About this book
The basic principle of electron crystallography is to calculate a 3D density map by combining the amplitudes obtained from electron diffraction patterns with the experimental phases calculated from images of two-dimensional crystals of membrane or soluble proteins. This technology is very well developed and has produced a number of atomic models of membrane proteins in a lipid environment. Focused on comprehensive experimental protocols, Electron Crystallography of Soluble and Membrane Proteins: Methods and Protocols covers the entire range of techniques used in electron crystallography, including protein sample preparation, 2D crystallization, and screening in negative stain over electron cryo-microscopy (cryo-EM) and data processing, as well as modeling of conformational changes.
Additional chapters provide perspective on past, present, and future challenges as well as complementary methods. Written for the popular Methods in Molecular Biology series, the work contains the kind of detailed descriptions and implementation advice necessary to ensure successful results. Comprehensive and cutting-edge, Electron Crystallography of Soluble and Membrane Proteins: Methods and Protocols serves laboratories new to the methods as well as state-of-the-art facilities pursuing this exciting area of protein science.
Contents
1. Introduction to Electron Crystallography Werner Kuhlbrandt
2. Practical Aspects in Expression and Purification of Membrane Proteins for Structural Analysis Kutti R. Vinothkumar, Patricia C. Edwards, and Joerg Standfuss
3. Two-Dimensional Crystallization of Membrane Proteins by Reconstitution through Dialysis Matthew C. Johnson, Tina M. Dreaden, Laura Y. Kim, Frederik Rudolph, Bridgette Barry, and Ingeborg Schmidt-Krey
4. Monolayer Two-Dimensional Crystallization Luc Lebeau and Catherine Venien-Bryan
5. Screening for Two-Dimensional Crystals by Transmission Electron Microscopy of Negatively Stained Samples Tina M. Dreaden, Maureen Metcalfe, Laura Y. Kim, Matthew C. Johnson, Bridgette A. Barry, and Ingeborg Schmidt-Krey
6. Low Dose Techniques and Cryo-Electron Microscopy Yoshinori Fujiyoshi
7. Grid Preparation for Cryo-Electron Microscopy Nobuhiko Gyobu
8. Recording High-Resolution Images of Two-Dimensional Crystals of Membrane Proteins Agustin Avila-Sakar, Xueming Li, Shawn Q. Zheng, and Yifan Cheng
9. The Collection of High-Resolution Electron Diffraction Data Tamir Gonen
10. Image Processing of 2D Crystal Images Marcel Arheit, Daniel Castano-Diez, Raphael Thierry, Bryant R. Gipson, Xiangyan Zeng, and Henning Stahlberg
11. Merging of Image Data in Electron Crystallography Marcel Arheit, Daniel Castano-Diez, Raphael Thierry, Priyanka Abeyrathne, Bryant R. Gipson, and Henning Stahlberg
12. Evaluation of Electron Crystallographic Data From Images of Two-Dimensional Crystals Vinzenz M. Unger
13. Modeling, Docking, and Fitting of Atomic Structures to 3D Maps from Cryo-Electron Microscopy Gregory S. Allen and David L. Stokes
14. Phasing Electron Diffraction Data by Molecular Replacement: Strategy for Structure Determination and Refinement Goragot Wisedchaisri and Tamir Gonen
15. High-Throughput Methods for Electron Crystallography David L. Stokes, Iban Ubarretxena-Belandia, Tamir Gonen, and Andreas Engel
16. Automated Grid Handling and Image Acquisition for Two-Dimensional Crystal Screening Anchi Cheng
17. Automation of Data Acquisition in Electron Crystallography Anchi Cheng
18. Automation of Image Processing in Electron Crystallography Marcel Arheit, Daniel Castano-Diez, Raphael Thierry, Bryant R. Gipson, Xiangyan Zeng, and Henning Stahlberg
19. Choice and Maintenance of Equipment for Electron Crystallography Deryck J. Mills and Janet Vonck
20. Future Developments in Instrumentation for Electron Crystallography Kenneth H. Downing
21. Tubular Crystals and Helical Arrays: Structural Determination of HIV-1 Capsid Assemblies Using Iterative Helical Real-Space Reconstruction Peijun Zhang, Xin Meng, and Gongpu Zhao
22. Single Particle Electron Microscopy Wilson C.Y. Lau and John L. Rubinstein
23. Electron Tomography of Paracrystalline 2D Arrays Hanspeter Winkler, Shenping Wu, and Kenneth A. Taylor
24. High-Resolution Imaging of 2D Outer Membrane Protein F (OmpF) Crystals by Atomic Force Microscopy Dimitrios Fotiadis and Daniel J. Muller
25. Determination of Soluble and Membrane Protein Structures by X-Ray Crystallography Raquel L. Lieberman, Mary E. Peek, and J. Derrick Watkins
26. Solution Nuclear Magnetic Resonance (NMR) Spectroscopy James J. Chou and Remy Sounier
27. Structure-Function Insights of Membrane and Soluble Proteins Revealed by Electron Crystallography Tina M. Dreaden, Bharanidharan Devarajan, Bridgette A. Barry, and Ingeborg Schmidt-Krey
28. Lipid Monolayer and Sparse Matrix Screening for Growing Two-Dimensional Crystals for Electron Crystallography: Methods and Examples Mark Yeager, Kelly A. Dryden, and Barbie K. Ganser-Pornillos
29. Processing of Electron Diffraction Patterns with the XDP Program Kaoru Mitsuoka
30. Future Directions of Electron Crystallography Yoshinori Fujiyoshi
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