| Preface |
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vii | |
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xix | |
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Part 1 How Lipids Shape Proteins |
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Lipid Bilayers, Translocons and the Shaping of Polypeptide Structure |
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3 | (24) |
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3 | (2) |
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Membrane Proteins: Intrinsic Interactions |
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5 | (9) |
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Physical Determinants of Membrane Protein Stability: The Bilayer Milieu |
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5 | (4) |
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Physical Determinants of Membrane Protein Stability: Energetics of Peptides in Bilayers |
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9 | (4) |
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Physical Determinants of Membrane Protein Stability: Helix--Helix Interactions in Bilayers |
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13 | (1) |
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Membrane Proteins: Formative Interactions |
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14 | (7) |
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Connecting Translocon-assisted Folding to Physical Hydrophobicity Scales: The Interfacial Connection |
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14 | (2) |
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Connecting Translocon-assisted Folding to Physical Hydrophobicity Scales: Transmembrane Insertion of Helices |
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16 | (5) |
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21 | (6) |
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22 | (5) |
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Folding and Stability of Monomeric β-Barrel Membrane Proteins |
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27 | (30) |
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27 | (2) |
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Stability of β-Barrel Membrane Proteins |
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29 | (3) |
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Thermodynamic Stability of FepA in Detergent Micelles |
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29 | (1) |
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Thermodynamic Stability of OmpA in Phospholipids Bilayers |
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30 | (1) |
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Thermal Stability of FhuA in Detergent Micelles |
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31 | (1) |
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Insertion and Folding of Transmembrane β-Barrel Proteins |
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32 | (3) |
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Insertion and Folding of β-Barrel Membrane Proteins in Micelles |
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32 | (1) |
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Oriented Insertion and Folding into Phospholipid Bilayers |
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32 | (1) |
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Assemblies of Amphiphiles Induce Structure Formation in β-Barrel Membrane Proteins |
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33 | (1) |
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Electrophoresis as a Tool to Monitor Insertion and Folding of β-Barrel Membrane Proteins |
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34 | (1) |
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pH and Lipid Headgroup Dependence of the Folding of β-Barrel Membrane Proteins |
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35 | (1) |
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Kinetics of Membrane Protein Folding |
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35 | (2) |
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Rate Law for β-Barrel Membrane Protein Folding and Lipid Acyl Chain Length Dependence |
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35 | (1) |
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Synchronized Kinetics of Secondary and Tertiary Structure Formation of the β-Barrel OmpA |
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36 | (1) |
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Interaction of OmpA with the Lipid Bilayer is Faster than the Formation of Folded OmpA |
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36 | (1) |
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Folding Mechanism of the β-Barrel of OmpA into DOPC Bilayers |
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37 | (5) |
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Multistep Folding Kinetics and Temperature Dependence of OmpA Folding |
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37 | (1) |
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Characterization of Folding Intermediates by Fluorescence Quenching |
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38 | (2) |
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The β-Barrel Domain of OmpA Folds and Inserts by a Concerted Mechanism |
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40 | (2) |
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Protein-Lipid Interactions at the Interface of β-Barrel Membrane Proteins |
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42 | (1) |
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Stoichiometry of the Lipid--Protein Interface |
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42 | (1) |
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Lipid Selectivity of β-Barrel Membrane Proteins |
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42 | (1) |
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Orientation of β-Barrel Membrane Proteins in Lipid Bilayers |
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43 | (2) |
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Lipid Dependence of the β-Barrel Orientation Relative to the Membrane |
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43 | (1) |
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Inclination of the β-Strands Relative to the β-Barrel Axis in Lipid Bilayers |
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44 | (1) |
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Hydrophobic Matching of the β-Barrel and the Lipid Bilayer |
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44 | (1) |
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In vivo Requirements for the Folding of OMPs |
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45 | (6) |
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Amino Acid Sequence Constraints for OmpA Folding in vivo |
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45 | (1) |
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45 | (1) |
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Insertion and Folding of the β-Barrel OmpA is Assisted by Skp and LPS |
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46 | (2) |
