Note: Intro -- Bacterial and Eukaryotic Porins -- Contents -- Preface -- References -- List of Contributors -- 1 Regulation of Porin Gene Expression by the Two-component Regulatory System EnvZ/OmpR -- 1.1 Introduction -- 1.2 The Structure of EnvZ -- 1.3 Biochemical Activities of EnvZ underlie Signaling -- 1.4 What is the EnvZ Activity Regulated by the Stimulus? -- 1.5 How is the Signal Propagated? -- 1.6 Is there a Role for Acetyl-phosphate in OmpR-P Production? -- 1.7 The OmpR Subfamily -- 1.8 OmpR Binding Sites -- 1.9 Recruitment of RNA Polymerase to OmpR-dependent Promoters -- 1.10 OmpR-RNAP Interaction Surface -- 1.11 Affinity Model of Porin Gene Regulation -- 1.12 A Test of the Affinity Model -- 1.13 Conformational Changes in OmpR Contribute to Differential Regulation of the Porin Genes -- 1.14 Other Factors that Regulate ompF and ompC -- 1.15 OmpR is a Global Regulator -- 1.15.1 Flagellar Biosynthesis -- 1.15.2 Curli Fimbriae Production -- 1.15.3 Virulence -- Acknowledgments -- References -- 2 The Structures of General Porins -- 2.1 Bacterial Outer Membrane Proteins -- 2.2 Construction of General Porins -- 2.3 Trimer Association and Folding -- 2.4 Pore Geometry -- 2.5 Permeation -- 2.6 Conclusion -- Acknowledgments -- References -- 3 Role of Bacterial Porins in Antibiotic Susceptibility of Gram-negative Bacteria -- 3.1 Introduction -- 3.2 Role of Porins in Antibiotic Resistance -- 3.2.1 Evolution of Clinical Isolates -- 3.2.2 Expression of a Modified Porin -- 3.3 In Vitro Mutagenesis Analyses of Porins and Modeling -- 3.3.1 Mutations in the Loop 3 Domain -- 3.3.2 Mutations in the Anti-loop 3 Domain -- 3.3.3 Modeling of β-Lactam in the OmpF Eyelet -- 3.4 Conclusion -- Acknowledgments -- References -- 4 Porins of the Outer Membrane of Pseudomonas aeruginosa -- 4.1 Introduction -- 4.2 The Outer Membrane Permeability Defect in P. aeruginosa. , 4.3 Porins Identified in the Genome Sequence -- 4.4 The General Porins -- 4.4.1 OprF -- 4.4.2 Other General Porins -- 4.5 Efflux -- 4.5.1 OprM -- 4.5.2 OprM Homologs -- 4.6 Specific Porins -- 4.6.1 OprB -- 4.6.2 OprP and OprO -- 4.6.3 OprD -- 4.6.4 OprD Homologs -- 4.7 TonB-dependent Receptors -- 4.7.1 FpvA -- 4.7.2 FptA -- 4.7.3 PfeA and PirA -- 4.7.4 HasR, PhuR and OptI -- 4.7.5 Other TonB-dependent Receptors -- 4.8 Conclusions -- Acknowledgments -- References -- 5 Regulation of Bacterial Porin Function -- 5.1 Introduction -- 5.2 Voltage Dependence -- 5.2.1 L3 and the Constriction Zone -- 5.2.2 Extracellular Loops -- 5.2.3 Modulation of Voltage Gating -- 5.3 Effect of pH -- 5.4 Polyamine Modulation -- 5.5 Others -- 5.6 Concluding Remarks -- Acknowledgements -- References -- 6 Reconstitution of General Diffusion Pores from Bacterial Outer Membranes -- 6.1 Introduction -- 6.2 Planar Lipid Bilayer Technique -- 6.3 Intrinsic Properties of General Diffusion Channels -- 6.3.1 Single-channel Analysis of OmpF Gating -- 6.3.2 Molecular Origin of Voltage Gating -- 6.3.3 Effect of Membrane Composition and OmpF-LPS Interactions -- 6.3.4 Open-channel Conductance -- 6.3.5 Voltage Effect and Channel Orientation -- 6.3.6 Ion Selectivity -- 