Molecular simulations and biomembranes : from biophysics to function

Contents......Page 12
1.1 Introduction......Page 18
1.2 Force Fields/Descriptions of Interactions......Page 21
1.2.1 Current Atomistic Force Fields......Page 22
1.2.2 Development of Force Field Parameters......Page 23
1.3 Starting Structures......Page 24
1.3.1 Bilayers......Page 25
1.3.3 Embedding Proteins in Bilayers......Page 26
1.4 Sampling......Page 28
1.4.2 Coarse Graining......Page 31
1.5 Pressure Coupling......Page 33
1.6 Electrostatics......Page 35
1.7 Periodicity......Page 36
1.8 Future Developments......Page 37
References......Page 38
2.1 Introduction......Page 43
2.2.1 Lateral Pressure Profile......Page 48
2.2.2 Calculation of Lateral Pressure Profile from Simulation......Page 49
2.2.3 Elastic Properties......Page 50
2.2.4 Interplay of Pressure Profile and Membrane Protein Activation......Page 51
2.3 Gauging Pressure Profile......Page 52
2.4.1 Dependence on Unsaturation Level......Page 55
2.4.2 Effects of Different Sterols in Two-component Membranes......Page 56
2.4.3 Pressure Profiles in Three-component Bilayers......Page 58
2.4.4 Implications of Anesthetics on Pressure Profile......Page 60
2.4.5 Elastic Properties Calculated from Lateral Pressure Profile......Page 62
2.4.6 Free Energy of Protein Activation and Lateral Pressure Profile......Page 65
2.5 Concluding Remarks......Page 67
References......Page 68
3.1 Introduction......Page 73
3.2.1 CG-MD and Lipid Bilayers......Page 74
3.2.2 CG-MD and Membrane Peptides and Proteins......Page 76
3.3 Evaluation of CG-MD: Model Membrane Peptides......Page 78
3.4.1 Glycophorin A......Page 81
3.4.2 Influenza M2 Channels......Page 83
3.5.1 Vesicle Simulations......Page 84
3.5.2 More Complex Membrane Proteins......Page 86
References......Page 90
4.1 Introduction......Page 93
4.2.2 Drugs......Page 95
4.3 The Solubility–Diffusion Model......Page 97
4.3.1 The z-Constraint Method......Page 98
4.4 Small Molecules......Page 99
4.5 Drugs......Page 100
4.6 Fullerene......Page 102
4.8 Conclusions......Page 104
References......Page 105
5.1 Introduction......Page 108
5.2.1 Overview......Page 111
5.2.2 Implicit Membrane Models forStudying Membrane Protein Folding......Page 112
5.2.3 The Generalized Born Model......Page 113
5.2.4 Non-polar Interactions......Page 116
5.2.5 Accuracy and Partitioning Properties......Page 117
5.2.7 Thermodynamic Analysis......Page 119
5.3.2 Transbilayer Peptide Folding......Page 121
5.3.3 Peptide Adsorption, Insertion and Folding......Page 128
5.3.4 Comparison with Explicit Methods......Page 141
5.3.5 Sampling Performance......Page 145
5.3.6 Conclusions......Page 151
References......Page 152
6.1 Introduction......Page 163
6.2 Methods......Page 165
6.3 All-atom Simulations......Page 167
6.4 Residue-based Coarse-grained Simulations......Page 168
6.5 Shape-based Coarse-grained Simulations......Page 169
6.6 Continuum Elastic Membrane Model......Page 174
6.8 Simulations of a Single N-BAR Domain......Page 176
6.9 Comparison of RBCG and SBCGSimulations for Systems with Six N-BAR Domains......Page 178
6.10 Effect of Different N-BAR Domain Lattices on Membrane Curvatures......Page 181
6.11 Comparing All-atom and SBCG Simulations of an N-BAR Domain Lattice......Page 184
6.13 Elastic Membrane Computations......Page 186
6.14 Conclusion......Page 189
References......Page 190
7.1 Introduction......Page 194
7.2.1 The Poisson–Boltzmann (PB) Equation......Page 197
7.2.2 Calculation of Electrostatic Free Energies and Decomposition......Page 198
7.2.3 The Modified PB Equation for Treatment of Transmembrane Voltage......Page 199
7.3.1 Electrostatics in the Intracellular Vestibule of K + Channels......Page 201
7.3.2 Long-pore Electrostatics in K + Channels......Page 208
7.3.3 K + Channels and the Transmembrane Potential......Page 212
7.4 Conclusion......Page 217
References......Page 218
8.1 Introduction......Page 220
8.2 The Amino-terminal Domain......Page 222
8.3.1 Selectivity and Modulation......Page 224
8.3.2 Dynamics......Page 226
8.4 The Transmembrane Domain......Page 233
References......Page 235
9.1 Introduction......Page 242
9.2 Outer Membrane Proteins......Page 243
9.3.1 OmpA and Its Homologues......Page 244
9.3.2 Simple OMPs in Diverse Environments......Page 247
9.5 Transporting Barrels......Page 249
9.5.1 TonB- dependent Transporters......Page 250
9.5.2 Autotransporters......Page 252
9.5.3 TolC......Page 254
9.6 Reacting Barrels......Page 256
9.7 Technological Barrels......Page 258
9.8 Conclusion......Page 260
References......Page 261
10.1 Introduction......Page 265
10.2 Computational Methodology......Page 267
10.2.2 Net Charge Density Distribution Calculation......Page 268
10.3 ATP-driven Transport in ABC Transporters......Page 269
10.4 Ion-driven Neurotransmitter Uptake by the Glutamate Transporter......Page 275
10.5 Substrate Binding and Selectivity in Glycerol-3-Phosphate Transporter......Page 280
10.6 Membrane Potential-driven Nucleotide Exchange in ADP/ATP Carrier......Page 285
10.7 Mechanically Driven Transport Across the Outer Membrane......Page 289
10.8 Conclusion......Page 294
References......Page 295
11.1 Introduction......Page 304
11.1.1 Carbon Nanotube Structure......Page 305
11.2 Molecular Dynamics Simulations......Page 306
11.2.2 Parameterization of CNT Models......Page 307
11.3 CNT Interactions with Lipids and Related Molecules......Page 309
11.4 Interaction of CNTs with Lipid Bilayers......Page 313
11.5 CNTs as Nanopores......Page 315
11.5.1 Transport of Water and Ions Through CNT Nanopores......Page 316
11.5.2 Nanopores as Nanosyringes......Page 318
References......Page 319
Subject Index......Page 323