Molecules : nucleation, aggregation and crystallization : beyond medical and other implications

Contents......Page 10
Preface......Page 6
Infectious amyloid nucleants......Page 14
Fossils show accurate speciation in paleobotany and paleozoology......Page 15
Twinning of minerals......Page 16
Any β-pleated polymeric assembly as a two-dimensional
sheet or as a fibril may act as a heteronucleant for
different amyloidogenic proteins......Page 17
Synthesis of prion-like infectious nucleants......Page 18
Biological macromolecules all interact strongly with SiO2, the most common solid mineral on the surface of Earth. Montmorillonite clay deposits cause delayed neurodegenerative diseases......Page 19
References......Page 20
2. Gels Mimicking Antibodies in Their Selective Recognition of Proteins and Its Potential Use for Protein Crystallization Jan Sedzik, Nasim Ghasemzadeh, Fred Nyberg and Stellan Hjertén......Page 24
Introduction......Page 25
Preparation of a ribonuclease-specific gel......Page 26
Can a bed be designed with selectivity for more than one protein?......Page 28
Selective bed with higher flow rate......Page 31
The selectivity of the artificial gel antibodies......Page 34
Do some protein molecules become attached covalently to the gel matrix?......Page 35
What conclusions can be drawn from the finding that (bio-)affinity methods do not always give the selectivity theoretically expected?......Page 36
Classification of chromatographic techniques in terms of the number of bonds between the solute and the stationary phase and the strength of these bonds......Page 37
Some comments on the mechanism of selective recognition......Page 38
Artificial gel antibodies for detection of biomarkers......Page 39
Selectivity, protein capacity and imprinting of bioparticles......Page 40
Potential applications......Page 42
Conclusions......Page 43
References......Page 44
Introduction......Page 48
The Basis of Biological Membranes......Page 49
Basic Bioinformatics......Page 50
Focus on the Myelin Membrane......Page 52
Myelin basic protein......Page 53
P0 protein......Page 54
PLP protein......Page 57
MOG......Page 60
Summary......Page 63
References......Page 64
Introduction......Page 68
Proteomics......Page 70
Techniques and strategies......Page 71
Peptide mass fingerprinting......Page 72
Post-translational and Chemical Modifications......Page 73
MALDI Imaging......Page 74
MS in structural biology......Page 75
Fibroblast growth factor (FGF) and fibroblast growth factor receptor (FGFR)......Page 76
RNA polymerase......Page 77
Ribosome......Page 78
Protein-lipid interactions......Page 81
Acknowledgments......Page 82
References......Page 83
Introduction......Page 88
Electron Density Profile on an Absolute Scale......Page 92
Method......Page 95
Model calculation......Page 98
References......Page 103
Introduction......Page 108
Why Two-Dimensional Crystals?......Page 109
Electron Crystallography: Initial Characterization......Page 110
Membrane proteins......Page 111
Symmetry......Page 114
Size......Page 116
Stacking, multilayers......Page 117
Specimen preparation and temperature......Page 119
Data processing......Page 120
2D or 3D Crystallization?......Page 121
Acknowledgments......Page 122
References......Page 123
7. Crystallization of Proteins: Principles and Methods Lata Govada......Page 126
The crystallization phase diagram......Page 127
Precipitation zone......Page 128
Nucleation zone......Page 129
Crystallization Methodologies......Page 130
Batch crystallization......Page 131
Sitting drop......Page 133
Liquid-liquid interface diffusion......Page 134
Granada crystallization box® (GCB)......Page 135
Dialysis......Page 136
Microdialysis......Page 137
Conclusions......Page 138
References......Page 139
Introduction......Page 142
The Microbatch Techniques......Page 143
The mechanism of crystallization under oil......Page 144
The contribution of oil to the control of heterogeneous nucleation......Page 148
Cleanliness of trials......Page 149
Effect of surface contact......Page 150
Application of organic molecules as precipitants and/or additives......Page 152
Crystallization of membrane proteins under oil......Page 153
References......Page 154
Introduction......Page 158
Fundamentals......Page 159
