Foundations of Structural Biology
Regular price
32.250 KD
inc. VAT
Couldn't load pickup availability
Table of contents
- Foundations of Structural Biologyiii
- Copyright Pageiv
- Contentsv
- Prefacexi
- CHAPTER 1. Introduction to Protein Structure1
- PROBLEMS5
- REFERENCES5
- CHAPTER 2. Solid-State and Solution Methods for Determining Biological Macromolecular Structure6
- DIFFRACTION METHODS6
- X-RAY CRYSTALLOGRAPHY7
- CRYSTALLIZATION8
- X-RAY DATA COLLECTION9
- RESOLUTION11
- STRUCTURE FACTORS, PHASES, AND REFINEMENT12
- MATHEMATICAL RELATIONSHIPS13
- DETERMINING THE POSITIONS OF HEAVY ATOMS14
- MOLECULAR REPLACEMENT: CALCULATING PHASES USING A HOMOLOGOUS STRUCTURE17
- TEMPERATURE FACTORS18
- REFINEMENT19
- ELECTRON DENSITY MAPS AND DIFFERENCE ELECTRON DENSITY MAPS19
- SUMMARY: DETERMINATION OF THE CRYSTAL STRUCTURE OF PROTEINS21
- NUCLEAR MAGNETIC RESONANCE METHODS FOR DETERMINING SOLUTION STRUCTURE21
- PROBLEMS24
- REFERENCES24
- CHAPTER 3. Crystallographic Coordinates and Stereodrawings25
- INTRODUCTION25
- HEADER RECORDS OF PDB FILES26
- COORDINATES29
- ATOM RECORDS IN A PDB FILE30
- ATOM LABELS30
- STEREODRAWINGS32
- STEREOGLASSES34
- DIVERGENT EYES36
- CROSSED EYES37
- THE AMINO ACIDS37
- VIEWING PROTEIN MODELS WITH A COMPUTER39
- THE FOUR-LETTER IDENTIFICATION CODE39
- DOWNLOADING COORDINATES WITH FTP40
- WORLD WIDE WEB PAGE FOR PDB40
- DISPLAYING PDB COORDINATES41
- PREKIN AND MAGE41
- SUMMARY46
- PROBLEMS46
- REFERENCES47
- APPENDIX 1: KINEMAGE COLOR PALETTE (DCR)47
- APPENDIX 2: MAGE KEYWORDS AND PARAMETERS (DCR)48
- CHAPTER 4. Properties of Biomacromolecules in the Crystalline State50
- INTRODUCTION50
- PROTEIN CRYSTALS50
- PHYSICAL PROPERTIES51
- CHEMISTRY OF CRYSTALLINE PROTEINS52
- CHEMICAL REACTIVITY53
- ENZYMATIC AND BIOLOGICAL ACTIVITY54
- CRYSTAL VERSUS SOLUTION NMR STUDIES55
- CRYSTALLOGRAPHIC TEMPERATURE FACTORS56
- STRUCTURAL HETEROGENEITY IN PROTEIN CRYSTALS58
- SUMMARY59
- PROBLEMS59
- REFERENCES60
- CHAPTER 5. Quaternary Structure of Proteins61
- INTRODUCTION61
- ASSOCIATION OF PROTEIN SUBUNITS61
- HELICAL OR CONTINUOUS PROTEIN POLYMERS62
- THE QUATERNARY STRUCTURE OF CLOSED AGGREGATES: OLIGOMERIC ENZYMES64
- BIOLOGICAL IMPLICATIONS OF QUATERNARY STRUCTURE68
- SURFACE ACCESSIBILITY69
- GENERATING COORDINATES FOR OTHER SUBUNITS71
- SUMMARY72
- PROBLEMS72
- REFERENCES73
- CHAPTER 6. Secondary Structure of Proteins75
- INTRODUCTION75
- THE CHEMICAL NATURE OF A POLYPEPTIDE CHAIN75
- DEFINITIONS OF SECONDARY STRUCTURE78
- B STRUCTURE81
- TURNS82
- THE COLLAGEN TRIPLE HELIX82
- PREDICTION OF SECONDARY STRUCTURE83
- SUMMARY83
- PROBLEMS84
- REFERENCES84
- CHAPTER 7. Domains and Supersecondary Structure86
- INTRODUCTION86
- DOMAINS87
- SUMMARY97
- PROBLEMS97
- REFERENCES98
- CHAPTER 8. Conformational States in Crystal and Nuclear Magnetic Resonance Structures99
- INTRODUCTION99
- COMPARISON OF TWO CONFORMATIONAL STATES100
- THE OXYGENATION OF HEMOGLOBIN: TWO CRYSTAL CONFORMATIONS102
- CONFORMATIONAL STATES IN OTHER CRYSTALLOGRAPHIC ANALYSES109
- SUMMARY110
- PROBLEMS111
- REFERENCES111
- APPENDIX112
