Chung / Anderson / Krishnamurthy Biological Membrane Ion Channels

Dynamics, Structure, and Applications
2007
ISBN: 978-0-387-68919-7
Verlag: Springer US
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 658 Seiten

Reihe: Biological and Medical Physics, Biomedical Engineering

This book deals with recent breakthroughs in ion-channel research that have been brought about by the combined effort of experimental biophysicists and computational physicists, who together are beginning to unravel the story of these exquisitely designed biomolecules. With chapters by leading experts, the book is aimed at researchers in nanodevices and biosensors, as well as advanced undergraduate and graduate students in biology and the physical sciences.

Autoren/Hrsg.

Chung, Shin-Ho

Krishnamurthy, Vikram

Anderson, Olaf S.

Krishnamurthy, Vikram V.

Inhaltsverzeichnis

1;Preface;6
2;Contents;9
3;List of Contributors;11
4;Part I Introduction;15
4.1;1 Ion Channels, from Fantasy to Fact in Fifty Years1;16
4.1.1;1.1 Introduction;16
4.1.2;1.2 Classical Biophysics;17
4.1.3;1.3 Pharmacology and Single Channels;20
4.1.4;1.4 Patch Clamp, Sequencing, and Mutagenesis;22
4.1.5;1.5 Structure;24
4.1.6;1.6 Spectroscopy;27
4.1.7;1.7 Theory;29
4.1.8;1.8 WhatÌs Next?;32
4.1.9;Acknowledgments;33
4.1.10;References;33
5;Part II Specific Channel Types;43
5.1;2 Gramicidin Channels: Versatile Tools;44
5.1.1;2.1 Overview;44
5.1.2;2.2 Introduction;44
5.1.3;2.3 Structure;45
5.1.4;2.4 Channel Function;60
5.1.5;2.5 Molecular Dynamics Analysis of Ion Permeation;75
5.1.6;2.6 Conclusion;78
5.1.7;Acknowledgments;79
5.1.8;References;79
5.2;3 Voltage-Gated Ion Channels;92
5.2.1;3.1 Introduction;92
5.2.2;3.2 Voltage-Dependent Ion Channels Are Membrane Proteins;93
5.2.3;3.3 The Parts of the Voltage-Dependent Channel;94
5.2.4;3.4 Gating Charge and the Voltage Sensor;97
5.2.5;3.5 Structural Basis of the Gating Charges;106
5.2.6;3.6 Structural Basis of the Voltage Sensor;107
5.2.7;3.7 Coupling of the Sensor to the Gate;120
5.2.8;3.8 Concluding Remarks;120
5.2.9;3.9 Outlook;122
5.2.10;Acknowledgments;123
5.2.11;References;123
5.3;4 Voltage-Gated Potassium Channels;130
5.3.1;Part I. Overview;130
5.3.2;4.1 Basics of K+ Channel Structure;131
5.3.3;4.2 Functional Classification;134
5.3.4;4.3 Summary;137
5.3.5;Part II. K+ Channel Operation 4.4 Control of Single- Channel Conductance;138
5.3.6;4.5 Activation Gates;140
5.3.7;4.6 Functions of the Outer Vestibule;144
5.3.8;4.7 Functions of the N-Terminal Domain;148
5.3.9;4.8 Modulation at the C-Terminal Domain;150
5.3.10;4.9 The MinK/MiRP Family of Accessory Subunits;152
5.3.11;Part III. Specific Properties of Voltage-Gated Channels 4.10 Diversity of Function;154
5.3.12;4.11 Kv1 Channels;155
5.3.13;4.12 Kv2 Channels;158
5.3.14;4.13 Kv3 Channels;162
5.3.15;4.14 Kv4 Channels;164
5.3.16;Acknowledgments;168
5.3.17;References;168
5.4;5 BKCa- Channel Structure and Function;182
5.4.1;5.1 Introduction;182
5.4.2;5.2 BKCa- Channel Topology;182
5.4.3;5.3 The Origin of the BKCa ChannelÌs Large Conductance;184
