Hydration Structures of Proteins
Description
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.
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Person
Masayoshi Nakasako is a professor at Keio University, and his work involves structural analysis of soft matter. He received his Doctor of Science from Tohoku University in 1990. After his doctoral program, he was a research associate at the Faculty of Pharmaceutical Sciences, The University of Tokyo; a researcher at RIKEN; a lecturer at the Institute of Molecular and Cellular Biosciences, The University of Tokyo; and an assistant professor at Keio University in 2002. In 2005, he was promoted to his present position. Currently, he also serves Spring-8 Center, RIKEN, as a guest researcher.
His research interest is in imaging of protein hydration, protein structures, and cells by various physicochemical experimental techniques including X-ray imaging using synchrotron radiation and X-ray free electron laser and molecular dynamics simulations.
Content
1. Introduction
1.1 Water: the cradle of life
1.2 Structure and interaction of water molecules
1.2.1 Structure of water molecules
1.2.2 Interactions between water molecules
1.2.3 Hydrogen bond between water molecules
1.3 Phase diagram of water
1.3.1 Three phases of water
1.3.2 Hexagonal ice and amorphous ice
1.4 Properties of liquid water1.4.1 Unusual physical properties
1.4.2 Brownian motion in liquid water
1.4.3 Structure of liquid water
1.5 Hydration
1.5.1 Solvation
1.5.2 Hydration
1.5.3 Hydration of hydrophobic molecules
1.6 Hydration structures of proteins
1.6.1 Proteins
1.6.2 Hydration structures of proteins
1.7 Scope of this monograph
References
2. Biophysical methods to visualize hydration structures of proteins
2.1 Introduction
2.2 X-ray crystallography at cryogenic temperatures
2.2.1 Outline
2.2.2 Crystallographic structure refinement
2.2.3 Difference Fourier map
2.2.4 X-ray crystallography at cryogenic temperatures
2.3 Cryogenic electron microscopy
2.3.1 Outline2.3.2 Specimen preparation and image collection
2.3.3 Image processing and single-particle analysis
2.4 Time-resolved fluorescence measurement2.4.1 Outline
2.4.2 Up-conversion method
2.5 Molecular dynamic simulation2.5.1 Outline
2.5.2 Force field
References
3. Hydration structures inside proteins
3.1 Introduction
3.2 Water molecules inside proteins
3.2.1 Tightly-bound water molecules3.2.2 Water molecules confined inside proteins
3.3 Hydration water molecules as glue in protein complexes
3.3.1 Hydration at the subunit interface of a protein complex
3.3.2 Hydration sites conserved in protein families
3.4 Hydration water molecules as lubricant at protein interface
3.5 Hydration water molecules in the ligand-binding sites
References
4. Hydration layer around proteins
4.1 Introduction
4.2 Hydration layer
4.2.1 First- and second-layer classes
4.2.2 Distance distribution and positional fluctuation
4.2.3 Monolayer hydration
4.2.4 Contact class
4.3 Local patterns in protein hydration
4.3.1 Patterns on hydrophilic surfaces
4.3.2 Hydration on hydrophobic surfaces4.3.3 Tetrahedral hydrogen bond geometry of water molecules
4.4 Hydration structures in molecular dynamics simulation4.4.1 Computation of solvent density
4.4.2 Characteristic of solvent density
References
5. Structural characteristics in local hydration
5.1 Introduction
5.2 Empirical hydration distribution around polar atoms
5.2.1 Construction5.2.2 Distribution around polar protein atoms
5.2.3 Hydration of aromatic acceptors
5.2.4 Characteristics and benefits of the empirical hydration distributions.5.2.5 Tetrahedral hydrogen bond geometry
5.3 Assessment of force fields of polar protein atoms
5.3.1 Models of water molecule suitable for simulation
5.3.2 Hydration of deprotonated polar atoms in sp 2-hybridization
