The Role Of Water In Atp Hydrolysis Energy Transduction By Protein Machinery

Author : Makoto Suzuki
Publisher : Springer
Page : 353 pages
File Size : 43,7 Mb
Release : 2018-05-07
Category : Science
ISBN : 9789811084591

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The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery by Makoto Suzuki Pdf

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.

Author : Makoto Suzuki
Publisher : Unknown
Page : 128 pages
File Size : 47,9 Mb
Release : 2018
Category : Adenosine triphosphate
ISBN : 9811084602

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The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery by Makoto Suzuki Pdf

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.

Author : Masahiro Kinoshita
Publisher : Springer Nature
Page : 87 pages
File Size : 52,6 Mb
Release : 2020-12-30
Category : Science
ISBN : 9789813362321

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Mechanism of Functional Expression of F1-ATPase by Masahiro Kinoshita Pdf

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.

Author : Francisco Rivero
Publisher : MDPI
Page : 274 pages
File Size : 55,5 Mb
Release : 2020-12-02
Category : Science
ISBN : 9783039365654

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Frontiers in the Actin Cytoskeleton by Francisco Rivero Pdf

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.

Author : Anonim
Publisher : Academic Press
Page : 410 pages
File Size : 48,6 Mb
Release : 2020-02-22
Category : Science
ISBN : 9780128192153

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Neutron Crystallography in Structural Biology by Anonim Pdf

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

Author : Bruce Alberts
Publisher : Unknown
Page : 0 pages
File Size : 46,5 Mb
Release : 2002
Category : Cytology
ISBN : 0815332181

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Molecular Biology of The Cell by Bruce Alberts Pdf

Author : Katsura Nishiyama,Tsuyoshi Yamaguchi,Toshiyuki Takamuku,Norio Yoshida
Publisher : Springer Nature
Page : 469 pages
File Size : 45,8 Mb
Release : 2022-01-03
Category : Science
ISBN : 9789811653957

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Molecular Basics of Liquids and Liquid-Based Materials by Katsura Nishiyama,Tsuyoshi Yamaguchi,Toshiyuki Takamuku,Norio Yoshida Pdf

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.

Author : Ron Milo,Rob Phillips
Publisher : Garland Science
Page : 400 pages
File Size : 50,7 Mb
Release : 2015-12-07
Category : Science
ISBN : 9781317230694

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Cell Biology by the Numbers by Ron Milo,Rob Phillips Pdf

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

Author : Yuji Mochizuki,Shigenori Tanaka,Kaori Fukuzawa
Publisher : Springer Nature
Page : 606 pages
File Size : 54,5 Mb
Release : 2021-01-04
Category : Science
ISBN : 9789811592355

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Recent Advances of the Fragment Molecular Orbital Method by Yuji Mochizuki,Shigenori Tanaka,Kaori Fukuzawa Pdf

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.

Author : Ernst-Georg Krause,Roland Vetter
Publisher : Springer Science & Business Media
Page : 313 pages
File Size : 45,7 Mb
Release : 2012-12-06
Category : Science
ISBN : 9781461312796

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Biochemical Mechanisms in Heart Function by Ernst-Georg Krause,Roland Vetter Pdf

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.

Author : Robert A. Alberty
Publisher : John Wiley & Sons
Page : 482 pages
File Size : 48,6 Mb
Release : 2006-03-31
Category : Science
ISBN : 9780470036457

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Biochemical Thermodynamics by Robert A. Alberty Pdf

Navigate the complexities of biochemical thermodynamics with Mathematica(r) Chemical reactions are studied under the constraints of constant temperature and constant pressure; biochemical reactions are studied under the additional constraints of pH and, perhaps, pMg or free concentrations of other metal ions. As more intensive variables are specified, more thermodynamic properties of a system are defined, and the equations that represent thermodynamic properties as a function of independent variables become more complicated. This sequel to Robert Alberty's popular Thermodynamics of Biochemical Reactions describes how researchers will find Mathematica(r) a simple and elegant tool, which makes it possible to perform complex calculations that would previously have been impractical. Biochemical Thermodynamics: Applications of Mathematica(r) provides a comprehensive and rigorous treatment of biochemical thermodynamics using Mathematica(r) to practically resolve thermodynamic issues. Topics covered include: * Thermodynamics of the dissociation of weak acids * Apparent equilibrium constants * Biochemical reactions at specified temperatures and various pHs * Uses of matrices in biochemical thermodynamics * Oxidoreductase, transferase, hydrolase, and lyase reactions * Reactions at 298.15K * Thermodynamics of the binding of ligands by proteins * Calorimetry of biochemical reactions Because Mathematica(r) allows the intermingling of text and calculations, this book has been written in Mathematica(r) and includes a CD-ROM containing the entire book along with macros that help scientists and engineers solve their particular problems.

Author : Uwe Bergmann,Vittal Yachandra,Junko Yano
Publisher : Royal Society of Chemistry
Page : 490 pages
File Size : 53,6 Mb
Release : 2017-08-11
Category : Science
ISBN : 9781788012027

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X-Ray Free Electron Lasers by Uwe Bergmann,Vittal Yachandra,Junko Yano Pdf

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.

Author : Byung Hong Kim,Geoffrey Michael Gadd
Publisher : Cambridge University Press
Page : 509 pages
File Size : 53,6 Mb
Release : 2019-05-16
Category : Medical
ISBN : 9781107171732

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Prokaryotic Metabolism and Physiology by Byung Hong Kim,Geoffrey Michael Gadd Pdf

Extensive and up-to-date review of key metabolic processes in bacteria and archaea and how metabolism is regulated under various conditions.

Author : J. Robin Harris,Jon Marles-Wright
Publisher : Springer Nature
Page : 580 pages
File Size : 41,9 Mb
Release : 2020-11-30
Category : Science
ISBN : 9783030589714

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Macromolecular Protein Complexes III: Structure and Function by J. Robin Harris,Jon Marles-Wright Pdf

This book covers important topics such as the dynamic structure and function of the 26S proteasome, the DNA replication machine: structure and dynamic function and the structural organization and protein–protein interactions in the human adenovirus capsid, to mention but a few. The 18 chapters included here, written by experts in their specific field, are at the forefront of scientific knowledge. The impressive integration of structural data from X-ray crystallography with that from cryo-electron microscopy is apparent throughout the book. In addition, functional aspects are also given a high priority. Chapter 1 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Author : Dominik Marx,Jürg Hutter
Publisher : Cambridge University Press
Page : 503 pages
File Size : 45,7 Mb
Release : 2009-04-30
Category : Science
ISBN : 9781139477192

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Ab Initio Molecular Dynamics by Dominik Marx,Jürg Hutter Pdf

Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car–Parrinello approach, correcting various misconceptions currently found in research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages and enabling developers to improve and add new features in their code.