6.3.7 The Permeating Cations Interact with Specific Elements along the Ionic Pathway -- 6.3.8 Single-channel Recordings versus Free Energy Calculation -- 6.4 OmpF as a Specific Channel: Antibiotic Translocation -- 6.5 Application: Nanoreactor -- Acknowledgments -- References -- 7 OmpA/OprF: Slow Porins or Channels Produced by Alternative Folding of Outer Membrane Proteins -- 7.1 Introduction -- 7.2 Controversies on OprF as the Major Porin of P. aeruginosa -- 7.2.1 Is the OprF Channel Wider than those of E. coli Porins? -- 7.2.2 Is OprF a Porin? -- 7.2.3 Is OprF the Major Porin in P. aeruginosa?. , 7.3 Similarity between OmpA and OprF -- 7.3.1 OmpA is also an Inefficient Porin -- 7.3.2 The Majority of OmpA and OprF Folds into Two-domain Conformers -- 7.4 The Minority, Open-channel Conformers of OmpA/OprF -- 7.5 The Nature of the Open Conformer -- 7.6 Regulation of Expression of ompA and oprF Genes -- References -- 8 Drug Efflux and Protein Export through Channel-tunnels -- 8.1 Introduction -- 8.2 Channel-tunnel-dependent Export Systems -- 8.2.1 The Type I Secretion System -- 8.2.1.1 Substrates -- 8.2.1.2 The Inner Membrane Transporters of Type I Secretion Systems -- 8.2.1.3 The Accessory Protein of the Type I Secretion System -- 8.2.2 Efflux Pumps -- 8.2.2.1 The Inner Membrane Transporters of Channel-tunnel-dependent Efflux Pumps -- 8.2.2.2 Accessory Proteins of Multidrug Efflux Pumps -- 8.2.3 Comparison of Channel-tunnel-dependent Export Systems in E. coli and P. aeruginosa -- 8.3 Channel-Tunnels -- 8.3.1 The Structure of TolC -- 8.3.1.1 The Channel Domain -- 8.3.1.2 The Tunnel Domain -- 8.3.2 Electrophysiological Characterization of TolC -- 8.3.2.1 The Role of Aspartate Residues at the Periplasmic Entrance -- 8.3.2.2 Opening of the Periplasmic Entrance -- 8.4 Model for TolC-dependent Export -- 8.4.1 The Role of the Accessory Protein -- 8.4.2 The Mechanism of Protein Secretion -- 8.4.3 The Mechanism of Efflux Pumps -- 8.4.3.1 Substrate Binding of Different Transporters -- 8.4.3.2 Export of Substances by RND Transporters Exclusively from the Periplasm? -- 8.5 Conclusion -- Acknowledgments -- References -- 9 Structure-Function Relationships in Sugar-specific Porins -- 9.1 Introduction -- 9.2 Maltoporin and Sucrose Porin -- 9.3 Probing Function by Site-directed Mutagenesis -- 9.3.1 Ionic Tracks -- 9.3.2 Greasy Slide -- 9.3.3 Tyrosine 118 -- 9.3.4 Translocation Kinetics -- 9.3.5 Changing Substrate Specificity -- 9.3.6 N-terminal Domain of ScrY. , 9.3.7 Probing the Role of the External Loops -- 9.4 Simulation of Maltoporin Function -- References -- 10 Functional Reconstitution of Specific Porins -- 10.1 Introduction -- 10.2 Isolation and Purification of Specific Porins -- 10.3 Reconstitution of Specific Porins in Lipid Bilayer Membranes -- 10.4 Analysis of Substrate Transport through Specific Porin Channels -- 10.4.1 Study of Ion Transport through the Phosphate-specific OprP of P. aeruginosa -- 10.4.2 Evaluation of the Stability Constant for Binding of Neutral Solutes to the Binding Site inside Specific Porins -- 10.4.3 Investigation of Substrate-binding Kinetics using the