1;Contents;6 2;Contributors;8 3;99 Understanding the Logic of I kappa B:NF- kappa B Regulation in Structural Terms;10 3.1;Abstract;10 3.2;1...Introduction;11 3.3;2...NF- kappa B and I kappa B;13 3.4;3...NF- kappa B Structure and Dimer Formation;16 3.4.1;3.1 Regulation of NF- kappa B Dimerization at the Interface;17 3.4.2;3.2 Regulation of NF- kappa B Dimerization at a Distance;17 3.4.3;3.3 Conditional NF- kappa B Dimerization;18 3.5;4...I kappa B Structure and Regulation of NF- kappa B;19 3.5.1;4.1 I kappa B alpha Binding to the NF- kappa B p50:RelA Heterodimer;19 3.5.2;4.2 Regulation of I kappa B alpha :NF- kappa B Complex Formation;20 3.5.3;4.3 The I kappa B beta :RelA Homodimer Complex;21 3.5.4;4.4 NF- kappa B Regulation by I kappa B epsilon ;22 3.5.5;4.5 The Non-Classical I kappa B Proteins p105 and p100;22 3.5.6;4.6 Post-Induction Repression of NF- kappa B by I kappa B;23 3.5.7;4.7 Kinetics of I kappa B Degradation;24 3.6;5...Recognition of DNA by NF- kappa B;24 3.6.1;5.1 NF- kappa B:DNA Complex Structures;25 3.6.2;5.2 NF- kappa B Recognition of kappa B DNA at the 5vprime-end;26 3.6.3;5.3 NF- kappa B Binding to the Inner Bases of kappa B DNA;27 3.6.4;5.4 Stabilization of NF- kappa B:DNA Complexes;27 3.6.5;5.5 Post-Translational Modification and NF- kappa B:DNA Complex Regulation;28 3.6.6;5.6 NF- kappa B Subunit Exchange in the Nucleus;29 3.7;Acknowledgments;29 3.8;References;30 4;107 NF- kappa B/Rel Proteins and the Humoral Immune Responses of Drosophila melanogaster;34 4.1;Abstract;34 4.2;1...Introduction;35 4.3;2...Microbial Recognition and Humoral Responses;36 4.3.1;2.1 Anti-microbial Peptides;36 4.3.2;2.2 Peptidoglycan Recognition and Immune Activation;37 4.3.2.1;2.2.1 Activation of the Toll Pathway;38 4.3.2.2;2.2.2 Activation of the IMD Pathway;41 4.4;3...Intracellular Signaling in the Toll and IMD Pathways;42 4.4.1;3.1 Toll Pathway;42 4.4.2;3.2 IMD Pathway;43 4.5;4...NF- kappa B Proteins;45 4.5.1;4.1 Dorsal and DIF;48 4.5.2;4.2 Relish;49 4.5.3;4.3 Transcriptional Regulation of NF- kappa B Targets;50 4.6;5...Co-activators of Drosophila Rel Proteins;53 4.7;6...Negative Regulators of the Toll and IMD Pathways;54 4.7.1;6.1 Catalytic PGRPs;54 4.7.2;6.2 Negative Regulators of Toll Signaling;55 4.7.3;6.3 Negative Regulators of IMD Signaling;56 4.8;7...Beyond AMPs;58 4.8.1;7.1 Anti-viral Immunity;58 4.8.2;7.2 Adaptive Immunity in Drosophila;59 4.9;8...Concluding Remarks;59 4.10;References;60 5;106 Specialized Chromatin Patterns in the Control of Inflammatory Gene Expression;70 5.1;Abstract;70 5.2;1...Specialization and Selectivity in the Inflammatory Gene Expression Programs;71 5.3;2...Specialized Chromatin Organizations at Different Groups of Inflammatory Genes;71 5.4;3...The Genomic Determinants of Nucleosomal Organization at Inflammatory Genes;72 5.5;4...A Role of the Nucleosome Barrier in Stimulus-selective Gene Induction;76 5.6;5...Chromatin Remodeling and Kinetics of NF- kappa B Activation: A Complex Interplay;77 5.7;6...Conclusions;79 5.8;Acknowledgments;79 5.9;References;79 6;98 IKK Regulation and Human Genetics;82 6.1;Abstract;82 6.2;1...Introduction;83 6.3;2...The Kinase Subunits;83 6.4;3...The NEMO/IKK gamma Regulatory Subunit: Structure and Function;85 6.5;4...Other Post-translational Modifications of NEMO;90 6.6;5...IKK-Related Genetic Diseases;91 6.6.1;5.1 Incontinentia Pigmenti (IP);92 6.6.1.1;5.1.1 Main Features of IP;92 6.6.1.2;5.1.2 Genetics of IP;92 6.6.1.3;5.1.3 Pathophysiology of IP;93 6.6.2;5.2 Anhidrotic Ectodermal Dysplasia with Immunodeficiency;94 6.6.3;5.3 Molecular Basis of NEMO-Related Pathologies;97 6.7;6...Are there other Components in the IKK Complex?;98 6.8;References;99 7;101 Control of NF- kappa B Activity by Proteolysis;105 7.1;Abstract;105 7.2;1...Regulation of NF- kappa B Activity by the Proteasome;106 7.2.1;1.1 The Ubiquitin and Proteasome System;106 7.2.2;1.2 Degradation of ''small'' I kappa Bs;106 7.2.3;1.3 Processing and Degradation of NF- kappa B1 and NF- kappa B2 Precursors;108 7.2