Download or read book Protein Structure Determination on Lipid Substrates by Electron Microscopy written by Elizabeth Morrison Wilson-Kubalek and published by . This book was released on 2005 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the impressive growth in gene sequence data and advances in genetics the number of proteins and macromolecular assemblies for structural studies are increasing at a rapid rate. Structural biology will help to unravel the function of the newly discovered proteins and their molecular interactions within the cell and will ultimately provide the framework for developing new therapeutic drugs. Electron crystallography has become a valuable method for the structure determination of proteins and macromolecular complexes that are large or heterogeneous, difficult to obtain, unstable, insoluble, or that fail to yield crystals suitable for X-ray crystallographic analysis. Although electron microscopy (EM) and image analysis methods are rapidly improving and continuing to prove their value, advances in sample preparation have been limited, and general methods for obtaining ordered arrays of proteins for EM analysis are needed. In this thesis, I have described a method for promoting the formation of helical protein arrays. Helical crystallization on lipid nanotubes presents an alternative platform to explore fundamentals of protein ordering, intermolecular protein interaction and phase behavior. Three-dimensional (3-D) maps of wild-type and mutant streptavidin (SA) show that the molecular packing arrangements of SA on the surface of the lipid nanotubes differ from previously reported lattice packing of SA on biotinylated monolayers. His-tagged Perfringolysin O (PFO), a soluble toxin was used to demonstrate the utility of nickel-lipid nanotubes as a tool for structural studies of His-tagged proteins. Cryo-EM and image analysis of PFO helical arrays were used to reconstruct a 3-D density map. These studies have demonstrated that lipid nanotubes offer a robust and reproducible substrate for forming helical protein arrays which present a means for studying protein structure and structure-function relationships. Using EM and single-particle image analysis I calculated 2-D projection maps from images of oligomeric PFO prepore and pore complexes formed on lipid layers and identified an apparent conformational change from the prepore to the pore. In addition, I identified specific domains of the toxin molecule within the image and have thus determined the orientation of PFO monomers within the oligomeric complex.

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 Strategies For Two dimensional Crystallization Of Proteins Using Lipid Monolayers written by Jens Dietrich and published by World Scientific. This book was released on 2005-06-16 with total page 154 pages. Available in PDF, EPUB and Kindle. Book excerpt: Strategies for Two-Dimensional Crystallization of Proteins Using Lipid Monolayers presents an overview of different methods that lead to structure determination by electron microscopy. These methods have proven to be extremely successful, especially for elucidating the structure of membrane proteins. Electron crystallography has become an important tool for structure determination of such proteins. This book covers the different practical approaches to two-dimensional crystallization of soluble as well as membrane proteins. From there it takes the reader to equally important issues, such as sample transfer and sample preparation for electron microscopy. In addition, the text provides an introduction to membrane protein structural biology and cryo-electron crystallography, as well as an in-depth discussion on two-dimensional crystallization and surface crystallization./a

Download or read book Protein Structure Determination by Electron Microscopy written by Grant Jay Jensen and published by . This book was released on 1999 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Structural Analysis of Proteins on Lipid Substrates written by E. M. Wilson-Kubalek and published by . This book was released on 2000 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Protein Structure Determination from Cryo electron Microscopy Density Maps written by Yu-Ruei Wang and published by . This book was released on 2015 with total page 71 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-particle cryo-electron microscopy (cryo-EM) has emerged as a powerful tool in structure determination of macromolecular complexes that are not suitable for crystallographic studies. Recent advances in direct electron detectors and image-processing techniques have allowed cryo-EM to reach near-atomic resolution (3--5 Å) from small particles with low or even no symmetry. However, tools to determine structures from cryo-EM maps have lagged behind. In this dissertation we describe approaches that apply Rosetta high-resolution structure prediction methods to model-building from cryo-EM maps. Using knowledge-based information gathered from proteins of known atomic structure, we describe the development of novel tools for de novo model-building from near-atomic resolution cryo-EM maps, and for architecture determination of multi-component macromolecular assemblies from medium- to low-resolution (5--15 Å) cryo- EM maps. We demonstrate that these new computational tools have shown usefulness in determining the structures from newly reconstructed cryo-EM maps, which would otherwise be difficult or impossible for human to do. These methods should enable rapid and reliable structure determination from cryo-EM maps.

Download or read book Protein Structure Determination by Electron Diffraction of Protein Microcrystals written by Matthew Gregory Iadanza and published by . This book was released on 2014 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: Crystallographic methods for protein structure determination are well established and have provided valuable insight into the workings of the biological world. X-ray crystallography of three dimensional crystals has benefited from the development of high throughput screening methods, but the method still requires the production of large well ordered crystals. Crystal screening and optimization is an extremely time consuming bottleneck and many proteins, often of high biological interest, are simply not able to be crystallized. Electron crystallography of two dimensional crystals is a much more limited method applicable only to extremely thin two-dimensional crystals, usually composed of protein and lipid. This method has provided insight into the structures and protein-lipid interactions of some integral membrane proteins but is extremely low throughput and not broadly applicable. This work presents a new method for protein structure determination which is essentially a hybrid of these two methods. A focused electron beam is diffracted by very small three dimensional protein microcrystals allowing for diffraction data to be collected from crystals at least six orders of magnitude smaller than those used for traditional X-ray crystallography. This method allows data collection and subsequent structure determination using crystals that would be considered `initial hits' in a crystallization screen and would normally require a great deal of optimization before yielding data for structure determination. As proof of principle the structure of hen egg white lysozyme determined to 3.0 Å resolution by microcrystal electron diffraction is presented. The procedures for data collection are detailed as well as an explanation of new software developed for processing the resulting data and possible future refinements and improvements to the technique. With further refinement microcrystal electron diffraction may prove useful for many proteins that are currently considered intractable because of their failure to form large well ordered three dimensional crystals.

