Textbook of Ion Channels Volume I: Fundamental Mechanisms and Methodologies

Cover
Half Title
Title Page
Copyright Page
Table of Contents
Preface
Editors
Contributors
Section 1 Fundamental Mechanisms
	Chapter 1 Ion Selectivity and Conductance
		1.1 Introduction
		1.2 Structural Basis for Selectivity in K+ Channels
		1.3 Structural Basis for Selectivity in Na+ Channels
		1.4 Mechanistic Models for Selectivity in Cation Channels
			1.4.1 The Close-Fit Model for Selectivity
			1.4.2 The Field-Strength Model for Selectivity
			1.4.3 The Coordination Model for Selectivity
			1.4.4 Kinetic Model for Selectivity
			1.4.5 The Site Number Model of Selectivity
			1.4.6 Other K+ Channel Selectivity Determinants
		1.5 Conductance
		Suggested Readings
	Chapter 2 Voltage-Dependent Gating of Ion Channels
		2.1 Introduction
		2.2 Basic Principles of Voltage Sensing
			2.2.1 Two-State Model of Voltage Gating
			2.2.2 Multistate Models of Voltage Gating
			2.2.3 Model-Free Methods for Estimating Free Energy of Channel Gating
		2.3 Biophysical Methods to Probe Voltage-Sensing Mechanisms
			2.3.1 Gating Charge per Channel
			2.3.2 Substituted Cysteine Accessibility Method (SCAM)
			2.3.3 Voltage-Clamp Fluorometry (VCF)
			2.3.4 Gating Pore Currents
			2.3.5 Thermodynamic Mutant Cycle Analysis of Interaction Energies
			2.3.6 Structural Approaches
			2.3.7 Computational Approaches
		2.4 Voltage-Sensor Motions
		2.5 Coupling of Voltage-Sensor Motion to Pore Opening
		2.6 Concluding Remarks
		Acknowledgments
		Suggested Readings
	Chapter 3 Ligand-Dependent Gating Mechanism
		3.1 Introduction
		3.2 Energetics of Ligand Gating
		3.3 Steady-State Properties of Ligand Gating
		3.4 Cooperativity
		3.5 Separate Ligand Binding and Opening Transitions
		3.6 Partial Agonists
		3.7 MWC Model
		3.8 Macroscopic Gating Kinetics
		3.9 Single-Channel Gating Kinetics
		3.10 Phi Analysis
		Suggested Readings
	Chapter 4 Mechanosensitive Channels and Their Emerging Gating Mechanisms
		4.1 Introduction
		4.2 Diversity of MS Channels
			4.2.1 The Auditory Mechanotransduction Channel
			4.2.2 Phenomenological Patch-Clamp Studies of MS Channels in Non-Sensory Cells
			4.2.3 The DEG/ENaC/MEC Family
			4.2.4 Bacterial Channels
			4.2.5 MS Channels in Plants
			4.2.6 Two-Pore Potassium (K2P, TPK) Channels
			4.2.7 TRP Channels
			4.2.8 Volume-Regulated Anion Channels
			4.2.9 Piezo Channels
		4.3 The Ways External Forces Are Conveyed to the Channel and the Energetics of Gating
		4.4 Transient Responses: Adaptation, Desensitization and Inactivation
		4.5 Experimental Parameters of MS Channel Gating
			4.5.1 The Auditory Transduction Channel
			4.5.2 Bacterial MS Channels as Models for Gating by Membrane Tension
			4.5.3 The Large-Conductance Channel MscL
			4.5.4 MscS Channel and Its Adaptive Gating Mechanism
		4.6 Conclusions and Perspectives
		Acknowledgments
		Suggested Readings
	Chapter 5 Inactivation and Desensitization
		5.1 Introduction
		5.2 Energetics of Inactivation and Desensitization
		5.3 Na+ Channel Inactivation
		5.4 K+ Channel N-Type Inactivation
		5.5 K+ Channel C-Type Inactivation
		5.6 Ionotropic Glutamate Receptor Desensitization
		5.7 Type II and III Inactivation/Desensitization in Other Channels
		Suggested Readings
	Chapter 6 Ion Channel Inhibitors
		6.1 Mechanisms of Inhibition
