Cryo-Electron Microscopy in Structural Biology

Krishnarao Appasani trained as a molecular cell biologist, earning Masters and Doctoral degrees in Biochemistry and Molecular biology. He accepted a Lectureship at Boston University and taught cell and molecular biology courses to undergraduates and graduate students. He was a post-doc in the laboratory of Nobel Laureate, the late Prof. H. Gobind Khorana at the Massachusetts Institute of Technology. Subsequently, he joined the faculty of Harvard Medical School and directed the Thoracic Oncology Laboratory at the Brigham &Women’s Hospital and the Dana-Farber Cancer Institute in Boston. During this time he completed an MBA at Bryant University, Smithfield, RI, and then moved to Perkin Elmer and directed the Microarrays group. Dr Appasani has published about 60 research papers and abstracts in international journals, especially on Gene Expression. He was awarded the Outstanding Investigator Award by the American Federation for Medical Research, Washington D.C., competed globally for the Ranbaxy Research Medal, and was honored with the 1997-Ranbaxy Research Award in the field of Applied Medical Sciences. At Perkin Elmer, Dr Appasani organized a global Biomics Seminar series to educate scientists and to initiate and develop collaborations with researchers in academia and other industries. For about 15 years he ran a multi-million-dollar knowledge management enterprise and served as an international authority in bridging Academia and Industry by fostering inter-disciplinary and translational science. In 2016 Dr Appasani was inducted as a Life Fellow of the Royal Society of Biology, England, for his global efforts in promoting science education.

Editor

List of contributors

Foreword

Preface

SECTION I Cryo-EM in Cell Biology: Structure Determination of Protein Assemblies and Cellular Organelle

Chapter 1 Introduction on Cryogenic Electron Microscopy in Structural Biology

Krishnarao Appasani

Chapter 2 Structural Dynamics of Proteasome Regulation by Cryo-EM

Youdong Mao

Chapter 3 Cryo-EM Structures of a Ubiquitin-Specific Protease in Complex with Substrate

Martin Rennie

Chapter 4 Structural Biology of Protein Kinases and Their Regulation

Samrat Mitra, Pranita Ray, Prateeka Borar, and Smarajit Polley

Chapter 5 The Life and Times of p53: Structural Advancements to Decipher the Guardian of the Genome

Maria J. Solares, Samantha Berry, and Deborah F. Kelly

SECTION II Technology Platform and Evolving Technologies

Chapter 6 Single-Particle Cryo-EM: What Happens Inside the Black Box?

Sayan Bhakta and Marin van Heel

Chapter 7 Streptavidin Affinity Grids in the Study of Macromolecular Complexes Using Cryo-Electron Microscopy

Nils Marechal and Patrick Schultz

Chapter 8 Running a Cost-Effective Modern Cryo-EM Facility for SPA Analysis

Lijia Jia

Chapter 9 Computational Methods for Bimolecular Structure Modeling for Cryo-EM

Javad Baghirov, Xiao Wang, Genki Terashi, Shu Li, and Daisuke Kihara

Chapter 10 Artificial Intelligence-Driven Data Acquisition for Single-Particle Cryo-EM and Three-Dimensional Electron Diffraction

Koji Yonekura

Chapter 11 From Icy Specimens to Digital Insights: Integrating Sample Preparation, Data Analysis, and IT Infrastructure

Eric Shell, Karine Minari, and Vitor Hugo Balasco Serrão

SECTION III Cryo-EM in Virology and Enzymology: High-Resolution Structures of Chaperonins and Enzymes

Chapter 12 Cryo-EM Structures of Viral and Bacterial Chaperonins

Olga S. Sokolova and Tatiana B. Stanishneva-Konovalova

Chapter 13 Cryo-EM Structure of Monkeypox Virus DNA Polymerase Holoenzyme

Yi Shi and George F Gao

Chapter 14 Determining the High-Resolution Structure of the [NiFe]-hydrogenase Huc by Native Host Purification and Cryo-EM

Hari Venugopal, Ashleigh Kropp, Chris Greening, and Rhys Grinter

Chapter 15 Membrane Rupture and Lipid–Protein Interaction of γ-Hemolysin from Staphylococcus aureus Using Cryo-EM

Suman Mishra, Anupam Roy, Arnab Chatterjee, and Somnath Dutta

SECTION IV Cryo-EM in the Study of Membrane Biology: Probing the Structures of Membrane Proteins

Chapter 16 Historical Evolution and Perspective on Cryo-EM Analysis of Membrane Proteins

Youzhong Guo

Chapter 17 Single-Particle Cryogenic Electron Microscopy Unfolds Distinct Membrane Transporter

Folds: Focus on Autoinducer-2 Exporter Family

Radhika Khera

Chapter 18 Rhodopsin Dimers in the Retinal Rod Outer Segment

Sahil Gulati and Krzysztof Palczewski

Chapter 19 Cryo-EM Structures of the Fungal GPCR Dimer Ste2

Vaithish Velazhahan and Christopher G. Tate

Chapter 20 Human V-ATPases: Assembly, Function, and Regulation

Elizabeth Fosuah, Qingpeng Lin, and Tian-Min Fu

Chapter 21 Structure and Function of the Intracellular Calcium Channel Ryanodine Receptor

Marco C. Miotto

Chapter 22 Cryo-EM of Mitochondrial Membrane Proteins

Swati Yadav, Shaileshanand Jha, and Kutti R. Vinothkumar

SECTION V Cryo-EM in the Study of Molecular Biology: Structural Insights of Gene Machineries

Chapter 23 Imaging Structurally Dynamic Ribosomes with Cryogenic Electron Microscopy

Samantha M. Webster, Mira B. May, Barrett M. Powell, and Joseph H. Davis

Chapter 24 Cryo-EM in the Study of Ribosome Biogenesis

Ankita Arora and Prem S. Kaushal

Chapter 25 Cryo-EM Structures of Ribosomes from Human Pathogens: Implications for Drug Targeting

Ankit Dhur, Aneek Banerjee, Krishnamoorthi Srinivasan, and Jayati Sengupta

SECTION VI Cryo-EM in the Study of Neurobiology and Skin—Neuroreceptors to Ion Channels and Synaptic Transmission

Chapter 26 Cryo-EM Structural Features of Glutamate Receptors Involved in Synaptic Neurotransmission or Brain Pathology

Nebojša Bogdanović

Chapter 27 Cryo-EM Structures of Systemic Amyloid Fibrils

Binh An Nguyen, Maria del Carmen Fernandez-Ramirez, Shumaila Afrin, and Lorena Saelices

Chapter 28 Structural Insights into the 5-HT3A Receptor Revealed by Cryogenic Electron Microscopy (Cryo-EM)

Zhuowen Li, Nikhil Bharambe, and Sandip Basak

Chapter 29 Molecular Cryo-EM in the Study of Skin Tissue

Lars Norlén

SECTION VII Applications of Cryo-ET and Cryo-EM in the Biopharmaceutical Industry

Chapter 30 Emerging Technologies in Cryo-Electron Tomography

Kanika Khanna

Chapter 31 Cryo-Electron Tomographic Imaging of Membrane Proteins from Mitochondria and Chloroplasts

Tofayel Ahmed and Antara Saha

Chapter 32 Functional Studies of the Actin Cytoskeleton by Cryogenic Electron Tomography

Dorit Hanein and Niels Volkmann

Chapter 33 Cryo-EM in Drug Discovery

Youxin Kong, Maxime Killer, Madhumati Sevvana, and Chiara Rapisarda

Chapter 34 Applications of Single-Particle Analysis and Cryo-ET in Drug Discovery

Qing Yao

Index