This book introduces recent progress in biological energetics from ATP hydrolysis to molecular machineries. The role of water is now recognized to be essential in biological molecular energetics. Although energetics is a rather distant field to many biologists, any working models for protein machineries such as protein motors, transporters, and other enzymes must be consistent with their energetics. Therefore, the book is intended to help scientists build systematic models of biomolecular functions based on three categories: (1) ATP hydrolysis reactions including ionic hydration and protonation–deprotonation of biomolecules, (2) protein–ligand/protein–protein interactions including hydration–dehydration processes, and (3) functioning mechanisms of protein machineries based on water functions.

This book presents a new view of the mechanism of functional expression of ATP-driven motors (proteins or protein complexes). It is substantially different from the prevailing idea that the motor converts chemical energy to mechanical work. To facilitate understanding, the differences between the new and prevailing views are explained using many illustrations. The book is of interest to those who are not convinced of the notion of chemo–mechanical coupling. The claims presented are the following: The system, which comprises not only the motor but also water, does no mechanical work during the ATP hydrolysis cycle; a protein is moved or a protein in the complex is rotated by the entropic force generated by water. The highlight of the explanation in the book is that the mechanism of unidirectional rotation of the central shaft in F1-ATPase is discussed in detail on the basis of this new view. The hydration entropy of each β subunit to which a specific chemical compound (ATP, ADP and Pi, Pi, or nothing) is bound, the hydration entropy of the α3β3 complex, and the dependence of the hydration entropy of F1-ATPase on the orientation of the γ subunit play essential roles.

This Special Issue of IJMS covers a broad range of cutting-edge aspects related to the organization, function, and role in disease of the actin cytoskeleton. This cellular structure is of fundamental importance for the homeostasis of every eukaryotic cell, from the simplest unicellular organism to the most complex animal cell. The actin cytoskeleton contributes to developing and maintaining cell shape and tissue integrity and is crucial for cell migration, movement of organelles, vesicle trafficking, and the completion of cell division. Elaborate structures like the sarcomere, the inner ear cell stereocilia, and the brush border microvilli are built on actin filament scaffolds. Dozens of actin-binding proteins orchestrate the dynamic remodeling of the actin cytoskeleton and integrate it with microtubules and intermediate filaments and with the cell signaling machinery. Playing such fundamental roles in a plethora of cellular processes, it comes as no surprise that defects in actin and associated proteins have been found to be implicated in pathological conditions as diverse as myopathies and neurodegenerative diseases. This Special Issue gathers 15 contributions highlighting the impressive advances made in recent years in this exciting field.

Neutron Crystallography in Structural Biology, Volume 634, the latest volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Chapters in this updated release include Fundamentals of neutron crystallography in structural biology, Large crystal growth for neutron protein crystallography, Prospects for membrane protein crystals in NMX, IMAGINE: The neutron protein crystallography beamline at the high flux isotope reactor, The macromolecular neutron diffractometer at the spallation neutron source, Current status and near future plan of neutron protein crystallography at J-PARC, Neutron macromolecular crystallography at the European spallation source, and much more. - Provides the authority and expertise of leading contributors from an international board of authors - Presents the latest release in the Methods in Enzymology series - Includes the latest information on neutron crystallography in structural biology

A Top 25 CHOICE 2016 Title, and recipient of the CHOICE Outstanding Academic Title (OAT) Award. How much energy is released in ATP hydrolysis? How many mRNAs are in a cell? How genetically similar are two random people? What is faster, transcription or translation?Cell Biology by the Numbers explores these questions and dozens of others provid

This book sheds light on the molecular aspects of liquids and liquid-based materials such as organic or inorganic liquids, ionic liquids, proteins, biomaterials, and soft materials including gels. The reader discovers how the molecular basics of such systems are connected with their properties, dynamics, and functions. Once the use and application of liquids and liquid-based materials are understood, the book becomes a source of the latest, detailed knowledge of their structures, dynamics, and functions emerging from molecularity. The systems discussed in the book have structural dimensions varying from nanometers to millimeters, thus the precise estimation of structures and dynamics from experimental, theoretical, and simulation methods is of crucial importance. Outlines of the practical knowledge needed in research and development are helpfully included in the book.

This book covers recent advances of the fragment molecular orbital (FMO) method, consisting of 5 parts and a total of 30 chapters written by FMO experts. The FMO method is a promising way to calculate large-scale molecular systems such as proteins in a quantum mechanical framework. The highly efficient parallelism deserves being considered the principal advantage of FMO calculations. Additionally, the FMO method can be employed as an analysis tool by using the inter-fragment (pairwise) interaction energies, among others, and this feature has been utilized well in biophysical and pharmaceutical chemistry. In recent years, the methodological developments of FMO have been remarkable, and both reliability and applicability have been enhanced, in particular, for non-bio problems. The current trend of the parallel computing facility is of the many-core type, and adaptation to modern computer environments has been explored as well. In this book, a historical review of FMO and comparison to other methods are provided in Part I (two chapters) and major FMO programs (GAMESS-US, ABINIT-MP, PAICS and OpenFMO) are described in Part II (four chapters). dedicated to pharmaceutical activities (twelve chapters). A variety of new applications with methodological breakthroughs are introduced in Part IV (six chapters). Finally, computer and information science-oriented topics including massively parallel computation and machine learning are addressed in Part V (six chapters). Many color figures and illustrations are included. Readers can refer to this book in its entirety as a practical textbook of the FMO method or read only the chapters of greatest interest to them.

This special issue of Molecular and Cellular Biochemistry good source of information in this regard. contains original research papers as well as invited reviews We wish to thank all of the contributors for their help and dedicated, on the occasion of the 40th anniversary of the in cooperation. We also wish to thank Mrs. Verona Kuhle for auguration of the Heart Research Group in Beriin-Buch that her secretarial help. We are grateful to Dr. Naranjan S. Dhalla, today forms a part there ofthe Max Delbriick Center for Mo Editor-in-Chief of Molecular and Cellular Biochemistry for his lecular Medicine, to Professor Albert Wollenberger, founder interest and encouragement, and for agreeing to publish this of the Heart Research Group and for 21 years its head. issue in honor of Albert Wollenberger. The papers in this issue are written by researchers work ing in the field of cardiovascular research who together with ERNST-GEORG KRAUSE and ROLAND VETTER Albert Wollenberger share the belief that an integrative ap Max Delbriick Center for Molecular Medicine plication of advances in molecular and cellular biology will Robert-Rossle-StraBe 10 lead to new concepts for treatment and prevention of cardio 13122 Beriin-Buch vascular diseases. We hope that this special will serve as a Gennany ALBERT WOLLENBERGER, Professor, Ph. D. (Harvard), Dr. Sc. Med. (Berlin) The dedication is accorded to Prof.

The ultra-bright femtosecond X-ray pulses provided by X-ray free electron lasers (XFELs) open up opportunities to study the structure and dynamics of a wide variety of systems beyond what is possible with synchrotron sources. This book introduces the principles and properties of currently operating and future XFELs, before outlining applications in materials science, chemistry and biology. Edited by pioneers in this exciting field, and featuring contributions from leading researchers, this book is ideal for researchers working with XFELs, synchrotron radiation, ultrafast and femtosecond crystallography and femtosecond spectroscopy.