		6.2 Pore Blockers
		6.3 Perturbation of Pore Block
		6.4 One-Sided Pore Blockers
		6.5 Slowly Permeating Blocking Ions
		6.6 Gated Inhibitor Access
		6.7 Allosteric Inhibition
		6.8 Partial Inverse Agonism
		6.9 Use-Dependent Pore Block
		6.10 Inhibition by Lipid Bilayer Effects
		6.11 Concluding Remarks
		Acknowledgments
		Suggested Readings
Section 2 Methodologies
	Chapter 7 Expression of Channels in Heterologous Systems and Voltage-Clamp Recordings of Macroscopic Currents
		7.1 Introduction
		7.2 Heterologous Expression of Channels in Cultured Cells and Oocytes
			7.2.1 Xenopus laevis Oocytes
			7.2.2 Advantages and Disadvantages of Xenopus Oocytes
			7.2.3 Mammalian Cells
			7.2.4 Advantages and Disadvantages of Mammalian Cells
		7.3 Voltage Clamp
			7.3.1 Two-Electrode Voltage Clamp
			7.3.2 Cut-Open Oocyte Clamp
		7.4 Patch Clamp
			7.4.1 The Electronics
			7.4.2 Establishing the Gigaseal
			7.4.3 Configurations
			7.4.4 Compensation and Voltage Errors; Series Resistance
		7.5 Analysis of Macroscopic Ionic Currents
			7.5.1 Voltage Dependence, Activation, Deactivation
		7.6 Estimation of the Number of Channels Using Noise Analysis
		7.7 Gating Current Recording
		Appendix: Effect of p/n Subtraction on the Current Noise
		Acknowledgments
		Suggested Readings
	Chapter 8 Patch Clamping and Single-Channel Analysis
		8.1 Introduction
		8.2 Conditions for Single-Channel Recording
		8.3 Analysis of Single-Channel Signals
			8.3.1 Nonstationary Recordings
			8.3.2 Stationary Recordings
			8.3.3 Filtering the Data
			8.3.4 Resolution
			8.3.5 Detection of Events
			8.3.6 Dwell-Time Histograms and Fitting of Distributions
			8.3.7 Burst Analysis
		8.4 Inferring a Mechanism
		8.5 Conclusions
		Acknowledgments
		Suggested Readings
	Chapter 9 Patch-Clamp Recordings from Native Cells and Isolation of Membrane Currents
		9.1 Introduction
		9.2 Optimizing Conditions for Patch-Clamp Recordings from Native Cells
		9.3 Isolation of Voltage-Gated (Inward and Outward) Currents in Cardiac Myocytes
		9.4 Identification of Kinetically Distinct Myocardial Kv Current Components
		9.5 Pharmacological Separation of Co-Expressed Kv Current Components
		9.6 Molecular Dissection of Native Kv Currents: Kv Pore-Forming (α) Subunits
		9.7 Probing the Functional Roles of Kv (and Other) Channels in Native Cells
		Acknowledgments
		Suggested Readings
	Chapter 10 Models of Ion Channel Gating
		10.1 Introduction
		10.2 The Goals and Benefits of Modeling
		10.3 Model Generation
			10.3.1 Should I Build a (New) Gating Model?
			10.3.2 What Kind of a Model?
				10.3.2.1 Phenomenological Models
				10.3.2.2 Statistically Parsimonious Gating Schemes
				10.3.2.3 Semi-Mechanistic Models
		10.4 Examples of Semi-Mechanistic Models and Assumptions
			10.4.1 The Hodgkin and Huxley (HH) Model
			10.4.2 Modern Models of KV Channel Gating
			10.4.3 Allosteric Mechanisms and Models
				10.4.3.1 The MWC Model
				10.4.3.2 The HA Model of BK Channels
			10.4.4 Semi-Mechanistic Models Represent a Balanced Approach
		10.5 Simulations
		10.6 Parameter Optimization, Validation and Interpretation
		10.7 Summaries, Conclusions and Future Developments
		Acknowledgments
		Suggested Readings
	Chapter 11 Investigating Ion Channel Structure and Dynamics Using Fluorescence Spectroscopy
