Analytical Techniques for the Elucidation of Protein Function

Analytical Techniques for the Elucidation of Protein Function
Contents
Preface
Editor’s Biographies
List of Contributors
1 EPR Spectroscopy
	1.1 Outline of EPR Spectroscopy
		1.1.1 Overview
	1.2 Biological Applications of EPR
		1.2.1 Proteins and Their Structures: Domain and Intrinsically Disordered Region
		1.2.2 Introduction of Spin Probes on Proteins
		1.2.3 Measurement of Constant Wave (CW)-EPR Spectrum
		1.2.4 Application of CW-EPR to Protein (Clock Protein, Amyloid Proteins, and HP1)
			1.2.4.1 Clock Proteins
			1.2.4.2 Amyloid Proteins (Aβ Peptide, β2-microglobulin, α-synuclein,Tau, and Prion)
			1.2.4.3 Heterochromatin Protein 1 (HP1)
		1.2.5 Measurement of Longer Distance between Spin-spin (HP1, Tau, α-synuclein)
		1.2.6 Biophysical Functions of Protein Dynamics
		1.2.7 Summary/Conclusion
2 Introduction to Incoherent Neutron Scattering: A Powerful Technique to Investigate the Dynamics of Bio-macromolecules
	2.1 Introduction
	2.2 Basic Theory and Dynamical Information Obtained from iNS
		2.2.1 Basic Principle of iNS Experiments
		2.2.2 Incoherent Scattering Function
		2.2.3 Dynamical Information Obtained by iNS
			2.2.3.1 Elastic Incoherent Neutron Scattering (EINS)
			2.2.3.2 Quasi-elastic Neutron Scattering (QENS)
	2.3 Examples of Biological Applications of iNS
		2.3.1 Dynamical Modulation of Proteins Caused by a Disease-causing Point Mutation
		2.3.2 Dynamical Differences between Amyloid Polymorphic Fibrils Showing Different Levels of Cytotoxicity
		2.3.3 New Theoretical Framework to Describe the Dynamical Behavior of Lipid Molecules
		2.3.4 Separation of Dynamics of Protein-detergent Complexes
		2.3.5 Hydration Water Mobility around Proteins
	2.4 Summary
3 Elucidation of Protein Function Using Raman Spectroscopy
	3.1 Introduction
	3.2 Basic Principle and Working of Raman Spectroscopy
		3.2.1 Theory and Frequencies of Raman Spectroscopy
		3.2.2 Instrumentation
	3.3 Advances in Raman Spectroscopy Techniques
		3.3.1 Resonance Raman Spectroscopy for Protein Analysis
			3.3.1.1 Ultraviolet Resonance Raman Spectroscopy
			3.3.1.2 Time-resolved Resonance Raman Spectroscopy
		3.3.2 Surface-enhanced Raman Spectroscopy (SERS)
		3.3.3 Tip-enhanced Raman Spectroscopy
		3.3.4 Polarized Raman Spectroscopy
		3.3.5 Raman Crystallography
		3.3.6 2D-COS Raman Spectroscopy
	3.4 Applications
	3.5 Conclusion
4 Fundamental Principles of Impedance Spectroscopy and its Biological Applications
	4.1 Introduction
		4.1.1 Basic Concept of Impedance Spectroscopy
		4.1.2 Description of Impedance for Capacitors and Inductors
		4.1.3 Nyquist Plot
		4.1.4 Debye Model
		4.1.5 Constant Phase and Warburg Element to Model Distorted and Diffusive Components
	4.2 Biological Applications of Impedance Spectroscopy
		4.2.1 Detection of DNA Hybridization and Photodamage
		4.2.2 Detection and Analysis of Proteins
	4.3 Conclusion
5 Mass Spectrometry Imaging
	5.1 Introduction
	5.2 Workflow of MSI
	5.3 Mass Microscope
	5.4 Visualization of Small Molecules (Pharmaceutical)
	5.5 Structural Isomer Discrimination Imaging (Steroid Hormones)
	5.6 Visualization of Proteins (Intact, Digestion)
	5.7 Visualization of Protein Function (Enzymatic Activity Visualization)
	5.8 Summary
6 Elucidation of Protein Function Using Single-molecule Monitoring by Quantum Dots
	6.1 Introduction
		6.1.1 Introduction to Quantum Dots
		6.1.2 Types of Quantum Dots
			6.1.2.1 Core Type QDs
			6.1.2.2 Core/shell-type QDs
			6.1.2.3 Alloyed-type QDs
	6.2 Synthesis Methods
		6.2.1 Wet-chemical Methods
		6.2.2 Vapor-phase Methods
	6.3 Bioconjugation
	6.4 Analytical Methods for Single-molecule Monitoring by Quantum Dots
		6.4.1 Epifluorescence Microscopy
		6.4.2 Total Internal Reflection Fluorescence Microscope
		6.4.3 Confocal Microscopy
		6.4.4 pseudo-TIRFM
		6.4.5 Single-point Edge Excitation Subdiffraction Microscopy
	6.5 Applications
		6.5.1 Application of Single-molecule Monitoring Using QD for Enlightening Nanoscale Neuroscience
		6.5.2 Investigation of Diffusion Dynamics of Neuroreceptors in Cultured Neurons
		6.5.3 Single-molecule Tracking of Neuroreceptors in Intact Brain Slices (in Vivo)
		6.5.4 QD-tagged Neurotransmitter Transporters
		6.5.5 QD Labeled Serotonin Transporter (SERT) to Understand Membrane Dynamics
		6.5.6 Membrane Trafficking and Imaging of Dopamine Transporter (DAT) Using QDs
	6.6 Limitations of QDs
	6.7 Conclusion
7 Biological Solid-state NMR Spectroscopy
	7.1 Introduction
	7.2 Magnetic Interactions for NMR
		7.2.1 Zeeman Interaction
		7.2.2 Isotropic and Anisotropic Chemical Shifts
		7.2.3 Homo- and Heteronuclear Dipolar Interactions
	7.3 Methods for Solid-state NMR
		7.3.1 Sample Preparation of Solid-state NMR
		7.3.2 Experimental NMR Techniques for High-resolution Solid-state NMR
		7.3.3 Fast MAS for 1H NMR
		7.3.4 Multidimensional High-resolution NMR Experiments with Recoupling RF Pulse Sequences
		7.3.5 Paramagnetic Effects for Structural Analysis
		7.3.6 High-field DNP for Sensitivity Enhancement
		7.3.7 Oriented Molecular Systems
	7.4 Applications of Solid-state NMR to Biological Molecular Systems
		7.4.1 Membrane Proteins and Peptides
		7.4.2 Amyloid Fibrous Proteins
		7.4.3 In-situ Cellular Biomolecules
	7.5 Concluding Remarks
8 Electrically Induced Bubble Knife and Its Applications
	8.1 Introduction
	8.2 Electrically Induced Bubble Knife
	8.3 Electrically Induced Bubble Injector
		8.3.1 Bubble Formation with Reagent Interface
		8.3.2 Simultaneous Injection and Ablation
	8.4 Plasma-induced Bubble Injector
	8.5 Protein Crystallization by Electrically Induced Bubbles
	8.6 Protein Crystallization by Plasma-induced Bubbles
Index
EULA