemistry of Archaea (Archaebacteria)

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Publisher : Elsevier
ISBN 13 : 0080860869
Total Pages : 633 pages
Book Rating : 4.0/5 (88 download)

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Book Synopsis The Biochemistry of Archaea (Archaebacteria) by : M. Kates

Download or read book The Biochemistry of Archaea (Archaebacteria) written by M. Kates and published by Elsevier. This book was released on 1993-12-13 with total page 633 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last 10 years, considerable information has accumulated on the biochemistry of archaea. In this volume, the subject as a whole is treated in a comprehensive manner. The book brings together recent knowledge concerning general metabolism, bioenergetics, molecular biology and genetics, membrane lipid and cell-wall structural chemistry and evolutionary relations, of the three major groups of archaea: the extreme halophiles, the extreme thermophiles, and the methanogens.Subjects included are: the evolutionary relationship of these microorganisms to all other living cells; special metabolic features of archeaea; protein structural chemistry; cell envelopes; molecular biology in archaea including DNA structure and replication, transcription apparatus, translation apparatus, and ribosomal structure; and a final chapter on the molecular genetics of archaea. This comprehensive scope ensures its usefulness to researchers, and stimulates further study in this rapidly developing field.

Characterization of Membrane Protein Primary Structure and Protein Covalent Modification by MALDI-TOF-MS

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ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (93 download)

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Book Synopsis Characterization of Membrane Protein Primary Structure and Protein Covalent Modification by MALDI-TOF-MS by : Jian Huang

Download or read book Characterization of Membrane Protein Primary Structure and Protein Covalent Modification by MALDI-TOF-MS written by Jian Huang and published by . This book was released on 2005 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The subjects of this thesis were to illustrate membrane protein primary structure determination, protein covalent modification and protein-protein interaction by using matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDITOF- MS). First, in one mode of sample preparation referred to as wall-less sample preparation, an increase in sequence coverage of a model membrane protein, bacteriorhodopsin, increased from 81 % using traditional sample methodology to 89%. Second, chemical modification sites of proteins, pheromone binding protein 2 (PBP2) and cytochrome P45OCam (P45OCam), were characterized by MALDI-MS. This finding contributed to further studies of protein-ligand interaction of PBP2, and also provided information about native conformation of P45OC, . Third, co-imrnunoprecipitation and MALDI-MS was used to identify the interaction of synapse-associated protein (SAP97) with potassium voltage-gated ion channel Kv1.5. This study provided the first direct mass spectral evidence to support their protein-protein interaction. In addition, to better understand one of MALDI ionization pathways, a simple two-plate method was used to examine the MALDI gas-phase cationization.

Molecular Dynamics Studies of the Protein Bacteriorhodopsin

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Publisher :
ISBN 13 :
Total Pages : 314 pages
Book Rating : 4.:/5 (38 download)

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Book Synopsis Molecular Dynamics Studies of the Protein Bacteriorhodopsin by : William Fowler Humphrey

Download or read book Molecular Dynamics Studies of the Protein Bacteriorhodopsin written by William Fowler Humphrey and published by . This book was released on 1996 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular dynamics (MD) simulations are employed to study the structure and function of the protein bacteriorhodopsin (bR), a 26 kD protein which residues in the purple membrane of the bacterium Halobacterium halobium. Bacteriorhodopsin undergoes a light-driven cyclic process, which pumps protons across the membrane, in order to maintain a proton gradient necessary for ATP synthesis. The cycle is initiated through a $transto cis$ isomerization of the chromophore retinal, which is bound to a lysine residue via a protonated Schiff base linkage. The study of bR is facilitated through development of the program VMD for visualization of the simulation results, and the program NAMD for MD calculations on parallel computers. Initially, MD simulations are used to develop a refined three-dimensional structure of the protein, using the experimentally determined electron-microscopy structure of bR as a basis, and to determine equilibrium positions for several water molecules within the protein interior. MD simulations are then used to model the early isomerization reaction events in the bR photocycle, for both the native (wild-type) system and several bR mutants. The simulations reveal the possibility for bR to form two or three unique photoproducts, distinguished by the retinal isomeric state and the orientation of the Schiff base proton relative to nearby water molecules and negatively charged aspartic acids. One particular photoproduct is suggested to lead to successful proton pump activity, while the remaining structures return back to the initial state; this result is supported by simulations of non-functional bR mutants, which do not exhibit formation of the suggested functional photoproduct. The very fast initial retinal photoexcitation and subsequent isomerization reaction are also examined in detail using a combined quantum/classical simulation technique, in which the evolution of the density matrix for the retinal isomerization degree of freedom is computed using the Liouville-von Neumann equation. The simulations result in wild-type bR exhibiting a non-adiabatic crossing between excited states after 500 fs, while the computed excited-state lifetimes for mutants D85N and D212N are an order of magnitude longer. The results compare well with recent femtosecond spectroscopy data for these systems and demonstrate that the lifetime of the excited state is controlled by the position and slope of the first potential energy surface crossing point.

Membrane Protein Structure and Function Characterization

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Publisher : Humana
ISBN 13 : 9781493983995
Total Pages : 419 pages
Book Rating : 4.9/5 (839 download)

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Book Synopsis Membrane Protein Structure and Function Characterization by : Jean-Jacques Lacapere

Download or read book Membrane Protein Structure and Function Characterization written by Jean-Jacques Lacapere and published by Humana. This book was released on 2018-06-10 with total page 419 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this present volume, different approaches are detailed to produce membrane proteins, purify them, study their function, determine their structure, and model them in membrane. Since every membrane protein behaves mostly in a unique way /fashion, knowledge of guidelines and tricks may help to increase chances to express, purify and characterize a peculiar membrane protein. Production of correctly folded protein remains a challenge. Moreover, getting a functional and stable protein requires to optimize membrane mimicking environments that can be detergent or artificial membranes. In some cases, the finding of the correct ligand which will stabilize the desired conformation is needed. In other cases, stabilization can be obtained using specific antibodies. This volume also presents different techniques to analyze the functional status of membrane proteins. Written in the highly successful Methods in Molecular Biology series format, chapters in Membrane Protein Structure and Function Characterization: Methods and Protocols provide different techniques to analyze the functional and structural status of membrane proteins. 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. Authoritative and practical, Membrane Protein Structure and Function Characterization: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Membrane Spectroscopy

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Publisher : Springer Science & Business Media
ISBN 13 : 3642815375
Total Pages : 509 pages
Book Rating : 4.6/5 (428 download)

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Book Synopsis Membrane Spectroscopy by : E. Grell

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- .

Biophysics of Membrane Proteins

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Publisher :
ISBN 13 : 9781071607244
Total Pages : 336 pages
Book Rating : 4.6/5 (72 download)

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Book Synopsis Biophysics of Membrane Proteins by : Vincent L. G. Postis

Download or read book Biophysics of Membrane Proteins written by Vincent L. G. Postis and published by . This book was released on 2020 with total page 336 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides recent advances in the field of biophysics of membrane proteins. Chapters are divided into several parts: detailing biochemistry and functional analysis, experimental and theoretical structural determinations, membrane protein dynamics, and conformation studies. Written in the highly successful Methods in Molecular Biology 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. Authoritative and cutting-edge, Biophysics of Membrane Proteins: Methods and Protocols aims to provide comprehensive protocols with notes to help further the understanding of key membrane protein structure and function for students, academics, and industrial researchers.