Protein Structure Determination From Cryo Electron Microscopy Density Maps

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Protein Structure Determination from Cryo-electron Microscopy Density Maps

Author : Yu-Ruei Wang
Publisher :
ISBN 13 :
Total Pages : 71 pages
Book Rating : 4.:/5 (932 download)

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Book Synopsis Protein Structure Determination from Cryo-electron Microscopy Density Maps by : Yu-Ruei Wang

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.

The Resolution Revolution: Recent Advances In cryoEM

Author :
Publisher : Academic Press
ISBN 13 : 0128054352
Total Pages : 488 pages
Book Rating : 4.1/5 (28 download)

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Book Synopsis The Resolution Revolution: Recent Advances In cryoEM by :

Download or read book The Resolution Revolution: Recent Advances In cryoEM written by and published by Academic Press. This book was released on 2016-08-26 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: cryoEM, a new volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods and new developments in recording images, the creation, evaluation and validation of 3D maps from the images, model building into maps and refinement of the resulting atomic structures, and applications of essentially single particle methods to helical structures and to sub-tomogram averaging. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods that determine the structures of biological molecules, a vital step for understanding their function Contains the technical developments underpinning the advances of cryoEM and captures the exciting insights that have resulted

Protein Conformational Dynamics

Author : Ke-li Han
Publisher : Springer Science & Business Media
ISBN 13 : 3319029703
Total Pages : 488 pages
Book Rating : 4.3/5 (19 download)

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Book Synopsis Protein Conformational Dynamics by : Ke-li Han

Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.

Advances in Computer Aided Protein Structure Determination from Sparse Cryo Electron Microscopy Data

Author : Brandon Frenz
Publisher :
ISBN 13 :
Total Pages : 54 pages
Book Rating : 4.:/5 (13 download)

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Book Synopsis Advances in Computer Aided Protein Structure Determination from Sparse Cryo Electron Microscopy Data by : Brandon Frenz

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.

Three-dimensional Electron Microscopy of Macromolecular Assemblies

Author : Joachim Frank
Publisher : Oxford University Press
ISBN 13 : 0195150961
Total Pages : 427 pages
Book Rating : 4.1/5 (951 download)

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Book Synopsis Three-dimensional Electron Microscopy of Macromolecular Assemblies by : Joachim Frank

Download or read book Three-dimensional Electron Microscopy of Macromolecular Assemblies written by Joachim Frank and published by Oxford University Press. This book was released on 2006 with total page 427 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cryoelectron microscopy of biological molecules is among the hottest growth areas in biophysics and structural biology at present, and Frank is arguably the most distinguished practitioner of this art. CryoEM is likely over the next few years to take over much of the structural approaches currently requiring X-ray crystallography, because one can now get good and finely detailed images of single molecules down to as little as 200,000 MW, covering a substantial share of the molecules of greatest biomedical research interest. This book, the successor to an earlier work published in 1996 with Academic Press, is a natural companion work to our forthcoming book on electron crystallography by Robert Glaeser, with contributions by six others, including Frank. A growing number of workers will employ CryoEM for structural studies in their own research, and a large proportion of biomedical researchers will have a growing interest in understanding what the capabilities and limits of this approach are.

Protein Complex Structure Determination Guided by Low-resolution Cryo-electron Microscopy Maps

Author : Daniel P. Farrell
Publisher :
ISBN 13 :
Total Pages : 68 pages
Book Rating : 4.:/5 (13 download)

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Book Synopsis Protein Complex Structure Determination Guided by Low-resolution Cryo-electron Microscopy Maps by : Daniel P. Farrell

