Protein Structure and Diseases (eBook)

Front Cover 1
Protein Structure and Diseases 4
Copyright 5
Contents 6
Chapter 1: Graphical representation and mathematical characterization of protein sequences and applications to viral proteins 10
I. Introduction 11
II. Graphical Methods 18
III. Application to Viral Proteins 30
IV. Conclusion 41
References 41
Chapter 2: Structural, thermodynamic, and mechanistical studies in uroporphyrinogen III synthase:Molecular basis of congenita... 52
I. Introduction 53
II. Uroporphyrinogen III Synthase 56
III. Molecular Basis of CEP 63
IV. The Hotspot Mutation C73R-UROIIIS 71
V. Treatment of CEP 75
VI. Concluding Remarks 78
Acknowledgments 79
References 80
Chapter 3: Role of Fibrin Structure in Thrombosis and Vascular Disease 84
I. Introduction 85
II. The Coagulation Cascade 86
III. Fibrinogen Structure and Function 90
IV. Factor XIII Structure and Function 93
V. Clot Formation and Function 95
VI. Fibrinolysis 100
VII. Elastic Properties of Fibrin 103
VIII. Heterogeneity in Coagulation and Fibrin Structure 105
IX. Environmental Factors and Fibrin Structure 111
X. Fibrin Density and Thrombosis 114
XI. Interactions with Cells and Wound Healing 116
XII. Perspectives 118
References 119
Chapter 4: Structural, dynamic, and functional aspects of helix association in membranes... 138
I. Introduction 139
II. Prediction of Structure of HH Dimers 142
III. Free Energy of TM Helix-Helix Association 150
IV. Combination of Modeling and Experimental Techniques 155
V. Limitations and Shortcomings of the Computational Methods 157
VI. Comparison with NMR Models: How Reliable Is The Reference? 159
VII. Is an Accurate Structure Prediction Always Required? 160
VIII. What Makes TM Helices Suitable Pharmacological Targets? 161
IX. Modeling of TM Helical Dimers as a First Step Toward 3D Structure of Polytopic MPs 161
X. From Structure and Thermodynamics to Function and Design 162
XI. Conclusion 163
Acknowledgments 164
References 164
Chapter 5: Proteins MOVE! Protein dynamics and long-range allostery in cell signaling 172
I. Introduction 173
II. NHERF1 Modulates the Macromolecular Assembly, Cell Surface Retention, and Subcellular Localization of Membrane Proteins... 176
III. Signal Transduction by Allosteric Scaffolding Protein Interactions 180
IV. Structural Basis of Autoinhibition and Long-Range Allostery in NHERF1 187
V. Dynamic Propagation of Allosteric Signals by Nanoscale Protein Motion 195
VI. Summary and Perspective 222
Acknowledgments 222
References 223
Chapter 6: Structural diversity of class I MHC-like molecules and its implications in binding specificities 232
I. Introduction 233
II. Sequence Analysis 236
III. Structure Analysis 248
IV. Glycosyalation 267
V. Conclusion 270
Acknowledgments 270
References 271
Author Index 280
Subject Index 306
Colour Plate 314