5.4.4;5.4 BKCa- Channel Gating, Studies Before Cloning;187
5.4.5;5.5 BKCa- Channel Gating, Macroscopic Current Properties;188
5.4.6;5.6 A Simple Model of BKCa- Channel Gating;190
5.4.7;5.7 Interpreting Mutations;200
5.4.8;5.8 A Better Model of Voltage-Dependent Gating;200
5.4.9;5.9 Combining HCA and MWC;204
5.4.10;5.10 The BKCa Channel Has Low- Affinity Ca2+ Binding Sites;208
5.4.11;5.11 The BKCa Channel Has Two Types of High- Affinity Ca2+- Binding Sites;210
5.4.12;5.12 Is the BKCa Channel Like the MthK Channel?;213
5.4.13;5.13 The Discovery of;216
5.4.14;1;216
5.4.15;5.14 Four;217
5.4.16;Subunits Have Now Been Identified;217
5.4.17;5.15 Conclusions;221
5.4.18;References;221
5.5;6 Voltage-Gated Sodium Channels;230
5.5.1;6.1 Introduction;230
5.5.2;6.2 The Sodium Channel as a Protein;231
5.5.3;6.3 The Pore;232
5.5.4;6.4 Gating;237
5.5.5;6.5 Hereditary Sodium Channel Diseases;244
5.5.6;Acknowledgments;245
5.5.7;References;245
5.6;7 Calcium Channels;251
5.6.1;7.1 Introduction;251
5.6.2;7.2 Types of Ca2+ Channels;252
5.6.3;7.3 Roles of Ca2+ Channels;260
5.6.4;7.4 Ion Selectivity and Permeation;264
5.6.5;7.5 Channel Structure;268
5.6.6;7.6 Theoretical Models of Permeation and Selectivity;272
5.6.7;7.7 Channel Gating;277
5.6.8;7.8 Inactivation of HVA Channels;280
5.6.9;7.9 Regulation of Channel Function;284
5.6.10;7.10 Conclusions and Outlook;289
5.6.11;References;291
5.7;8 Chloride Transporting CLC Proteins1;310
5.7.1;8.1 Introduction;310
5.7.2;8.2 Overview Over the Family of CLC Proteins;312
5.7.3;8.3 Architecture of CLC Proteins;318
5.7.4;8.4 Gating of CLC-0 and Mammalian CLC Channels;321
5.7.5;8.5 Permeation of CLC-0 and Mammalian CLC Channels;324
5.7.6;8.6 The X-ray Structure and Its Functional Implication: A Pivot Glutamate Controls the Protopore Gate;324
5.7.7;8.7 The Function as a Cl-/ H+ Antiporter;326
5.7.8;8.8 Pharmacology;328
5.7.9;8.9 CBS Domains;330
5.7.10;8.10 Conclusion;331
5.7.11;Acknowledgment;331
5.7.12;References;331
5.8;9 Ligand-Gated Ion Channels: Permeation and Activation1;343
5.8.1;9.1 Introduction;343
5.8.2;9.2 Physicochemical Structure;347
5.8.3;9.3 Ion Conductances, Permeation and Selectivity;353
5.8.4;9.4 Ion Channel Gating;362
5.8.5;9.5 Conclusions and Some Questions Still Pending;369
5.8.6;Acknowledgments;369
5.8.7;References;370
5.9;10 Mechanosensitive Channels;376
5.9.1;10.1 Introduction;376
5.9.2;10.2 Evolutionary Origins of MS Channels;377
5.9.3;10.3 Bilayer and Tethered Model of MS Channel Gating by Mechanical Force;378
5.9.4;10.4 MS Channels of Bacteria and Archaea;383
5.9.5;10.5 MS Channels of Eukaryotes;386
5.9.6;10.6 The Role of MS Channels in Cell Physiology and Pathology of Disease;392
5.9.7;10.7 Conclusion;394
5.9.8;Acknowledgments;395
5.9.9;References;395
5.10;11 TRP Channels;406
5.10.1;11.1 Introduction;406
5.10.2;11.2 TRP Channel History;406
5.10.3;11.3 Classification;407
5.10.4;11.4 Structural Aspects;408
5.10.5;11.5 Activation Mechanisms;414
5.10.6;11.6 Concluding Remarks;421
5.10.7;Acknowledgments;422
5.10.8;References;422
5.11;12 Ion Channels in Epithelial Cells;431