Download or read book Protein Complex Structure Determination Guided by Low-resolution Cryo-electron Microscopy Maps written by Daniel P. Farrell and published by . This book was released on 2021 with total page 68 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cryo-electron microscopy of protein complexes often leads to moderate resolution maps (4-8 Ã ), with visible secondary structure elements but poorly resolved loops, making model-building challenging. In the absence of high-resolution structures of homologues, only coarse-grained structural features are typically inferred from these maps, and it is often impossible to assign specific regions of density to individual protein subunits. This dissertation describes a new method for overcoming these difficulties that integrates predicted residue distance distributions from a deep-learned convolutional neural network, computational protein folding using Rosetta, and automated EM-map-guided complex assembly. We will show how this method performs on a diverse benchmarking dataset in addition to describing how it was used to build models for three difficult protein complexes that would have been impossible to solve without this software. We anticipate that our approach will be broadly useful for cryoEM structure determination of large complexes containing many subunits for which there are no homologues of known structure.

Single-particle Cryo-electron Microscopy

Author : Joachim Frank
Publisher : World Scientific Publishing Company
ISBN 13 : 9789813234857
Total Pages : 0 pages
Book Rating : 4.2/5 (348 download)

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Book Synopsis Single-particle Cryo-electron Microscopy by : Joachim Frank

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.

Deciphering Protein Complex Structures from Cryo-electron Microscopy Maps Using Deep Learning

Author : Jonas Pfab
Publisher :
ISBN 13 :
Total Pages : 58 pages
Book Rating : 4.:/5 (123 download)

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Book Synopsis Deciphering Protein Complex Structures from Cryo-electron Microscopy Maps Using Deep Learning by : Jonas Pfab

Download or read book Deciphering Protein Complex Structures from Cryo-electron Microscopy Maps Using Deep Learning written by Jonas Pfab and published by . This book was released on 2020 with total page 58 pages. Available in PDF, EPUB and Kindle. Book excerpt: Information about macromolecular structure of protein complexes such as SARS-CoV-2, and related cellular and molecular mechanisms can assist the search for vaccines and drug development processes. To obtain such structural information, we present DeepTracer, a fully automatic deep learning-based method for fast de novo multi-chain protein complex structure determination from high-resolution cryo-electron microscopy (cryo-EM) density maps. We applied DeepTracer on a previously published set of 476 raw experimental density maps and compared the results with a current state of the art method. The residue coverage increased by over 30% using DeepTracer and the RMSD value improved from 1.29Å to 1.18Å. Additionally, we applied DeepTracer on a set of 62 coronavirus-related density maps, among them 10 with no deposited structure available in EMDataResource. We observed an average residue match of 84% with the deposited structures and an average RMSD of 0.93Å. Additional tests with related methods further exemplify DeepTracer's competitive accuracy and efficiency of structure modeling. DeepTracer allows for exceptionally fast computations, making it possible to trace around 60,000 residues in 350 chains within only two hours. The web service is globally accessible at https://deeptracer.uw.edu.

Efficient Geometric Approaches for Mining Protein Structure from Cryo-EM Density Maps

Author : Hang Dou
Publisher :
ISBN 13 :
Total Pages : 100 pages
Book Rating : 4.:/5 (13 download)

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Book Synopsis Efficient Geometric Approaches for Mining Protein Structure from Cryo-EM Density Maps by : Hang Dou

Download or read book Efficient Geometric Approaches for Mining Protein Structure from Cryo-EM Density Maps written by Hang Dou and published by . This book was released on 2017 with total page 100 pages. Available in PDF, EPUB and Kindle. Book excerpt: A protein's 3D structure is the key to understanding its biological function. In recent years, cryo-electron microscopy or cryo-EM has established itself as a mainstream technique to capture proteins' structure at near-native conditions. However the vast majority of cryo-EM data are at medium (5-10A) or low (>10A) resolutions, which is insufficient to capture a protein's atomic structure. Fortunately, at such resolutions, some intrinsic structures of a protein, such as secondary structure elements (SSEs) and smooth c-alpha backbone fragments (SCBFs), can be recognized or robustly detected. In this dissertation, we present efficient protein fitting pipelines to recover a protein's atomic structure given the protein's cryo-EM density map by leveraging the intrinsic structure information detected from the density map. Specifically, we first compute the correspondences between the protein features (SSEs or SCBFs) detected from the cryo-EM density map and those extracted from the template model. Then we fit the template model into the cryo-EM density map guided by the obtained correspondences.

