Hydration Structures of Proteins: Atomic Details

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 water

1.4.1 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 Outline

2.3.2 Specimen preparation and image collection

2.3.3 Image processing and single-particle analysis

2.4 Time-resolved fluorescence measurement

2.4.1 Outline

2.4.2 Up-conversion method

2.5 Molecular dynamic simulation

2.5.1 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 molecules

3.2.2 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 surfaces

4.3.3 Tetrahedral hydrogen bond geometry of water molecules

4.4 Hydration structures in molecular dynamics simulation

4.4.1 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 Construction

5.2.2 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 sp²-hybridization

5.3.3 Hydration of protonated nitrogen atoms in sp²- or sp³- hybridization

5.3.4 H