Download or read book Advances in Computer Aided Protein Structure Determination from Sparse Cryo Electron Microscopy Data written by Brandon Frenz and published by . This book was released on 2017 with total page 54 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-particle cryo-electron microscopy (cryoEM) has become a powerful tool for determining macromolecular structures. Thanks to recent advances in direct electron detectors and motion correction algorithms it can frequently deliver electron density maps in the range of 3-5Å resolution. To obtain as much atomic level detail of the structure as possible from this data an accurate atomic model must be built. This can be done manually however, it is laborious and error prone. To resolve this problem modelers have turned to computational tools which can make up for lack of experimental data. Here we describe several tools for modeling with sparse experimental data, including a novel sampling strategy for de novo model completion and a novel refinement strategy for glycans with near atomic resolution cryoEM and x-ray crystallography data.

Download or read book Single particle Cryo electron Microscopy written by Joachim Frank and published by World Scientific Publishing Company. This book was released on 2017-12-31 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book reproduces 55 of more than 300 articles written by the author, representing milestones in methods development of single-particle cryo-EM as well as important results obtained by this technique in the study of biological macromolecules and their interactions. Importantly, neither symmetries nor ordered arrangements (as in two-dimensional crystals, helical assemblies, icosahedral viruses) are required. Although the biological applications are mainly in the area of ribosome structure and function, the elucidation of membrane channel structures and their activation and gating mechanisms are represented, as well. The book is introduced by a commentary that explains the original development of concepts, describes the contributions of the author's colleagues and students, and shows how challenges were overcome as the technique matured. Along the way, the ribosome served as an example for a macromolecule with intricate structure and conformational dynamics that pose challenges for three-dimensional visualization. Toward the end of the book -- bringing us to the present time -- molecular structures with near-atomic resolution are presented, and a novel type of computational analysis, manifold embedding, is introduced. Single-particle cryo-EM is currently revolutionizing structural biology, presenting a powerful alternative to X-ray crystallography as a means to solve the structure of biological macromolecules. The book presents in one place a number of articles containing key advances in mathematical and computational methods leading up to the present time. Secondly, the development of the technique over the years is reflected by ever-expanding discoveries in the field of ribosome structure and function. Thirdly, as all histories of ideas, the history of concepts pertaining to this new method of visualization is fascinating all in itself.

Download or read book Membrane Protein Crystallization written by and published by Academic Press. This book was released on 2009-05-29 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume of Current Topics in Membranes focuses on Membrane Protein Crystallization, beginning with a review of past successes and general trends, then further discussing challenges of mebranes protein crystallization, cell free production of membrane proteins and novel lipids for membrane protein crystallization. This publication also includes tools to enchance membrane protein crystallization, technique advancements, and crystallization strategies used for photosystem I and its complexes, establishing Membrane Protein Crystallization as a needed, practical reference for researchers.

Download or read book Structure and Function of Membrane Proteins written by Ingeborg Schmidt-Krey and published by Humana. This book was released on 2021-04-21 with total page 358 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book examines detailed experimental and computational approaches for the analysis of many aspects vital to the understanding of membrane protein structure and function. Readers will receive guidance on the selection and use of methods for over-expression and purification, tools to characterize membrane proteins within different phospholipid bilayers, direction on functional studies, and approaches to determine the structures of membrane proteins. Detailed experimental steps for specific membrane proteins with critical notes allow the protocols to be modified to different systems. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of practical information and implementation advice that leads to excellent, reproducible results. Authoritative and up-to-date, Structure and Function Studies of Membrane Proteins serves as an ideal guide for biologists, biochemists, and biophysicists striving to further understand these essential proteins and their many biological roles.

Download or read book Free Energy Calculations written by Christophe Chipot and published by Springer Science & Business Media. This book was released on 2007-01-08 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Free energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability. This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.

Download or read book Crystallization of Membrane Proteins written by Hartmut Michel and published by CRC Press. This book was released on 2018-01-18 with total page 343 pages. Available in PDF, EPUB and Kindle. Book excerpt: The precise knowledge of the structure of biological macromolecules forms the basis of understanding their function and their mechanism of action. It also lays the foundation for rational protein and drug design. The only method to obtain this knowledge is still crystallography. At present, the structures of about 400 proteins are known at or nearly at atomic proteins. However, only two of them are membrane proteins or complexes of the membrane proteins. The reasons for the difference is not the crystals of membrane proteins resists forming special problems when being analysed. The reason is that the membrane proteins resist into forming into well-ordered crystals. The intention of this book is to help to produce well-ordered crystals proteins and to provide guidelines, it is aimed at both biochemists and protein crystallographer‘s.

Download or read book Three Dimensional Electron Microscopy of Macromolecular Assemblies written by Frank Joachim and published by Elsevier. This book was released on 1996-01-24 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: Three-Dimensional Electron Microscopy of Macromolecular Assemblies is the first systematic introduction to single-particle methods of reconstruction. It covers correlation alignment, classification, 3D reconstruction, restoration, and interpretation of the resulting 3D images in macromolecular assemblies. It will be an indispensable resource for newcomers to the field and for all using or adopting these methods. Key Features* Presents methods that offer an alternative to crystallographic techniques for molecules that cannot be crystallized* Describes methods that have been instrumental in exploring the three-dimensional structure of* the nuclear pore complex* the calcium release channel;* the ribosome* chaperonins

Download or read book Protein lipidation in health and disease written by Rebeca M. Mejias Estevez and published by Frontiers Media SA. This book was released on 2023-11-15 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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