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Cryo-EM. Part C, Analyses, interpretation, and case studies /

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, intrumentation, and methods underlying all cryo-EM approaches which allow practictioners to easily move between them. Within each section...

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Detalles Bibliográficos
Clasificación:Libro Electrónico
Otros Autores: Jensen, Grant J.
Formato: Electrónico eBook
Idioma:Inglés
Publicado: San Diego, Calif : Academic Press/Elsevier, �2010.
Colección:Methods in enzymology ; v. 483.
Temas:
Acceso en línea:Texto completo
Texto completo
Tabla de Contenidos:
  • 1.Introduction / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio
  • 2.Features in a Subnanometer Resolution Density Map / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio
  • 3.Tools: Analyzing a Subnanometer Resolution Density Map / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio
  • 4.Protocol: From Density Map to Atomic Model / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio
  • 5.Case Study: Mm-cpn / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio
  • 6.Discussion / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio
  • Acknowledgments / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio
  • References / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio
  • 1.Introduction / Niels Volkmann
  • 2.Noise Reduction / Niels Volkmann
  • 3.Segmentation / Niels Volkmann
  • 4.Detection and Mapping of Macromolecular Assemblies / Niels Volkmann
  • 5.Classification and Averaging / Niels Volkmann
  • 6.Validation / Niels Volkmann
  • Acknowledgments / Niels Volkmann
  • References / Niels Volkmann
  • 1.Introduction / Friedrich F�orster / Elizabeth Villa
  • 2.The Problem of Placing Assembly Subunits into Cryo-EM Maps / Friedrich F�orster / Elizabeth Villa
  • 3.Structure Prediction of Subunits / Friedrich F�orster / Elizabeth Villa
  • 4.Protein[-]Protein Interaction Data / Friedrich F�orster / Elizabeth Villa
  • 5.Model Building of a Complex Using Cryo-EM and Additional Data / Friedrich F�orster / Elizabeth Villa
  • 6.Refinement of Atomic Models Using High-Resolution Maps / Friedrich F�orster / Elizabeth Villa
  • 7.Conclusion and Outlook / Friedrich F�orster / Elizabeth Villa
  • References / Friedrich F�orster / Elizabeth Villa
  • 1.Introduction / Catherine L. Lawson
  • 2.EM Structural Data Archives / Catherine L. Lawson
  • 3.Deposition and Content / Catherine L. Lawson
  • 4.Access / Catherine L. Lawson
  • 5.Examples of Use / Catherine L. Lawson
  • 6.Future Prospects / Catherine L. Lawson
  • 7.Guide to Deposition of EM Structural Data / Catherine L. Lawson
  • Acknowledgments / Catherine L. Lawson
  • References / Catherine L. Lawson
  • 1.Electron Crystallography / Andreas D. Schenk / Richard K. Hite / Andreas Engel / Yoshinori Fujiyoshi / Thomas Walz
  • 2.Contributions of Electron Crystallography to the Structural Biology of Aquaporins / Andreas D. Schenk / Richard K. Hite / Andreas Engel / Yoshinori Fujiyoshi / Thomas Walz
  • 3.Contributions of Structural Studies on Aquaporins to Advances in Electron Crystallography / Andreas D. Schenk / Richard K. Hite / Andreas Engel / Yoshinori Fujiyoshi / Thomas Walz
  • Acknowledgments / Andreas D. Schenk / Richard K. Hite / Andreas Engel / Yoshinori Fujiyoshi / Thomas Walz
  • References / Andreas D. Schenk / Richard K. Hite / Andreas Engel / Yoshinori Fujiyoshi / Thomas Walz
  • 1.Introduction: The Role of Electron Microscopy in Tubulin Studies / Kenneth H. Downing / Eva Nogales
  • 2.Tubulin Studies by Electron Crystallography / Kenneth H. Downing / Eva Nogales
  • 3.Microtubule Structure / Kenneth H. Downing / Eva Nogales
  • 4.Structure of Microtubule Assembly/Disassembly Intermediates / Kenneth H. Downing / Eva Nogales
  • 5.Mechanism of Kinesin Movement Along Microtubule / Kenneth H. Downing / Eva Nogales
  • 6.Drug Binding Studied by Diffraction and Modeling / Kenneth H. Downing / Eva Nogales
  • 7.Tomography for Larger Structures / Kenneth H. Downing / Eva Nogales
  • 8.Conclusion / Kenneth H. Downing / Eva Nogales
  • Acknowledgments / Kenneth H. Downing / Eva Nogales
  • References / Kenneth H. Downing / Eva Nogales
  • 1.Helical Crystallization of the Bacterial Integral Membrane Protein, MsbA / John Paul Glaves / Lauren Fisher / Andrew Ward / Howard S. Young
  • 2.Helical Crystallization of the Sarcoplasmic Reticulum Ca2+-ATPase / John Paul Glaves / Lauren Fisher / Andrew Ward / Howard S. Young
  • 3.Discussion / John Paul Glaves / Lauren Fisher / Andrew Ward / Howard S. Young