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Role of Omp85 in Targeting or Assembly of β-Barrel Membrane Proteins |
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48 | (3) |
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51 | (6) |
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52 | (5) |
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A Paradigm of Membrane Protein Folding: Principles, Kinetics and Stability of Bacteriorhodopsin Folding |
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57 | (24) |
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57 | (2) |
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Principles of Transmembrane α-Helical Membrane Protein Folding: A Thermodynamic Model for Bacteriorhodopsin |
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59 | (1) |
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Bacteriorhodopsin Stability |
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60 | (3) |
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Side-chain Contributions to Helix Interactions and the Role of Pro |
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61 | (1) |
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62 | (1) |
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Pulling the Protein Out of the Membrane |
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63 | (1) |
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Bacteriorhodopsin Folding Kinetics |
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64 | (5) |
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Cotranslational Insertion |
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65 | (1) |
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Retinal Binding Studies to Apomembrane |
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65 | (2) |
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Unfolding, Refolding and Kinetic Studies in vitro |
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67 | (2) |
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Controlling Membrane Protein Folding |
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69 | (2) |
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71 | (10) |
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Summary of Bacteriorhodopsin Folding |
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71 | (2) |
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Implications for Transmembrane α-Helical Membrane Protein Folding |
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73 | (2) |
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75 | (6) |
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Post-integration Misassembly of Membrane Proteins and Disease |
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81 | (16) |
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81 | (1) |
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A Given IMP May be Subject to Numerous Disease-linked Mutations |
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82 | (2) |
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Ligand Rescue of Misassembly-prone Membrane Proteins: Implications |
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84 | (3) |
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What IMP Properties Affect Folding Efficiency in the Cell? |
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87 | (2) |
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Common Mutations in Transmembrane Domains That Lead to Misassembly and Disease |
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89 | (1) |
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Correlating Biophysical, Cell-biological and Biomedical Measurements |
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90 | (7) |
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91 | (6) |
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Part 2 How Proteins Shape Lipids |
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A Census of Ordered Lipids and Detergents in X-ray Crystal Structures of Integral Membrane Proteins |
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97 | (22) |
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97 | (1) |
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98 | (5) |
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Illustrative Examples of Selected Bound Lipids, Detergents and Related Molecules |
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103 | (11) |
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Integral Membrane Protein Structures Contain Ordered Native Lipids |
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103 | (4) |
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Structures of Lipids in Membrane Protein Co-crystals Differ from Those in Pure Lipid Crystals |
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107 | (1) |
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Native Lipids can Stabilize and Preserve Protein--Protein Interfaces |
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108 | (1) |
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Multiple Acyl Chain Conformations Exist for Efficient Packing with Protein Interfaces |
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108 | (1) |
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Lipid Acyl Chains Interact Primarily with Aliphatic and Aromatic Amino Acid Side-chains |
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109 | (1) |
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Unusual Lipid/Detergent Conformations Occur at the Protein--Lipid Interface |
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109 | (3) |
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A Bilayer Structure is Present in Crystals Grown from the LCP |
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112 | (2) |
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114 | (5) |
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115 | (4) |
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Lipid and Detergent Interactions with Membrane Proteins Derived from Solution Nuclear Magnetic Resonance |
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119 | (22) |
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119 | (1) |
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Heteronuclear Solution NMR of Protein/Detergent Complexes |
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120 | (2) |
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122 | (2) |
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Size and Shape of Pure Detergent Micelles and Detergent/Protein Complexes |
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124 | (1) |
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Sample Preparation for Solution NMR Measurements |
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125 | (3) |
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Protein/Detergent Interactions Monitored by NMR Spectroscopy |
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128 | (2) |
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Dynamics and Conformational Transitions of Membrane Proteins in Detergent Micelles |
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130 | (1) |
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MD Simulations of Protein/Detergent Complexes |
