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Table of contents
1 Introduction to Part I: Biomolecular hydration shell dynamics
1.1 How to probe water dynamics in hydration shells?
1.1.1 Experimental techniques
1.1.2 Molecular dynamics simulations
1.2 Water reorientation mechanism: Extended Jump Model
1.2.1 Bulk water reorientation mechanism
1.2.2 Hydrophobic solutes: transition-state excluded volume (TSEV) factor
1.2.3 Hydrophilic solutes: transition-state hydrogen-bond (TSHB) factor
1.2.4 Biomolecular hydration shells: spatial heterogeneity
1.3 Outline
2 Temperature dependence of hydrophobic hydration dynamics
2.1 Introduction
2.2 Methodology
2.3 Results
2.3.1 Temperature dependence of perturbation from simulations
2.3.2 Excluded volume with local structural fluctuations
2.3.3 Interpretation of the temperature dependence of the perturbation factor
2.3.4 Validity of the excluded-volume picture at room temperature
2.4 Concluding remarks
3 Hydration shell dynamics around a hyperactive antifreeze protein and ubiquitin
3.1 Introduction
3.2 Methodology
3.3 Hydration dynamics of ubiquitin
3.3.1 Average water reorientation dynamics in the hydration shell
3.3.2 Hydration dynamics distributions and mapping
3.3.3 Temperature dependence of the dynamical perturbation
3.4 Hydration Dynamics of CfAFP
3.4.1 Average retardation factor in the Cf AFP hydration shell
3.4.2 Site-resolved analysis of Cf AFP hydration dynamics
3.4.3 Local structural order
3.4.4 Short-ranged structural perturbation
3.4.5 Water–Cf AFP H-bond strength
3.5 Concluding remarks
4 Heterogeneous water dynamics in DNA hydration shell
4.1 Introduction
4.2 Methods
4.2.1 System preparation
4.2.2 Water dynamics analysis
4.2.3 Groove width analysis
4.3 Orientational dynamics in the hydration shell: spatial heterogeneity
4.3.1 Heterogeneity in hydration dynamics
4.3.2 Spatial heterogeneity
4.3.3 Mechanism for reorientation
4.4 Dynamical heterogeneity in the minor groove
4.4.1 Temporal heterogeneity
4.4.2 Hydration structure and kinetics in the A-tract
4.4.3 Minor groove fluctuations: dynamical heterogeneity
4.4.4 Dynamical heterogeneity model
4.5 Concluding remarks
5 Introduction to part II: Environmental effects in enzyme catalysis
5.1 Context of the study
5.1.1 Enzyme catalysis: controversies and challenges
5.1.2 Transition-State Theory
5.1.3 Outline
5.2 Computational approach
6 Role of active site residues in DHFR catalysis
6.1 Introduction
6.1.1 DHFR: a paradigm system
6.1.2 Recent experiments and open questions
6.2 Methodology
6.2.1 System Preparation
6.2.2 EVB simulations
6.2.3 pKa shifts calculations
6.3 Results
6.3.1 Hydride transfer step
6.3.2 Protonation step
6.3.3 Overall picture
6.4 Concluding remarks
7 Enzyme catalysis in organic solvents: role of water
7.1 Introduction
7.1.1 Non-aqueous enzymology
7.1.2 Subtilisin Carlsberg: a model system
7.2 Methodology
7.2.1 System preparation
7.2.2 EVB description
7.2.3 Equilibration procedure
7.2.4 Hydration levels
7.3 How does water affect the chemical rate constant?
7.3.1 Hydration level and activation free-energy Gz
7.3.2 Hydration level and transmission coefficient
7.3.3 Existence of a stable non-productive bound state at low hydration
7.4 Concluding remarks
