Protein Simulations (eBook)

Valerie Daggett (Herausgeber)

eBook Download: PDF

2003 | 1. Auflage
459 Seiten
Elsevier Science (Verlag)
978-0-08-049378-7 (ISBN)

Infos

Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function.

* Force Fields
* Ligand Binding
* Protein Membrane Simulation
* Enzyme Dynamics
* Protein Folding and unfolding simulations

Inhalt

Cover 1
Contents 6
Preface 10
Chapter 1. Assessment of the Role of Computations in Structural Biology 12
I. Introduction 12
II. Comparison of the Role of Computation in the Study of Small Molecules and Macromolecules 13
III. Comparison of Theory and Experiment 16
IV. Molecular Recognition and Docking 19
V. Error Estimation and Error Propagation in Experiment and Theory 21
VI. The Role of Models in Protein Simulations 24
VII. Parameterization 26
VIII. Testing of Theoretical Models for Structural Biology 27
IX. Conclusions 30
References 30
Chapter 2. Force Fields for Protein Simulations 38
I. Introduction 38
II. Protein Force Fields, 1980 to the Present 41
III. Beyond Fixed Atomic Point-Charge Electrostatics 56
IV. Modeling the Solvent Environment 73
V. Conclusions 88
References 89
Chapter 3. Protein Simulation and Drug Design 98
I. Introduction 98
II. Fixed-Conformation Models 99
III. Including Protein and Ligand Flexibility in Modeling Molecular Recognition 106
IV. Fast Approximate Simulation Methods for Calculating Binding Free Energies 114
V. Including Protein Flexibility in Virtual Screening 122
VI. Enhanced Sampling via the Replica-Exchange Method 126
VII. Conclusions 128
References 129
Chapter 4. Free Energy Calculations and Ligand Binding 134
I. Introduction 134
II. Free Energy Perturbation and Thermodynamic Integration 136
III. Extrapolation of Free Energies 146
IV. Linear Interaction Energy Approaches 148
V. MM-PBSA 158
VI. PROFEC 160
VII. Dynamics and Chemical MC/MD 162
VIII. Conclusions 165
References 166
Chapter 5. Membrane Protein Simulations: Ion Channels and Bacterial Outer Membrane Proteins 170
I. Introduction 170
II. Simulation Methods 173
III. Ion Channels 177
IV. Outer Membrane Proteins 185
V. Future Prospects 194
References 196
Chapter 6. Large Scale Simulation of Protein Mechanics and Function 206
I. Introduction 206
II. Technology for Simulation and Visualization of Large Biomolecular Systems 209
III. Aquaporins–Membrane Water Channels 212
IV. Energy Conversion in ATP Synthase 222
V. Mechanical Signaling in Fibronectin 243
VI. Outlook 248
References 250
Chapter 7. Structure/Function Correlations of Proteins Using MM, QM/MM and Related Approaches: Methods, Concepts, Pitfalls, and Current Progress 260
I. Introduction 260
II. Classical Force Fields and Their Use 261
III. Evaluation of Electrostatic Free Energies of Macromolecules 269
IV. Methods for Simulation of Chemical Processes in Enzymes 274
V. Studying Enzyme Catalysis 285
VI. Concluding Remarks 312
References 313
Chapter 8. Catalysis and Specificity in Enzymes: A Study of Triosephosphate Isomerase and Comparison with Methyl Glyoxal Synthase 326
I. Introduction 326
II. Computational Methods 331
III. Preparation of the Active Site: The TIM ‘‘Lid’’ Transition 335
IV. Analysis of Mechanisms of the TIM Catalyzed Reactions: The Effect on the Activation Barrier 338
V. Dynamic Effects in the TIM Reaction 355
VI. Catalytic Specificity: Comparison of TIM and MGS 369
VII. Conclusions 377
References 379
Chapter 9. All-Atom Simulations of Protein Folding and Unfolding 384
I. Background 384
II. Overview of Results 388
III. Conclusions/Summary 406
References 410
Author Index 416
Subject Index 440
Color Plate Section 461

Produkt-Details

• Erscheint lt. Verlag: 26.11.2003
• Sprache: englisch
• Themenwelt: Sachbuch/Ratgeber
• Themenwelt: Medizin / Pharmazie ► Gesundheitsfachberufe
• Themenwelt: Medizin / Pharmazie ► Medizinische Fachgebiete ► Pharmakologie / Pharmakotherapie
• Themenwelt: Medizin / Pharmazie ► Physiotherapie / Ergotherapie ► Orthopädie
• Themenwelt: Naturwissenschaften ► Biologie ► Biochemie
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Zellbiologie
• Themenwelt: Naturwissenschaften ► Physik / Astronomie ► Angewandte Physik
• Themenwelt: Technik ► Medizintechnik
• Themenwelt: Technik ► Umwelttechnik / Biotechnologie
• ISBN-10: 0-08-049378-5 / 0080493785
• ISBN-13: 978-0-08-049378-7 / 9780080493787