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131 | (2) |
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Implications on the Structure and Function of Membrane Proteins in Biological Membranes |
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133 | (8) |
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134 | (7) |
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Part 3 Membrane Penetration by Toxins |
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Lipid Interactions of a-Helical Protein Toxins |
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141 | (22) |
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141 | (4) |
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The Two Secondary Structures Compared |
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141 | (4) |
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Lessons from a Potassium Channel |
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145 | (1) |
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145 | (6) |
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Outer Membrane Interactions |
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146 | (1) |
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Colicin A Requires Acidic Lipids |
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147 | (1) |
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148 | (1) |
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The Colicin--Phospholipid Complex |
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149 | (1) |
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150 | (1) |
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151 | (5) |
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152 | (2) |
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154 | (1) |
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155 | (1) |
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156 | (7) |
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157 | (6) |
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Membrane Recognition and Pore Formation by Bacterial Pore-forming Toxins |
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163 | (24) |
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163 | (1) |
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Classification of Bacterial PFTs |
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163 | (3) |
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164 | (2) |
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166 | (1) |
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A General Mechanism of Pore Formation? |
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166 | (3) |
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169 | (6) |
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Recognition of Specific Membrane Lipids |
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170 | (2) |
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Recognition of Membrane-anchored Proteins or Carbohydrates |
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172 | (1) |
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The Role of Membrane Lipid Domains |
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173 | (2) |
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Oligomerization on the Membrane Surface |
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175 | (4) |
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Oligomerization Triggered by Lipid-induced Conformational Changes |
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176 | (2) |
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Oligomerization Following Proteolytic Activation of Toxins |
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178 | (1) |
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Membrane Penetration and Pore Formation |
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179 | (2) |
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181 | (6) |
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183 | (4) |
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Mechanism of Membrane Permeation and Pore Formation by Antimicrobial Peptides |
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187 | (34) |
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187 | (1) |
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The Cell Membrane is the Major Binding Site for Most Cationic Antimicrobial Peptides |
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188 | (4) |
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Non-receptor-mediated Interaction of Antimicrobial Peptides with their Target Cells |
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189 | (2) |
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A Receptor-mediated Interaction of Antimicrobial Peptides with their Target Cells |
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191 | (1) |
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Parameters Involved in the Selection of Target Cells by Antimicrobial Peptides |
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192 | (9) |
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The Role of the Composition of the Cell Wall and the Cytoplasmic Membrane |
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193 | (1) |
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The Role of the Peptide Chain and Its Organization |
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194 | (1) |
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The Extent of Hydrophobicity and Distribution of Positively-charged Amino Acids Along the Peptide Chain |
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194 | (1) |
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The Stability of the Amphipathic Structure |
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194 | (1) |
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The Ability of a Peptide to Self-associate in Solution and/or in Membranes |
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195 | (5) |
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Fatty Acid Modification can Compensate for the Hydrophobicity and Amphipathicity of the Peptide Chain |
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200 | (1) |
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The Lethal Event Caused by Antimicrobial Peptides |
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201 | (1) |
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How do Antimicrobial Peptides Damage the Integrity of the Target Cell Membrane? |
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202 | (7) |
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Membrane-imposed Amphipathic Structure |
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202 | (2) |
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Molecular Mechanisms of Membrane Permeation |
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204 | (1) |
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Pore Formation via the Barrel--Stave Model |
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204 | (1) |
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205 | (3) |
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The Molecular Architecture of the Permeation Pathway |
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208 | (1) |