		11.1 Introduction
		11.2 Modulation of Fluorescence
			11.2.1 Förster Resonance Energy Transfer
		11.3 Labeling Techniques
			11.3.1 Thiol-Reactive Chemistry
			11.3.2 Fluorescently Labeled Ligands or Toxins
			11.3.3 Genetically Encoded Fluorescent Labels
				11.3.3.1 Fluorescent Proteins
				11.3.3.2 Ligand-Binding Domains
				11.3.3.3 Fluorescent Unnatural Amino Acids
		11.4 Obtaining Structural and Dynamic Information from Fluorescence Measurements
			11.4.1 Kinetics of Local Structural Rearrangements
			11.4.2 Intra- and Intermolecular Distance Measurements
				11.4.2.1 Linking Distances to Structures and Models
				11.4.2.2 Lanthanide-Based RET and Transition-Metal FRET
			11.4.3 Ligand Binding
			11.4.4 Single-Channel Fluorescence
		11.5 Conclusions
		Suggested Readings
	Chapter 12 Ion Channel Structural Biology in the Era of Single-Particle Cryo-EM
		12.1 Introduction
		12.2 Why Single-Particle Cryo-EM?
		12.3 Sample Preparation of Ion Channels for Single-Particle Cryo-EM
		12.4 Cryo-EM Experiment: Data Acquisition and Interpretation
		12.5 Foundations of Microscopy and Data Processing
			12.5.1 Fourier Theory
			12.5.2 Central Slice Theorem
			12.5.3 Contrast Transfer Function
			12.5.4 Box Size
			12.5.5 Defocus Range
			12.5.6 Refinement
			12.5.7 Classification
			12.5.8 Masking during Refinement
			12.5.9 Resolution Estimation
				12.5.9.1 Local Resolution Estimation
				12.5.9.2 Directional Resolution Estimation
			12.5.10 Masking
			12.5.11 Filtering and Sharpening
		12.6 What Structural Information Can Cryo-EM Provide?
		12.7 Further Technological Advancement and Challenges ahead in Ion Channel Structural Biology
		Suggested Readings
	Chapter 13 Protein Crystallography
		13.1 Ion Channels Physiology in the Era of Structural Biology
		13.2 Why Crystallization?
		13.3 Enhancing Crystallization Likelihood
		13.4 Protein Crystallization
		13.5 The Diffraction Experiment and Phasing Techniques
		13.6 Structure Determination and Quality Metrics
		13.7 Structure Analysis and Visualization
		13.8 The Developing Role of X-Ray Crystallography in the Structural Biology Toolbox
		Suggested Readings
	Chapter 14 Rosetta Structural Modeling
		14.1 Introduction
		14.2 Rosetta Molecular Modeling
			14.2.1 Scoring
				14.2.1.1 Rosetta Standard Full-Atom Scoring Function
				14.2.1.2 Rosetta Membrane Full-Atom Scoring Function
				14.2.1.3 Other Scoring Functions
			14.2.2 Sampling
			14.2.3 Packing
			14.2.4 Minimization
		14.3 Homology Modeling of Ion Channels
		14.4 Symmetry Modeling of Ion Channels
		14.5 Modeling of Ion Channels with Experimental Data
		14.6 Modeling of Ion Channels Interaction with Modulators
			14.6.1 Rosetta Protein–Ligand Docking
			14.6.2 Rosetta Protein–Protein Docking
		14.7 De Novo Protein Design
		14.8 Future Directions
		Resources for Learning Rosetta
		Suggested Readings
	Chapter 15 Molecular Dynamics
		15.1 Introduction
			15.1.1 Basic Introduction to MD Simulations
			15.1.2 Force Fields and the Potential Energy Function
			15.1.3 MD Simulations Analysis and the Notion of Free Energy
			15.1.4 Enhanced Sampling Simulations Schemes
		15.2 Applying External Stimuli in MD Simulations
			15.2.1 Transmembrane Potential (∆V    )
			15.2.2 Mechanical Force
			15.2.3 pH, Temperature and Others
		15.3 Sensing
			15.3.1 Voltage
			15.3.2 Temperature
		15.4 Gating and Conformational Changes
		15.5 Ion Conduction and Selectivity
			15.5.1 Enhanced Sampling Free Energy Calculation Methods
			15.5.2 Methods Where Conduction Is Modeled Explicitly
		15.6 Small Molecule Modulation
		15.7 Lipid Modulation
		15.8 Allostery
		15.9 In Silico Mutagenesis
		15.10 Conclusion
		Suggested Readings
	Chapter 16 Genetic Models and Transgenics
		16.1 Introduction
		16.2 Linking Ion Channels to Phenotypes: Forward Genetics
			16.2.1 Model Organisms
			16.2.2 Cloning
			16.2.3 Phenotypic Screens
		16.3 Targeted Alteration of Ion Channel Function: Reverse Genetics
			16.3.1 Nontargeted Transgenics
			16.3.2 Targeted Homologous Recombination
			16.3.3 Gene Editing
			16.3.4 Conditional Site-Specific Recombination
			16.3.5 Genetically Encoded Tools for Studying Ion Channel Function
			16.3.6 Genetic Integrity and Maintenance of Mouse Lines
			16.3.7 Phenotypic Characterization
		16.4 Ion Channels in Human Physiology and Disease
			16.4.1 Linkage and Single-Nucleotide Polymorphisms
		16.5 Summary
		Suggested Readings
	Chapter 17 EPR and DEER Spectroscopy
		17.1 Introduction
		17.2 Site-Directed Spin Labeling (SDSL)
		17.3 CW EPR Spectroscopy
			17.3.1 Mobility
			17.3.2 Solvent Accessibility
		17.4 DEER Spectroscopy
			17.4.1 Principles
		17.5 Practical Aspects
		17.6 Applications to Ion Channels
			17.6.1 Local Dynamics and Solvent Environment
			17.6.2 Oligomerization
			17.6.3 Structure and Conformational Changes
		Suggested Readings
Index