Cryo-EM Part B: 3-D Reconstruction

Author :
Publisher : Academic Press
ISBN 13 : 0123849926
Total Pages : 472 pages
Book Rating : 4.1/5 (238 download)

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Book Synopsis Cryo-EM Part B: 3-D Reconstruction by :

Download or read book Cryo-EM Part B: 3-D Reconstruction written by and published by Academic Press. This book was released on 2010-09-30 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is dedicated to a description of the instruments, samples, protocols, and analyses that belong to cryo-EM. It emphasizes the relatedness of the ideas, instrumentation, and methods underlying all cryo-EM approaches, which allow practitioners to easily move between them. Within each section, the articles are ordered according to the most common symmetry of the sample to which their methods are applied. Includes time-tested core methods and new innovations applicable to any researcher Methods included are useful to both established researchers and newcomers to the field Relevant background and reference information given for procedures can be used as a guide

Introduction to Conventional Transmission Electron Microscopy

Author : Marc De Graef
Publisher : Cambridge University Press
ISBN 13 : 0521620066
Total Pages : 741 pages
Book Rating : 4.5/5 (216 download)

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Book Synopsis Introduction to Conventional Transmission Electron Microscopy by : Marc De Graef

Download or read book Introduction to Conventional Transmission Electron Microscopy written by Marc De Graef and published by Cambridge University Press. This book was released on 2003-03-27 with total page 741 pages. Available in PDF, EPUB and Kindle. Book excerpt: A graduate level textbook covering the fundamentals of conventional transmission electron microscopy, first published in 2003.

cryoEM

Author : Tamir Gonen
Publisher : Humana
ISBN 13 : 9781071609682
Total Pages : 350 pages
Book Rating : 4.6/5 (96 download)

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Book Synopsis cryoEM by : Tamir Gonen

Download or read book cryoEM written by Tamir Gonen and published by Humana. This book was released on 2021-12-28 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details the most up-to-date cryo-EM techniques from leading researchers. Chapters are organized into four parts with emphasis on electron cryotomography, single particle analysis, and the crystal based cryo-EM methods of 2D electron crystallography, and MicroED for the study of 3D crystals. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, CryoEM: Methods and Protocols aims to serve as an excellent resource on cryo-EM and can serve as the foundation for new researchers to this growing field in structural biology.

Deep Learning to Predict Protein Backbone Structure from High-resolution Cryo-EM Density Maps

Author : Spencer Moritz
Publisher :
ISBN 13 :
Total Pages : 42 pages
Book Rating : 4.:/5 (11 download)

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Book Synopsis Deep Learning to Predict Protein Backbone Structure from High-resolution Cryo-EM Density Maps by : Spencer Moritz

Download or read book Deep Learning to Predict Protein Backbone Structure from High-resolution Cryo-EM Density Maps written by Spencer Moritz and published by . This book was released on 2019 with total page 42 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Determining [alpha]-helix Correspondence for Protein Structure Prediction from Cryo-EM Density Maps

Author : Sasakthi Senanayaka Abeysinghe
Publisher :
ISBN 13 :
Total Pages : 112 pages
Book Rating : 4.:/5 (135 download)

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Book Synopsis Determining [alpha]-helix Correspondence for Protein Structure Prediction from Cryo-EM Density Maps by : Sasakthi Senanayaka Abeysinghe

Download or read book Determining [alpha]-helix Correspondence for Protein Structure Prediction from Cryo-EM Density Maps written by Sasakthi Senanayaka Abeysinghe and published by . This book was released on 2007 with total page 112 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Protein Structure Determination on Lipid Substrates by Electron Microscopy

Author : Elizabeth Morrison Wilson-Kubalek
Publisher :
ISBN 13 : 9780542002434
Total Pages : 344 pages
Book Rating : 4.0/5 (24 download)

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Book Synopsis Protein Structure Determination on Lipid Substrates by Electron Microscopy by : Elizabeth Morrison Wilson-Kubalek

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.