5.11.1;12.1 Ion Channels and Epithelial Function;431
5.11.2;12.2 Structural and Evolution of Epithelial Channels;435
5.11.3;12.3 Functional Specializations of Epithelial Ion Channels;439
5.11.4;12.4 Regulation of Epithelial Ion Channels;443
5.11.5;12.5 Summary;447
5.11.6;References;447
6;Part III Theoretical Approaches;452
6.1;13 PoissonÒNernstÒPlanck Theory of Ion Permeation Through Biological Channels;453
6.1.1;13.1 Introduction;453
6.1.2;13.2 Basic (Primitive) PNP Theory (and Its Limitations);455
6.1.3;13.3 Numerical Algorithms for Solving the 3D PNP Equations;463
6.1.4;13.4 Application of Primitive PNP to Gramicidin A in Charged/ Dipolar Lipid Bilayers;465
6.1.5;13.5 Incorporating Ion (De)Hydration Energy Effects into PNP: DSEPNP;468
6.1.6;13.6 Incorporating Effects of Channel Protein Fluctuation in PNP: PMFPNP;472
6.1.7;13.7 Conclusions and Outlook;481
6.1.8;Acknowledgments;483
6.1.9;References;483
6.2;15 Brownian Dynamics: Simulation for Ion Channel Permeation1;510
6.2.1;15.1 Introduction;510
6.2.2;15.2 Stochastic Dynamics Simulations;512
6.2.3;15.3 Application of Brownian Dynamics in Ion Channels;516
6.2.4;15.4 Mathematical Formulation of Brownian Dynamics Algorithm;523
6.2.5;15.5 Probabilistic Characterization of Channel Conductance;529
6.2.6;15.6 Brownian Dynamics Simulation;535
6.2.7;15.7 Adaptive Controlled Brownian Dynamics Simulation;537
6.2.8;15.8 Concluding Remarks;539
6.2.9;References;542
6.3;16 Molecular Dynamics Simulation Approaches to K Channels;547
6.3.1;16.1 Introduction: Potassium Channels;547
6.3.2;16.2 Homology Modeling;548
6.3.3;16.3 MD Simulations of Ion Channels;550
6.3.4;16.4 Essential Dynamics of Ion Channels;551
6.3.5;16.5 What Can Simulations Tell Us?;554
6.3.6;16.6 Future Perspectives;562
6.3.7;Acknowledgments;563
6.3.8;References;563
7;Part IV Emerging Technologies;570
7.1;17 Patch-Clamp Technologies for Ion Channel Research;571
7.1.1;17.1 Introduction;571
7.1.2;17.2 Recordings of Ion Channel Activity;573
7.1.3;17.3 Planar Patch-Clamp Technologies;579
7.1.4;17.4 Simultaneous Electrical and Fluorescence Measurements;586
7.1.5;17.5 The Grand Challenge: Single-Charge Detection;586
7.1.6;17.6 Future Prospects;589
7.1.7;Acknowledgment;590
7.1.8;References;590
7.2;18 Gated Ion Channel-Based Biosensor Device;594
7.2.1;18.1 Introduction;594
7.2.2;18.2 Membrane-Based Biosensors;594
7.2.3;18.3 The Ion Channel Switch ICSTM Biosensor;595
7.2.4;18.4 Fabrication of a Membrane-Based Biosensor;596
7.2.5;18.5 Mechanism of Operation;604
7.2.6;18.6 Biosensor Characterization;611
7.2.7;18.7 Further Developments;614
7.2.8;Acknowledgments;615
7.2.9;References;615
7.3;19 Signal Processing Based on Hidden Markov Models for Extracting Small Channel Currents;621
7.3.1;19.1 Introduction;621
7.3.2;19.2 General Description of the HMM Method;622
7.3.3;19.3 HMM Formulation and Estimation Problems;627
7.3.4;19.4 Problem 1: Bayesian State Estimation of HMM;633
7.3.5;19.5 Problem 2: HMM Maximum Likelihood Parameter Estimation;637
7.3.6;19.6 Discussion;641
7.3.7;Reference;645
8;Index;649