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E-book
Author Frank, Joachim.

Title NOVEL DEVELOPMENTS IN CRYO-EM OF BIOLOGICAL MOLECULES resolution in time and state space
Published [S.l.] : JENNY STANFORD PUB, 2023

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Description 1 online resource
Contents Cover -- Half Title -- Title Page -- Copyright Page -- Table of Contents -- Preface -- Acknowledgments -- Part I: Single-Particle Cryo-EM of Molecules in Thermal Equilibrium -- Chapter 1: Generalized Single-Particle Cryo-EM: A Historical Perspective -- Chapter 2: Advances in the Field of Single-Particle Cryo-Electron Microscopy Over the Last Decade -- 2.1: Improving the Resolution of Asymmetric Structures -- 2.2: The Development of Higher-Throughput Methodology -- 2.3: Looking to the Future -- Chapter 3: Single-Particle Reconstruction of Biological Molecules: Story in a Sample (Nobel Lecture)
3.1: The Background -- 3.2: Graduate Studies and Harkness Fellowship -- 3.3: Postdoctoral Work at the Cavendish Lab: The Concept of Single-Particle Averaging and Reconstruct -- 3.4: Move to the Wadsworth Center: From Concept to Practice -- 3.5: Determination of Angles and Three-Dimensional Reconstruction -- 3.6: Move to Columbia University: Story in a Sample -- 3.7: Conclusions -- Part II: Machine Learning Applied to Ensembles of Molecules in Thermal Equilibrium: Resolution in State Space -- Chapter 4: Structural Characterization of mRNA-tRNA Translocation Intermediates -- 4.1: Results
4.1.1: Summary of Reconstructions -- 4.1.2: Progression of Ribosomal Dynamics and tRNA Movements -- 4.1.3: Quantification of Conformational Changes -- 4.1.4: Coordination of the Dynamics Between the Ribosome and the tRNAs -- 4.1.5: Translating Relative Occupancies of the PRE States into Free-Energy Differences -- 4.2: Discussion -- 4.3: Materials and Methods -- 4.3.1: Image Processing -- 4.3.2: Fitting of Crystallographic Structures into Electron Microscopy Densities -- Chapter 5: Trajectories of the Ribosome as a Brownian Nanomachine -- 5.1: Conceptual Outline -- 5.2: Analytical Procedure
5.3: Results -- 5.4: Discussion -- 5.5: Conclusions -- Chapter 6: Continuous Changes in Structure Mapped by Manifold Embedding of Single-Particle Data in Cryo-EM -- 6.1: Introduction -- 6.2: Mapping of Heterogeneity by Manifold Embedding -- 6.3: Results Obtained for the Ribosome -- 6.4: Conclusions: Implications for Future Studies of Biological Macromolecules -- Chapter 7: New Opportunities Created by Single-Particle Cryo-EM: The Mapping of Conformational Space -- Chapter 8: POLARIS: Path of Least Action Analysis on Energy Landscapes -- 8.1: Introduction -- 8.2: Methods
8.2.1: Image Segmentation -- 8.2.2: Permutational Analysis -- 8.2.3: Branching Recursion -- 8.2.4: Pathway Pruning -- 8.3: Results -- 8.3.1: Comparison of Results from POLARIS and MEPSA -- 8.4: Discussion -- 8.4.1: Completeness -- 8.4.2: Accuracy -- 8.4.3: Complexity -- Chapter 9: Propagation of Conformational Coordinates Across Angular Space in Mapping the Continuum of States from Cryo-EM Data by Manifold Embedding -- 9.1: Introduction -- 9.2: Methods -- 9.2.1: Overall Approach -- 9.2.2: Formulating the Selection of Conformational Coordinate as an Optimization Problem
Summary Cryo-EM, as it is currently practiced in many laboratories, is limited to the visualization of molecules that are in thermal equilibrium at the time before freezing. A further limitation is that the existing software does not fully exploit the information that is contained in the images of large ensembles of molecules in thermal equilibrium. This book is a collection of recent articles by the author, reprinted with introductions, and they mainly describe two novel methods in cryo-EM, one computational and the other experimental that requires the use of a microfluidic device. Both methods have the capacity to shed light on the dynamic behavior of biomolecules. Combined, they greatly expand the range of applications of cryo-EM. The book describes a successful approach in which, based on cryo-EM data, all states visited by the molecule in thermal equilibrium are mapped by manifold embedding--a method of geometric machine learning--and the energy landscape of the molecule is derived. It also discusses methods and biological results of time-resolved cryo-EM, following a reaction in a non-equilibrium system over a short period of time and resulting in the capture of short-lived states that have been inaccessible by standard methods of cryo-EM
Notes Joachim Frank is a professor of biochemistry and molecular biophysics and of biological sciences at Columbia University, USA. Dr. Frank's lab has developed techniques of single-particle reconstruction of biological macromolecules, specializing in mathematical and computational approaches. He has applied these techniques of visualization to explore the structure and dynamics of the ribosomes during the process of protein synthesis and to elucidate the structure and function of several ion channels. He is a member of the National Academy of Sciences and of the American Academy of Microbiology. He is also a fellow of the American Academy of Arts and Sciences and of the American Association for the Advancement of Science. In 2014, he was honored with the Franklin Medal for Life Sciences. In 2017, he shared the Wiley Prize in Biomedical Sciences with Richard Henderson and Marin van Heel. He was awarded the 2017 Nobel Prize in Chemistry together with Jacques Dubochet and Richard Henderson for "developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution."
Subject Proteins -- Structure
Genomics.
Electron microscopy -- Technique.
SCIENCE / Life Sciences / Biology / General
SCIENCE / Life Sciences / Biophysics
Electron microscopy -- Technique.
Genomics.
Proteins -- Structure.
Form Electronic book
ISBN 9781000989441
1000989445
9781003456100
1003456103
9781000989489
1000989488