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208 | (1) |
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Channel Aggregates/Hydrophobic Pores |
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208 | (1) |
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209 | (12) |
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210 | (11) |
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Part 4 Mechanisms of Membrane Fusion |
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Cell Fusion in Development and Disease |
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221 | (24) |
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221 | (1) |
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Developmental Cell Fusion for Health |
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221 | (12) |
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222 | (1) |
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222 | (1) |
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223 | (3) |
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226 | (1) |
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Epithelial Cell Fusion Assay in C. elegans |
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227 | (1) |
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227 | (1) |
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Developmental Genetics of Cell Fusion in C. elegans |
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227 | (1) |
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eff-1 Mutant Epidermal Cells do not Initiate Cell Membrane Fusion |
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228 | (1) |
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eff-1-mediated Cell Fusion is Essential for Healthy Organogenesis |
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228 | (2) |
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eff-1 Encodes Novel Type I Membrane and Secreted Proteins |
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230 | (1) |
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eff-1 is Highly Expressed in Epidermal Cells Ready to Fuse |
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230 | (1) |
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eff-1 is Sufficient for Cell Membrane Fusion in vivo |
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230 | (1) |
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Tissue-specific Fusogenic Activity of eff-1 in Pharyngeal Muscles |
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231 | (1) |
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Comparison between Cell Fusion in a Worm, a Fly and Vertebrates |
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231 | (2) |
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233 | (6) |
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Cell Fusion Mediated by Enveloped Viruses |
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233 | (1) |
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Dissection of Viral Membrane Fusion |
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234 | (1) |
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Initiation and Expansion of Membrane Fusion |
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234 | (1) |
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Protein--Protein and Protein--Lipid Interactions in Membrane Fusion |
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235 | (1) |
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The Role of Fusion Proteins Outside the Fusion Site |
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236 | (1) |
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HA Insiders Initiate Hemifusion and HA Outsiders Expand Fusion Pores |
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236 | (1) |
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Models for Final Expansion of Fusion Pores |
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237 | (2) |
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Dissection of Developmental Fusion Based on Viral Fusion Analogies |
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239 | (1) |
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Activation of a Developmental Fusogen |
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239 | (1) |
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Dissection of Developmental Cell Fusion |
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239 | (1) |
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Direct Cell Fusion Promotion or Indirect Relaxation of Fusion Blocks |
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240 | (1) |
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240 | (5) |
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241 | (4) |
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Molecular Mechanisms of Intracellular Membrane Fusion |
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245 | (34) |
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245 | (1) |
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Intracellular Fusion Reactions -- An Overview |
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246 | (1) |
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247 | (2) |
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SNARE Proteins -- The Fusion Catalysts? |
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249 | (13) |
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Assembly--Disassembly Cycle of SNARE Proteins |
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249 | (2) |
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N-terminal Domains of SNAREs -- Recruiting Proteins or Regulating SNARE Function? |
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251 | (1) |
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``Zippering'' Model for SNARE-mediated Membrane Fusion |
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252 | (1) |
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Trans-complexes -- Intermediates in the Fusion Pathway? |
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253 | (3) |
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Acceptor Complexes, Topology and Specificity |
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256 | (1) |
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256 | (1) |
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257 | (1) |
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258 | (1) |
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Challenges of the SNARE Hypothesis |
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259 | (1) |
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Persistence of Fusion in Spite of SNARE Deletions |
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260 | (1) |
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Late-acting Factors Uncovered in Yeast Vacuolar Fusion |
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260 | (2) |
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Exocytosis of Cortical Granules in Sea Urchin Oocytes |
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262 | (1) |
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SM Proteins and Other Regulators |
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262 | (2) |
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263 | (1) |