5.3.3 Hydration of protonated nitrogen atoms in sp 2- or sp 3- hybridization
5.3.4 Hydration of protonated oxygen atoms in sp 2- or sp 3- hybridization
5.3.5 Molecular dynamics simulation of proteins using force field with lone-pair electrons
References
6. Prediction of hydration structures
6.1 Introduction
6.2. Computation of probability distribution of water molecules
6.3 Prediction for soluble proteins
6.3.1 On solvent exposed surfaces and in cavities
6.3.2 At interface in protein complex
6.4 Prediction for membrane proteins
6.4.1 For surfaces of membrane proteins6.4.2 For channels in transmembrane regions
6.5 Accuracy of prediction
6.6 Comparison of the prediction with theory of liquid
6.7 Utilization of probability distribution in structure analysis
6.7.1. Assessment on hydration water sites 6.7.2 Probability distribution-weighted electron density map6.8 Prediction of hydration structures on hydrophobic surfaces
References
7. Network of hydrogen bonds around proteins
7.1. Introduction7.2 Network of hydrogen bonds
7.2.1 Chain connection of hydrogen bonds
7.2.2 Percolation property
7.3 Probability of hydrogen-bond formation
7.4 Network of hydrogen bonds in simulation trajectory
7.5 Influence of networks of hydrogen bons on protein motions
References
8. Dipole-Dipole interactions in hydration layer
8.1 Introduction
8.2 Orientational ordering of hydration water molecules
8.2.1 Coherent patterns of time-averaged water dipoles8.2.2 Solvent dipoles and networks of hydrogen bonds
8.2.3 Solvent dipole in drug design
8.2.4 Poisson-Boltzmann equation and orientation ordering of water molecules8.3 Fluorescence from tryptophan side chains exposed to solvent
8.3.1 Fluorescence from photo-excited tryptophan of protein
8.3.2 Interpretation of dynamic Stokes shift8.3.3 Orientation ordering of hydration water molecules around tryptophan side chains
8.3.4 Origin of dynamic Stokes shift
References
9. Hydration structure changes of proteins at work
9.1. Introduction9.2 Experimental evidence on hydration-regulated protein motion
9.2.1 Domain motion in glutamate dehydrogenase9.2.2 Hydration structure changes in domain motion
9.2.3 Model for hydration coupled domain motion
9.3 Molecular mechanism in hydration-coupled domain motion
9.3.1 Domain motion observed in simulation
9.3.2 Simultaneous changes in conformation and hydration9.3.3 Hydration changes in the hydrophobic pocket
9.3.4 Drying transition in the hydrophobic pocket
9.3.5 Hydration changes in hydrophilic crevice
9.3.5 Mechanism of hydration regulated domain motion
9.4 Manipulation of conformation and hydration of proteins in crystals9.4.1 Conformational changes of proteins in different molecular packing
9.4.2 hydration changes in different molecular packingReferences
10. Energy landscape and hydration of proteins
10.1 Introduction
10.1.1 Protein conformation manifold and energy landscape
10.2 X-ray diffraction imaging
10.2.1 Structure analysis using X-ray diffraction imaging
10.2.2 X-ray diffraction imaging using X-ray laser
10.3 Cryogenic electron microscopy10.3.1 Classification of protein structures
10.3.2 Energy landscape in protein motions
10.3.3 Prediction of hydration structure by neural network10.4 Future prospect
References
Appendix
A. Three and one letter codes of amino acids
B. X-ray diffraction by crystalB.1 Thomson scattering
B.2 Interference of X-rays emitted from electrons
B.3 Diffraction from crystalB.4 Ewald sphere
C. The image obtained by electron microscopy
C.1 Electron scattering by weak-phase objectC.2 Contrast transfer function
D. The Principle of the up-conversion method
D.1 Higher-order dielectric polarization
D.2 Radiation by non-linear dielectric polarization
D.3 The phase-matching condition and birefringence
E. The symplectic integrator
F. The geometries of the polar groups in amino acid residues.