Joachim Frank - Böcker

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.

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.

Electron tomography has become a standard technique with applications in cell biology, structural biology, and materials science. This definitive work provides a comprehensive treatment of the mathematical background and working methods of three-dimensional reconstruction from tilt series, with special emphasis on the problems presented by limitations of data collection in the transmission electron microscope. In addition to chapters that are applicable to 3D reconstruction in all fields of science, such as radiological imaging in medicine and electron tomography in materials science, Electron Tomography also focuses on specimen preparation and imaging unique to biological electron microscopy. This extensively revised second edition updates key contributions on the mathematics of 3D reconstruction, and includes new topics such as automated tomography, frozen sectioning of cells, and the interpretation of density maps through methods of fitting, docking, denoising, and segmentation. Each chapter is a self-contained treatise by a world expert in the author's field of research, resulting in an indispensable resource and companion for laboratories that practice electron tomography or seek to implement electron tomography as a tool for visualization of cells and cell components. Key FeaturesPresents the mathematical background and working methods for three-dimensional reconstruction from projections Takes the reader from biological specimen preparation to three-dimensional images of the cell and its components Revised and updated extensively from the first edition published in 1992 The definitive work in the field written by leading international experts

The concept of molecular machines in biology has transformed the medical field in a profound way. Many essential processes that occur in the cell, including transcription, translation, protein folding and protein degradation, are all carried out by molecular machines. This volume focuses on important molecular machines whose architecture is known and whose functional principles have been established by tools of biophysical imaging (X-ray crystallography and cryo-electron microscopy) and fluorescence probing (single-molecule FRET). This edited volume includes contributions from prominent scientists and researchers who understand and have explored the structure and functions of these machines. This book is essential for students and professionals in the medical field who want to learn more about molecular machines.

Electron tomography has become a standard technique with applications in cell biology, structural biology, and materials science. This definitive work provides a comprehensive treatment of the mathematical background and working methods of three-dimensional reconstruction from tilt series, with special emphasis on the problems presented by limitations of data collection in the transmission electron microscope. In addition to chapters that are applicable to 3D reconstruction in all fields of science, such as radiological imaging in medicine and electron tomography in materials science, Electron Tomography also focuses on specimen preparation and imaging unique to biological electron microscopy. This extensively revised second edition updates key contributions on the mathematics of 3D reconstruction, and includes new topics such as automated tomography, frozen sectioning of cells, and the interpretation of density maps through methods of fitting, docking, denoising, and segmentation. Each chapter is a self-contained treatise by a world expert in the author's field of research, resulting in an indispensable resource and companion for laboratories that practice electron tomography or seek to implement electron tomography as a tool for visualization of cells and cell components. Key FeaturesPresents the mathematical background and working methods for three-dimensional reconstruction from projections Takes the reader from biological specimen preparation to three-dimensional images of the cell and its components Revised and updated extensively from the first edition published in 1992 The definitive work in the field written by leading international experts

Computational Methods for Three-Dimensional Microscopy Reconstruction

Approaches to the recovery of three-dimensional information on a biological object, which are often formulated or implemented initially in an intuitive way, are concisely described here based on physical models of the object and the image-formation process. Both three-dimensional electron microscopy and X-ray tomography can be captured in the same mathematical framework, leading to closely-related computational approaches, but the methodologies differ in detail and hence pose different challenges. The editors of this volume, Gabor T. Herman and Joachim Frank, are experts in the respective methodologies and present research at the forefront of biological imaging and structural biology.Computational Methods for Three-Dimensional Microscopy Reconstruction will serve as a useful resource for scholars interested in the development of computational methods for structural biology and cell biology, particularly in the area of 3D imaging and modeling.

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.

The aim of this book is to make available, to students and experts, a compendium of important articles covering (1) the development of single-article reconstruction techniques, and (2) the progress in the exploration of structural basis of translation in bacteria and eukaryotes by cryo-EM and single-particle reconstruction.For novice and expert alike, a good overview of the development of tools and the ensuing discoveries spanning almost half a century has been lacking. Review articles attempting such an endeavor normally a very limited scope. The purpose of this book is to give the reader access to a selection of original articles spanning this period, from which he or she can form his or her opinion, the introductory text serving as a guide.There is no competing book. The author has made pioneering contributions both in the development of the technique, which is now on the verge of attaining atomic resolution, and to the exploration of ribosome structure and function.Selected reprints of key papers in the development of single-particle reconstruction methods, and in the research of ribosome structure and dynamics making use of these new methods. The reprints cover the period of 1969-2013.

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.