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264 | (3) |
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Measuring Fusion Pore Opening and Closure |
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265 | (1) |
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The Role of Proteins in Controlling Fusion Pore Opening |
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266 | (1) |
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267 | (12) |
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267 | (1) |
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268 | (11) |
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Interplay of Proteins and Lipids in Virus Entry by Membrane Fusion |
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279 | (28) |
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279 | (2) |
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Fusion of Pure Lipid Bilayers |
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281 | (3) |
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Viral Protein Sequences that Mediate Lipid Bilayer Fusion |
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284 | (2) |
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284 | (1) |
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285 | (1) |
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Other Regions of the Fusion Protein |
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285 | (1) |
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Interactions of Fusion Peptides with Lipid Bilayers |
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286 | (6) |
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HIV Fusion Peptide--Bilayer Interactions |
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287 | (1) |
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Influenza Fusion Peptide Structure |
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288 | (2) |
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Influenza Fusion Peptide Mutants |
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290 | (1) |
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Binding of Fusion Peptides to Lipid Bilayers |
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290 | (1) |
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Sendai, Measles and Ebola Fusion Peptide--Bilayer Interactions |
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290 | (1) |
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Perturbation of Bilayer Structure by Fusion Peptides |
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291 | (1) |
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Interactions of Transmembrane Domains with Lipid Bilayers |
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292 | (2) |
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Structure--Function (Fusion) Relationships of Membrane-interactive Viral Fusion Protein Domains |
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294 | (2) |
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294 | (1) |
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Transmembrane Domain Mutants |
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295 | (1) |
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Possible Mechanisms for Initiating the Formation of Viral Fusion Pores |
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296 | (11) |
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300 | (7) |
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Part 5 Cholesterol, Lipid Rafts, and Protein Sorting |
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Protein--Lipid Interactions in the Formation of Raft Microdomains in Biological Membranes |
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307 | (30) |
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Many Plasma Membrane Functions are Mediated by Molecular Complexes, Microdomains and Membrane Skeleton-based Compartments |
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307 | (2) |
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309 | (1) |
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Four Types of Membrane Domains |
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310 | (4) |
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The Cell Membrane is a Two-dimensional Non-ideal Liquid Containing Dynamic Structures on Various Time-Space Scales |
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314 | (1) |
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A Definition of Raft Domains |
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315 | (1) |
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The Original Raft Hypothesis |
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316 | (1) |
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Are there Raft Domains in Steady-state Cells in the Absence of Extracellular Stimulation? |
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316 | (8) |
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Standard Immunofluorescence or Immunoelectron Microscopy Failed to Detect Raft-like Domains in the Plasma Membrane of Steady-state Cells |
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317 | (1) |
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The Recovery of a Molecule in Detergent-resistant Membrane (DRM) Fractions Might Infer its Raft Association in the Cell Membrane, but the Relationship between DRM Fractions and Raft Domains is Complicated |
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317 | (2) |
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The Size of Rafts in Plasma Membranes of Steady-state Cells may be 10 nm or Less |
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319 | (3) |
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Mushroom Model for the Steady-state Raft |
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322 | (2) |
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Stabilized Rafts Induced by Protein Clustering in Plasma and Golgi Membranes |
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324 | (2) |
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Clustering of Raft Molecules by Ligand Binding or Crosslinking Induces Stabilized Rafts (``Receptor-cluster Rafts'') |
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324 | (1) |
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How can Raft Molecule Clustering Induce Stabilized Rafts? |
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324 | (2) |
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Can Receptor-cluster Rafts Work as Platforms to Facilitate the Assembly of Raftophilic Molecules? |
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326 | (3) |
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Benchmarks for Experiments Examining the Colocalization of Raftophilic Molecules |
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326 | (1) |
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Simultaneous Crosslinking of Two GPI-anchored Receptors |
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327 | (1) |
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Sequential Crosslinking of One Species of GPI-anchored Receptors Followed by Crosslinking of a Second Species without Fixation |
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328 | (1) |
