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This book describes hydration structures of proteins by combining
experimental results with theoretical considerations. It is
designed to introduce graduate students and researchers to
microscopic views of the interactions between water and biological
macromolecules and to provide them with an overview of the field.
Topics on protein hydration from the past 25 years are examined,
most of which involve crystallography, fluorescence measurements,
and molecular dynamics simulations. In X-ray crystallography and
molecular dynamics simulations, recent advances have accelerated
the study of hydration structures over the entire surface of
proteins. Experimentally, crystal structure analysis at cryogenic
temperatures is advantageous in terms of visualizing the positions
of hydration water molecules on the surfaces of proteins in their
frozen-hydrated crystals. A set of massive data regarding hydration
sites on protein surfaces provides an appropriate basis, enabling
us to identify statistically significant trends in geometrical
characteristics. Trajectories obtained from molecular dynamics
simulations illustrate the motion of water molecules in the
vicinity of protein surfaces at sufficiently high spatial and
temporal resolution to study the influences of hydration on protein
motion. Together with the results and implications of these
studies, the physical principles of the measurement and simulation
of protein hydration are briefly summarized at an undergraduate
level. Further, the author presents recent results from statistical
approaches to characterizing hydrogen-bond geometry in local
hydration structures of proteins. The book equips readers to better
understand the structures and modes of interaction at the interface
between water and proteins. Referred to as "hydration structures",
they are the subject of much discussion, as they may help to answer
the question of why water is indispensable for life at the
molecular and atomic level.
In this book, the author describes the development of the
experimental diffraction setup and structural analysis of
non-crystalline particles from material science and biology. Recent
advances in X-ray free electron laser (XFEL)-coherent X-ray
diffraction imaging (CXDI) experiments allow for the structural
analysis of non-crystalline particles to a resolution of 7 nm, and
to a resolution of 20 nm for biological materials. Now XFEL-CXDI
marks the dawn of a new era in structural analys of non-crystalline
particles with dimensions larger than 100 nm, which was quite
impossible in the 20th century. To conduct CXDI experiments in both
synchrotron and XFEL facilities, the author has developed
apparatuses, named KOTOBUKI-1 and TAKASAGO-6 for cryogenic
diffraction experiments on frozen-hydrated non-crystalline
particles at around 66 K. At the synchrotron facility, cryogenic
diffraction experiments dramatically reduce radiation damage of
specimen particles and allow tomography CXDI experiments. In
addition, in XFEL experiments, non-crystalline particles scattered
on thin support membranes and flash-cooled can be used to
efficiently increase the rate of XFEL pulses. The rate, which
depends on the number density of scattered particles and the size
of X-ray beams, is currently 20-90%, probably the world record in
XFEL-CXDI experiments. The experiment setups and results are
introduced in this book. The author has also developed software
suitable for efficiently processing of diffraction patterns and
retrieving electron density maps of specimen particles based on the
diffraction theory used in CXDI.
In this book, the author describes the development of the
experimental diffraction setup and structural analysis of
non-crystalline particles from material science and biology. Recent
advances in X-ray free electron laser (XFEL)-coherent X-ray
diffraction imaging (CXDI) experiments allow for the structural
analysis of non-crystalline particles to a resolution of 7 nm, and
to a resolution of 20 nm for biological materials. Now XFEL-CXDI
marks the dawn of a new era in structural analys of non-crystalline
particles with dimensions larger than 100 nm, which was quite
impossible in the 20th century. To conduct CXDI experiments in both
synchrotron and XFEL facilities, the author has developed
apparatuses, named KOTOBUKI-1 and TAKASAGO-6 for cryogenic
diffraction experiments on frozen-hydrated non-crystalline
particles at around 66 K. At the synchrotron facility, cryogenic
diffraction experiments dramatically reduce radiation damage of
specimen particles and allow tomography CXDI experiments. In
addition, in XFEL experiments, non-crystalline particles scattered
on thin support membranes and flash-cooled can be used to
efficiently increase the rate of XFEL pulses. The rate, which
depends on the number density of scattered particles and the size
of X-ray beams, is currently 20-90%, probably the world record in
XFEL-CXDI experiments. The experiment setups and results are
introduced in this book. The author has also developed software
suitable for efficiently processing of diffraction patterns and
retrieving electron density maps of specimen particles based on the
diffraction theory used in CXDI.
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