TheTextbook of Ion Channelsis a set of three volumes providing a wide-ranging reference source on ion channels for students, instructors and researchers. Ion channels are membrane proteins that control the electrical properties of neurons and cardiac cells; mediate the detection and response to sensory stimuli like light, sound, odor, and taste; and regulate the response to physical stimuli like temperature and pressure. In non-excitable tissues, ion channels are instrumental for the regulation of basic salt balance that is critical for homeostasis. Ion channels are located at the surface membrane of cells, giving them the unique ability to communicate with the environment, as well as the membrane of intracellular organelles, allowing them to regulate internal homeostasis. Ion channels are fundamentally important for human health and diseases, and are important targets for pharmaceuticals in mental illness, heart disease, anesthesia, pain and other clinical applications. The modern methods used in their study are powerful and diverse, ranging from single ion-channel measurement techniques to models of ion channel diseases in animals, and human clinical trials for ion channel drugs.
Volume I, Part 1 covers fundamental topics such as the basic principles of ion permeation and selectivity, voltage-dependent, ligand-dependent, and mechano-dependent ion channel activation mechanisms, the mechanisms for ion channel desensitization and inactivation, and basic ion channel pharmacology and inhibition. Volume I, Part 2 offers a practical guide of cardinal methods for researching ion channels, including heterologous expression and voltage-clamp and patch-clamp electrophysiology; isolation of native currents using patch clamping; modeling ion channel gating, structures, and its dynamics; crystallography and cryo-electron microscopy; fluorescence and paramagnetic resonance spectroscopy methods; and genetics approaches in model organisms.
All three volumes give the reader an introduction to fundamental concepts needed to understand the mechanism of ion channels; a guide to the technical aspects of ion channel research; a modern guide to the properties of major ion channel families; and includes coverage of key examples of regulatory, physiological and disease roles for ion channels.
Author(s): Jie Zheng, Matthew C. Trudeau
Publisher: CRC Press
Year: 2023
Language: English
Pages: 330
City: Boca Raton
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