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Examination of the Recruitment of Non-crosslinked Second Raftophilic Molecules to Crosslinked GPI-anchored Receptor Clusters |
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328 | (1) |
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Difficulty in Colocalization Experiments using Raftophilic Molecules: Low Levels of Colocalization and Quantitative Reproducibility Due to Sensitivity to Subtle Differences in Experimental Conditions and Protocols |
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329 | (1) |
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Timescales Again! Transient Colocalization of Raftophilic Molecules |
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329 | (2) |
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331 | (6) |
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332 | (5) |
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Protein and Lipid Partitioning in Locally Heterogeneous Model Membranes |
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337 | (32) |
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Introduction: Why Should We Use Simple Model Membranes to Gain Insight into Complex Membrane Organization? |
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337 | (3) |
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Relation of Domain Structure to a Biological Function |
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337 | (1) |
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An Accessible Detection Method |
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338 | (1) |
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338 | (2) |
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340 | (3) |
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GUVs: Properties and Preparation |
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342 | (1) |
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Methods of Investigation of Domain Formation in Biomimetic Membranes |
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343 | (2) |
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343 | (1) |
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Atomic Force Microscopy (AFM) |
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343 | (1) |
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Near-field Scanning Optical Microscopy (NSOM) |
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344 | (1) |
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Fluorescence Imaging (Confocal, Multi-photon) |
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344 | (1) |
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Fluorescence Photobleaching Recovery (FPR) or Fluorescence Recovery after Photobleaching (FRAP) |
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344 | (1) |
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Single Particle Tracking (SPT) |
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344 | (1) |
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Fluorescence Correlation Spectroscopy (FCS) |
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345 | (1) |
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Lipid Domain Assembly in GUVs |
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345 | (12) |
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345 | (1) |
|
Can Cellular Membrane Domains be Regarded as Phase Domains? |
|
|
345 | (2) |
|
Properties of Lipid Bilayer Phases |
|
|
347 | (1) |
|
Co-existence of Lipid Bilayer Phases |
|
|
348 | (1) |
|
|
|
348 | (1) |
|
|
|
348 | (3) |
|
|
|
351 | (2) |
|
Effect of Sterols on Lipid Segregation |
|
|
353 | (1) |
|
Lipid Dynamics in Domain-exhibiting GUVs |
|
|
354 | (1) |
|
``Fluidizing'' Effect of Cholesterol for High-Tm Lipids |
|
|
355 | (1) |
|
``Condensing'' Effect of Cholesterol for Low-Tm Lipids |
|
|
356 | (1) |
|
Spatial Organization and Dynamics of Membrane Proteins in GUVs |
|
|
357 | (1) |
|
From Model to Cellular Membranes |
|
|
358 | (11) |
|
Model Membranes Constitute Test Systems for Developing New and Improving Existing Detection Techniques |
|
|
358 | (3) |
|
Direct Comparison Between Results Obtained on Model and Native Membranes |
|
|
361 | (1) |
|
Model Membranes Demonstrate What Structures Can be Potentially Formed by Lipids and Proteins, and Suggest Mechanisms for Fulfilling in vivo Functions |
|
|
361 | (1) |
|
|
|
362 | (7) |
|
Part 6 Targeting of Extrinsic Membrane Protein Modules to Membranes and Signal Transduction |
|
|
|
In vitro and Cellular Membrane-binding Mechanisms of Membrane-targeting Domains |
|
|
369 | (34) |
|
|
|
|
|
|
|
369 | (1) |
|
Membrane Interactions of Membrane-targeting Domains |
|
|
370 | (3) |
|
Interfacial Location of Membrane-targeting Domains |
|
|
370 | (1) |
|
Energetics and Kinetics of Membrane--Protein Interactions |
|
|
371 | (2) |
|
|
|
373 | (3) |
|
|
|
373 | (1) |
|
|
|
374 | (1) |
|
Membrane-binding Mechanisms |
|
|
374 | (1) |
|
|
|
375 | (1) |
|
|
|
376 | (2) |
|
|
|
376 | (1) |
|
|
|
376 | (1) |
|
Membrane Binding Mechanisms |
|
|
377 | (1) |
|
|
|
378 | (1) |
|
|
|
378 | (2) |
|
Occurrence, Structure and Lipid Specificity |
|
|
378 | (2) |
|
Membrane-binding Mechanisms |
|
|
380 | (1) |
|
|
|
380 | (1) |
|
|
|
380 | (4) |
|
Occurrence, Structure and Lipid Specificity |
|
|
380 | (2) |
|
Membrane-binding Mechanism |
|
|
382 | (1) |
|
|
|
383 | (1) |
|
|
|
384 | (3) |
|
Occurrence, Structure and Lipid Specificity |
|
|
384 | (1) |
|
Membrane-binding Mechanism |
|
|
385 | (1) |
|
|
|
385 | (2) |
|
|
|
387 | (2) |
|
Occurrence, Structure and Lipid Specificity |
|
|
387 | (1) |
|
Membrane-binding Mechanism |
|
|
387 | (2) |
|
|
|
389 | (1) |
|
|
|
390 | (1) |
|
|
|
391 | (1) |
|
Other Phosphoinositide-binding Domains |
|
|
391 | (1) |
|
|
|
392 | (11) |
|
|
|
393 | (10) |
|
Structure and Interactions of C2 Domains at Membrane Surfaces |
|
|
403 | (20) |
|
|
|
|
|
403 | (1) |
|
C2 Domains: Ca2+-dependent and Ca2+-independent Membrane Binding |
|
|
404 | (1) |
|
What Drives Membrane Targeting of C2 Domains? |
|
|
405 | (1) |
|
Electrostatic Binding of Simple Linear Protein Motifs |
|
|
406 | (2) |
|
The Results of Electrostatic Calculations of C2 Domains |
|
|
408 | (2) |
|
Determining the Interactions and Positions of C2 Domains |
|
|
410 | (6) |
|
Site-directed Mutagenesis |
|
|
410 | (1) |
|
|
|
410 | (1) |
|
|
|
411 | (1) |
|
Site-directed Spin Labeling (SDSL) to Determine C2 Domain Orientation |
|
|
411 | (5) |
|
Proteins with Multiple C2 Domains |
|
|
416 | (1) |
|
Interactions of Phosphoinositides with C2 Domains |
|
|
417 | (6) |
|
|
|
418 | (5) |
|
Structural Mechanisms of Allosteric Regulation by Membrane-binding Domains |
|
|
423 | (14) |
|
|
|
|
|
|
|
|
|
423 | (1) |
|
How Membranes and PH Domains Regulate Rho Family-specific Guanine Nucleotide Exchange Factors (GEFs) |
|
|
424 | (5) |
|
DH and PH Domain Rho GEFs |
|
|
425 | (1) |
|
Regulation of GEF Activity by PH Domains |
|
|
425 | (4) |
|
Regulation of G-protein Receptor Kinase (GRK) 2 Activity by Lipids and the Gβγ Subunit at the Membrane |
|
|
429 | (3) |
|
Lipid Activation of Rac-GAP Activity: β2-Chimaerin |
|
|
432 | (5) |
|
The C1 Domain of β2-Chimaerin is Buried |
|
|
432 | (2) |
|
Mechanism of Allosteric Rac-GTPase Activation by the C1 Domain |
|
|
434 | (1) |
|
|
|
435 | (2) |
| Subject Index |
|
437 | |
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