Structural Biology in Drug Discovery

Author : Jean-Paul Renaud
Publisher : John Wiley & Sons
ISBN 13 : 1118900502
Total Pages : 1367 pages
Book Rating : 4.1/5 (189 download)

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Book Synopsis Structural Biology in Drug Discovery by : Jean-Paul Renaud

Download or read book Structural Biology in Drug Discovery written by Jean-Paul Renaud and published by John Wiley & Sons. This book was released on 2020-01-09 with total page 1367 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the most comprehensive and up-to-date overview of structure-based drug discovery covering both experimental and computational approaches, Structural Biology in Drug Discovery: Methods, Techniques, and Practices describes principles, methods, applications, and emerging paradigms of structural biology as a tool for more efficient drug development. Coverage includes successful examples, academic and industry insights, novel concepts, and advances in a rapidly evolving field. The combined chapters, by authors writing from the frontlines of structural biology and drug discovery, give readers a valuable reference and resource that: Presents the benefits, limitations, and potentiality of major techniques in the field such as X-ray crystallography, NMR, neutron crystallography, cryo-EM, mass spectrometry and other biophysical techniques, and computational structural biology Includes detailed chapters on druggability, allostery, complementary use of thermodynamic and kinetic information, and powerful approaches such as structural chemogenomics and fragment-based drug design Emphasizes the need for the in-depth biophysical characterization of protein targets as well as of therapeutic proteins, and for a thorough quality assessment of experimental structures Illustrates advances in the field of established therapeutic targets like kinases, serine proteinases, GPCRs, and epigenetic proteins, and of more challenging ones like protein-protein interactions and intrinsically disordered proteins

Hydrogen Exchange Mass Spectrometry of Proteins

Author : David D. Weis
Publisher : John Wiley & Sons
ISBN 13 : 1118616499
Total Pages : 422 pages
Book Rating : 4.1/5 (186 download)

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Book Synopsis Hydrogen Exchange Mass Spectrometry of Proteins by : David D. Weis

Download or read book Hydrogen Exchange Mass Spectrometry of Proteins written by David D. Weis and published by John Wiley & Sons. This book was released on 2016-03-21 with total page 422 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hydrogen exchange mass spectrometry is widely recognized for its ability to probe the structure and dynamics of proteins. The application of this technique is becoming widespread due to its versatility for providing structural information about challenging biological macromolecules such as antibodies, flexible proteins and glycoproteins. Although the technique has been around for 25 years, this is the first definitive book devoted entirely to the topic. Hydrogen Exchange Mass Spectrometry of Proteins: Fundamentals, Methods and Applications brings into one comprehensive volume the theory, instrumentation and applications of Hydrogen Exchange Mass Spectrometry (HX-MS) - a technique relevant to bioanalytical chemistry, protein science and pharmaceuticals. The book provides a solid foundation in the basics of the technique and data interpretation to inform readers of current research in the method, and provides illustrative examples of its use in bio- and pharmaceutical chemistry and biophysics In-depth chapters on the fundamental theory of hydrogen exchange, and tutorial chapters on measurement and data analysis provide the essential background for those ready to adopt HX-MS. Expert users may advance their current understanding through chapters on methods including membrane protein analysis, alternative proteases, millisecond hydrogen exchange, top-down mass spectrometry, histidine exchange and method validation. All readers can explore the diversity of HX-MS applications in areas such as ligand binding, membrane proteins, drug discovery, therapeutic protein formulation, biocomparability, and intrinsically disordered proteins.