Analysis of Current Fluctuations -- 10.5 Study of Carbohydrate Binding to the Specific Porins of the LamB Family -- 10.5.1 LamB of E. coli -- 10.5.1.1 Study of LamB (Maltoporin) Mutants -- 10.5.2 ScrY (Sucrose Porin) of Enteric Bacteria -- 10.5.2.1 Study of Carbohydrate Binding to ScrY Mutants -- 10.6 Properties of the Cyclodextrin (CD)-specific Outer Membrane Porin CymA of Klebsiella oxytoca -- 10.7 Porin OmpP2 of Haemophilus influenzae is a Specific Porin for Nicotinamide-derived Nucleotide Substrates -- 10.8 Study of the Nucleoside-specific Tsx of E. coli -- 10.9 Conclusions -- Acknowledgements -- References -- 11 Energy-coupled Outer Membrane Iron Transporters -- 11.1 Common Features of Outer Membrane Iron Transporters -- 11.1.1 Energy Coupling of Transport -- 11.1.2 Iron Sources -- 11.1.3 Regulation -- 11.1.4 Transport across the Cytoplasmic Membrane -- 11.2 Crystal Structures of Energy-coupled Outer Membrane Transport Proteins -- 11.2.1 FhuA Transporter and Receptor -- 11.2.1.1 The Transport Activity of FhuA -- 11.2.1.2 Substrate Specificity of the E. coli FhuA Transporter -- 11.2.1.3 The Receptor Activity of FhuA -- 11.2.1.4 Analysis of Previously Isolated Mutants in the Light of the FhuA Crystal Structure. , 11.2.2 FecA Transporter and Signaler -- 11.2.2.1 Transport Activity of FecA -- 11.2.2.2 Signaler Function of FecA -- 11.2.3 FepA Transporter and Receptor -- 11.2.3.1 FepA Transport Activity for Fe(3+) Enterobactin and Receptor Activity for Colicin B -- 11.3 Other Fe(3+) Siderophore Transporters -- 11.3.1 The Outer Membrane Protein FpvA of P. aeruginosa Transports Fe(3+) Pyoverdin -- 11.3.2 The IroN Protein Transports Salmochelin -- 11.3.3 FyuA Transports Fe(3+) Yersiniabactin -- 11.4 Outer Membrane Proteins that Transport Heme -- 11.5 Outer Membrane Proteins that Transport Iron Delivered as Transferrin and Lactoferrin -- 11.6 Perspectives -- Acknowledgments -- References -- 12 Structural and Functional Aspects of the Vitamin B(12) Receptor BtuB -- 12.1 Introduction -- 12.1.1 Overview -- 12.1.2 Cbl Uptake and Utilization -- 12.1.3 Transport Components -- 12.1.4 Colicins and Phages -- 12.2 BtuB Structure -- 12.2.1 Shared Structural Features -- 12.2.1.1 The β-barrel -- 12.2.1.2 Periplasmic Turns -- 12.2.1.3 External Loops -- 12.2.1.4 The Hatch Domain -- 12.2.2 Calcium Binding -- 12.2.3 Cbl-binding Surfaces -- 12.2.3.1 Comparison to Iron-Siderophore Binding Surfaces -- 12.2.4 The Ton Box -- 12.2.4.1 Interaction of the Ton Box and TonB -- 12.3 BtuB Dynamics -- 12.3.1 Site-directed Spin Labeling -- 12.3.2 Substrate-induced Changes in the Ton Box -- 12.3.3 Transmembrane Region and Barrel Dynamics -- 12.3.4 Comparison to Crystal Structure -- 12.4 Revisiting Old Data -- 12.4.1 phoA Fusions -- 12.4.2 Behavior of In-frame Deletions -- 12.5 Myths and Models about TonB-dependent Transport Mechanism -- 12.5.1 "Ligand-gated Pores"? -- 12.5.2 The Barrel is Sufficient for TonB-dependent Transport? -- 12.5.3 The Hatch Stays in the Barrel? -- 12.6 Conclusions -- Acknowledgments -- References -- 13 Structure and Function of Mitochondrial (Eukaryotic) Porins. , 13.1 Introduction.