  • 4.Conclusions / John Paul Glaves / Lauren Fisher / Andrew Ward / Howard S. Young
  • Acknowledgments / John Paul Glaves / Lauren Fisher / Andrew Ward / Howard S. Young
  • References / John Paul Glaves / Lauren Fisher / Andrew Ward / Howard S. Young
  • 1.Introduction / Justus Loerke / Jan Giesebrecht / Christian M.T. Spahn
  • 2.Dealing with Heterogeneity: 3D Sorting / Justus Loerke / Jan Giesebrecht / Christian M.T. Spahn
  • 3.Subnanometer Multiparticle Cryo-EM of Ribosomes in Practice / Justus Loerke / Jan Giesebrecht / Christian M.T. Spahn
  • 4.Interpretation / Justus Loerke / Jan Giesebrecht / Christian M.T. Spahn
  • 5.Conclusions / Justus Loerke / Jan Giesebrecht / Christian M.T. Spahn
  • Acknowledgments / Justus Loerke / Jan Giesebrecht / Christian M.T. Spahn
  • References / Justus Loerke / Jan Giesebrecht / Christian M.T. Spahn
  • 1.Electron Microscopy and the Next Frontier in Structural Biology / Edward J. Brignole / Francisco Asturias
  • 2.The Catalytic Cycle of FAS Requires Conformational Changes / Edward J. Brignole / Francisco Asturias
  • 3.Methods and Rationale Employed in the Conformational Analysis of FAS / Edward J. Brignole / Francisco Asturias
  • 4.EM and FAS: A Versatile Tool for a Flexible Macromolecule / Edward J. Brignole / Francisco Asturias
  • Acknowledgments / Edward J. Brignole / Francisco Asturias
  • References / Edward J. Brignole / Francisco Asturias
  • 1.Introduction / Dorit Hanein
  • 2.Testing the Lamella Hypothesis / Dorit Hanein
  • 3.Challenges / Dorit Hanein
  • Acknowledgments / Dorit Hanein
  • References / Dorit Hanein
  • 1.Introduction / Friedrich F�orster / Bong-Gyoon Han / Martin Beck
  • 2.Data Acquisition / Friedrich F�orster / Bong-Gyoon Han / Martin Beck
  • 3.Templates / Friedrich F�orster / Bong-Gyoon Han / Martin Beck
  • 4.Template Matching / Friedrich F�orster / Bong-Gyoon Han / Martin Beck
  • 5.Assessment of Performance / Friedrich F�orster / Bong-Gyoon Han / Martin Beck
  • 6.The Spatial Proteome of L. interrogans / Friedrich F�orster / Bong-Gyoon Han / Martin Beck
  • 7.Outlook / Friedrich F�orster / Bong-Gyoon Han / Martin Beck
  • Acknowledgments / Friedrich F�orster / Bong-Gyoon Han / Martin Beck
  • References / Friedrich F�orster / Bong-Gyoon Han / Martin Beck
  • 1.Introduction / Asaf Mader / Nadav Elad / Ohad Medalia
  • 2.Specimen Preparation / Asaf Mader / Nadav Elad / Ohad Medalia
  • 3.Relying on Correlative Light and Electron Microscope for Cellular Structural Study of Eukaryotic Cells / Asaf Mader / Ohad Medalia / Nadav Elad
  • 4.Cryoelectron Tomography of Cytoskeleton-Driven Processes / Asaf Mader / Nadav Elad / Ohad Medalia
  • 5.Cryotomography of Midbodies / Asaf Mader / Nadav Elad / Ohad Medalia
  • 6.Structural Analysis of the Nuclear Pore Complex by Cryo-ET / Asaf Mader / Nadav Elad / Ohad Medalia
  • 7.Concluding Remarks / Asaf Mader / Nadav Elad / Ohad Medalia
  • Acknowledgments / Asaf Mader / Nadav Elad / Ohad Medalia
  • References / Asaf Mader / Nadav Elad / Ohad Medalia
  • 1.Introduction / Jun Liu / Elizabeth R. Wright / Hanspeter Winkler
  • 2.Cryoelectron Tomography / Jun Liu / Elizabeth R. Wright / Hanspeter Winkler
  • 3.3D Visualization of Intact HIV Virion / Jun Liu / Elizabeth R. Wright / Hanspeter Winkler
  • 4.Conclusions and Perspective / Jun Liu / Elizabeth R. Wright / Hanspeter Winkler
  • Acknowledgments / Jun Liu / Elizabeth R. Wright / Hanspeter Winkler
  • References / Jun Liu / Elizabeth R. Wright / Hanspeter Winkler
  • 1.Introduction / Dmitry Lyumkis / Arne Moeller / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher
  • 2.Specimen Preparation / Dmitry Lyumkis / Arne Moeller / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher
  • 3.Autoloading and Robotic Screening / Dmitry Lyumkis / Arne Moeller / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher
  • 4.Microscopy / Dmitry Lyumkis / Arne Moeller / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L.
  • Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher
  • 5.Image Processing / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher / Dmitry Lyumkis / Arne Moeller
  • 6.Assessment and Integration / Dmitry Lyumkis / Arne Moeller / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher
  • 7.The Future of Automation / Dmitry Lyumkis / Arne Moeller / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher
  • Acknowledgments / Dmitry Lyumkis / Arne Moeller / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher
  • References / Arne Moeller / Dmitry Lyumkis / Bridget Carragher / Clinton S. Potter / Neil R. Voss / Joel D. Quispe / James Pulokas / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / Anchi Cheng.