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Author : John B. C. Findlay Publisher : Taylor & Francis Page : 240 pages File Size : 43,9 Mb Release : 1996-08 Category : Medical ISBN : STANFORD:36105018420021
Membrane Protein Models is an important collection of reviews, by internationally recognised researchers, of recent advances in the modelling of integral membrane proteins based on their structure/function relationship. The emphasis is on G protein-couple
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.
Molecular Modeling of Proteins by Andreas Kukol Pdf
Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions and notes on troubleshooting and avoiding common pitfalls. Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical and biosciences interested in utilizing this powerful technology.
Membrane Protein Structure and Function Characterization by Jean-Jacques Lacapere Pdf
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 Protein Structure Determination by Jean-Jacques Lacapère Pdf
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.
Structural Bioinformatics of Membrane Proteins by D. Frishman Pdf
This book is the first one specifically dedicated to the structural bioinformatics of membrane proteins. With a focus on membrane proteins from the perspective of bioinformatics, the present work covers a broad spectrum of topics in evolution, structure, function, and bioinformatics of membrane proteins focusing on the most recent experimental results. Leaders in the field who have recently reported breakthrough advances cover algorithms, databases and their applications to the subject. The increasing number of recently solved membrane protein structures makes the expert coverage presented here very timely. Structural bioinformatics of membrane proteins has been an active area of research over the last thee decades and proves to be a growing field of interest.
In this volume, a detailed description of cutting-edge computational methods applied to protein modeling as well as specific applications are presented. Chapters include: the application of Car-Parrinello techniques to enzyme mechanisms, the outline and application of QM/MM methods, polarizable force fields, recent methods of ligand docking, molecular dynamics related to NMR spectroscopy, computer optimization of absorption, distribution, metabolism and excretion extended by toxicity for drugs, enzyme design and bioinformatics applied to protein structure prediction. A keen emphasis is laid on the clear presentation of complex concepts, since the book is primarily aimed at Ph.D. students, who need an insight in up-to-date protein modeling. The inclusion of descriptive, color figures will allow the reader to get a pictorial representation of complicated structural issues.
The Next Generation in Membrane Protein Structure Determination by Isabel Moraes Pdf
This book reviews current techniques used in membrane protein structural biology, with a strong focus on practical issues. The study of membrane protein structures not only provides a basic understanding of life at the molecular level but also helps in the rational and targeted design of new drugs with reduced side effects. Today, about 60% of the commercially available drugs target membrane proteins and it is estimated that nearly 30% of proteins encoded in the human genome are membrane proteins. In recent years much effort has been put towards innovative developments to overcome the numerous obstacles associated with the structure determination of membrane proteins. This book reviews a variety of recent techniques that are essential to any modern researcher in the field of membrane protein structural biology. The topics that are discussed are not commonly found in textbooks. The scope of this book includes: Expression screening using fluorescent proteins The use of detergents in membrane protein research The use of NMR Synchrotron developments in membrane protein structural biology Visualisation and X-ray data collection of microcrystals X-ray diffraction data analysis from multiple crystals Serial millisecond crystallography Serial femtosecond crystallography Membrane protein structures in drug discovery The information provided in this book should be of interest to anyone working in the area of structural biology. Students will find carefully prepared overviews of basic ideas and advanced protein scientists will find the level of detail required to apply the material directly to their day to day work. Chapters 4, 5, 6, 8 and 9 of this book are published open access under a CC BY 4.0 license at link.springer.com.
Membrane Proteins: Structures, Interactions and Models by A. Pullman,Joshua Jortner Pdf
The 25th Jerusalem Symposium represents a most significant highlight in the development and history of these meetings. Living within the decimal system we have celebrated with much pleasure the lath and the 20th Jerusalem Symposia. With this one we experience a feeling of particular satisfaction because 25 years is different from, is more than, two decades and a half. It is a quarter of a century. It seems thus as if we have changed the dimension of our endeavour. In no way do we loose the sense of modesty with respect to the significance of these meetings. For the organizers, however, they do represent a continuity of efforts which we feel happy to have been able to carry out. At this occasion it seems useful to say a few words about the origin of the Jerusalem Symposia and to recall the name of a colleague who played an essential role in their creation and has been a most efficient and devoted co organizer of the seven first of them. This was Professor Ernst Bergmann, one of the most distinguished founders of Israeli Science and a world famous physico-organic chemist.
Introduction to Protein Structure Prediction by Huzefa Rangwala,George Karypis Pdf
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.
Techniques for the Analysis of Membrane Proteins by C. Ragan Pdf
A preface should justify the existence of the book it precedes and this is invariably done in scientific texts by reference to the explosive growth of the field since the last such volume appeared. In molecular biology, most fields can be justifiably described as growing explosively, as should be the case for a young and vigorous science, but the study of membrane proteins stands out as one which has taken giant strides in the last few years. Ignorance of the structure and function of membrane proteins at the molecular level was certainly not due to lack of interest but rather was a result of lack of appropriate techniques. It has above all been the development of new experimental methods which has wrenched membrane biochemistry out of what Anthony Martonosi fetchingly called its 'romantic phase' (Le. lots of ideas and few facts), into an era when the determination of membrane protein structure and mechanism is a reasonable goal. Membrane proteins are generally classified as peripheral or integral. Peripheral proteins are relatively easily dissociated from membranes by mild treatments whence their study is essentially no different to that of soluble proteins. This book therefore concentrates on integral proteins which are strongly bound to the membrane by hydrophobic interactions with lipids. A crucial step in their study is of necessity the d~velopment of methods of solubilization and purification under non-denaturing conditions.
Protein Actions by Ken Dill,Robert L. Jernigan,Ivet Bahar Pdf
Protein Actions: Principles and Modeling is aimed at graduates, advanced undergraduates, and any professional who seeks an introduction to the biological, chemical, and physical properties of proteins. Broadly accessible to biophysicists and biochemists, it will be particularly useful to student and professional structural biologists and molecular biophysicists, bioinformaticians and computational biologists, biological chemists (particularly drug designers) and molecular bioengineers. The book begins by introducing the basic principles of protein structure and function. Some readers will be familiar with aspects of this, but the authors build up a more quantitative approach than their competitors. Emphasizing concepts and theory rather than experimental techniques, the book shows how proteins can be analyzed using the disciplines of elementary statistical mechanics, energetics, and kinetics. These chapters illuminate how proteins attain biologically active states and the properties of those states. The book ends with a synopsis the roles of computational biology and bioinformatics in protein science.