Solubility and Supersaturation......Page 160
Nucleation......Page 162
Crystal Growth......Page 164
Productivity......Page 166
Solid phase......Page 167
Particle size......Page 168
Crystal shape......Page 170
Product purity......Page 173
The Process......Page 175
The role of agitation......Page 177
Control of the product crystal mean size......Page 178
References......Page 183
10. Myelin Basic Protein, A Saucy Molecule With High Responsiveness to the Environment or Just an Unusual Membrane Protein? Paolo Riccio......Page 186
Myelin Basic Protein: What Is It and What Does It Do?......Page 187
The IUPs......Page 188
MBP Ligands and Functions......Page 189
The absence of structure in the acid-extracted molecule......Page 190
MBP as a membrane protein: The discovery of lipid-bound MBP......Page 191
Partitioning of MBP in the Myelin Membrane......Page 193
Incorporation of myelin basic protein in liposomes made of myelin lipids......Page 194
Concluding Remarks......Page 196
Acknowledgments......Page 197
References......Page 198
Introduction......Page 208
Magnetic field orientation......Page 209
Magnetic force......Page 210
Generation of magnetic fields by various magnets......Page 212
Superconducting magnets for supplying uniform magnetic force......Page 213
Modes of operation of various magnets......Page 214
Historical Background......Page 215
Protein crystals grown in a magnetic field exhibit orientation......Page 219
Sedimenting crystals......Page 221
Other Studies on Magnetic Orientation of Protein Crystals......Page 222
Other Possible Mechanisms Through Which Homogeneous Magnetic Fields May Contribute to Quality Improvement......Page 223
Studies on Crystal Perfection in Homogeneous Magnetic Fields......Page 224
Our studies on the use of a magnetic force......Page 227
Summary......Page 231
References......Page 232
Introduction......Page 238
Pre-crystallization assumptions......Page 239
Rationale and design of the crystallization trials......Page 240
Algorithm......Page 241
Discussion......Page 242
Summary......Page 246
References......Page 247
13. Virtual Molecule: P0 Myelin Glycoprotein. I. Homology Modeling and Prediction of the Secondary and Tertiary Structure Jan Pawel Jastrzebski and Jan Sedzik......Page 250
Methods and Tools for Homology Prediction......Page 251
Construction and Analysis of a Three-Dimensional Atomic Model of P0 Glycoprotein......Page 252
The P0 extracellular domain — Soluble part......Page 253
The P0 transmembrane segment is 21 amino residues long......Page 256
The P0 intracellular part......Page 258
Hydrophobicity and Electrostatic Potential of P0 Protein......Page 260
Structural Effects of Breaking the Disulfide Bridge......Page 262
Summary and Discussion......Page 267
References......Page 268
Introduction......Page 272
Membrane Protein Crystallization: A Standard Approach......Page 273
Cubic phase crystallization......Page 276
Crystallization in the sponge phase......Page 281
Crystallization from vesicles......Page 284
Crystallization from bicelles......Page 287
Towards a General Method of Membrane Protein Crystallization......Page 289
References......Page 290
Introduction......Page 296
Amyloid in Alzheimer’s Disease......Page 299
Nuclear magnetic resonance spectroscopy......Page 301
Structure of A βin Fibrils......Page 303
Other Techniques......Page 304
A β Polymerization......Page 305
Gel Electrophoresis......Page 307
CD spectroscopy......Page 308
Fluorescence correlation spectroscopy (FCS)......Page 309
Inhibition of A β Polymerization......Page 310
Summary......Page 312
References......Page 313
16. Recent Advances in Structural Basis for Molecular Mimicry in Inflammatory Autoimmune Demyelinating Polyneuropathy Xin Yang......Page 318
Guillain–Barré syndrome......Page 319
A true case of molecular mimicry......Page 320
Campylobacter jejuni......Page 321
Hemophilus influenzae......Page 322
Oligosaccharides of LPSs that mimic ganglioside structure......Page 323
Oligosaccharides of LPSs or other molecules that mimic non-ganglioside structures......Page 332
Pathogenic auto-antibodies in CIDP......Page 335
Conclusion......Page 336
References......Page 337
17. Fresh Water Pearls of Wisdom on Protein Crystallization Jan Sedzik......Page 344
Glossary......Page 358
Index......Page 362