- CHAPTER 9. Hydrogen Bonds and Water Molecules in Crystalline Proteins114
- INTRODUCTION114
- HYDROGEN-BONDING POSITIONS IN PROTEINS115
- NEUTRON DIFFRACTION117
- WATER MOLECULES OBSERVED IN CRYSTALLINE PROTEINS119
- THE DISTRIBUTION OF PROTEIN-BOUND WATER120
- WATER NETWORKS IN CRYSTALLINE PROTEINS123
- SUMMARY124
- PROBLEMS124
- REFERENCES125
- CHAPTER 10. Protein and Nucleic Acid Complexes126
- INTRODUCTION126
- STRUCTURAL DATA DESCRIBING DNA127
- INTERACTION BETWEEN DNA AND SITE-SPECIFIC PROTEINS130
- DNA-BINDING MOTIFS130
- HELIX–TURN–HELIX131
- PHAGE 434 REPRESSOR–DNA COMPLEX132
- A LEUCINE ZIPPER132
- SUMMARY134
- PROBLEMS135
- REFERENCES135
- CHAPTER 11. Metal Ions Bound to Proteins137
- INTRODUCTION137
- COORDINATION OF METALS IN PROTEINS138
- FUNCTIONAL REASONS FOR METAL ION BINDING139
- A METAL ION PROVIDING A CONFORMATIONAL FUNCTION140
- METALLOPROTEINS FOR TRANSPORT AND STORAGE140
- METALLOPROTEINS AS REDOX INTERMEDIATES141
- METALLOPROTEINS THAT BIND DIOXYGEN144
- METALLOPROTEINS THAT SERVE A CATALYTIC FUNCTION144
- SUMMARY146
- PROBLEMS147
- REFERENCES147
- CHAPTER 12. Lipid–Protein Interactions148
- INTRODUCTION148
- ELECTRON MICROSCOPY, ELECTRON DIFFRACTION, AND MEMBRANE PROTEIN STRUCTURE149
- MEMBRANE PROTEIN STRUCTURE BY ELECTRON MICROSCOPY AND X-RAY METHODS150
- LIPID-METABOLIZING ENZYMES152
- LIPID TRANSPORT AND STORAGE PROTEINS154
- SUMMARY156
- PROBLEMS156
- REFERENCES157
- APPENDIX 1: Extra Reading in Structural Biology158
- APPENDIX 2: Macromolecular Structure Information Resources160
- Index163
Imagine trying to understand an engine without visualizing its moving parts. Biological processes involve far more complex chemical reactions and components than any engine. Furthermore, the parts work together to do many more functions than an engine which sole task is to turn a shaft. Understanding the implications of the three-dimensional coordinates for a molecule with several thousand atoms requires an understanding of, and practice with, 3D imaging. For many biologists, this means acquiring a whole new set of skills. Foundations of Structural Biology is aimed at helping the reader develop visualization skills for protein or DNA segments, while also describing the fundamental principles underlying the organization and interaction between these complex molecules.
Key Features
* Explains how to use coordinate databases and atomic coordinates of biological macromolecules
* Teaches the skills of stereoviewing
* Contains computer-generated stereographics
* Describes the principles of symmetry and handedness in proteins and DNA
* Introduces metal and lipid binding proteins and DNA-protein interactions
* Explains the principles involved in understanding secondary and quaternary structure
* Includes coverage of protein-metal, protein-nucleic acid, and protein-lipid interactions
Key Features
* Explains how to use coordinate databases and atomic coordinates of biological macromolecules
* Teaches the skills of stereoviewing
* Contains computer-generated stereographics
* Describes the principles of symmetry and handedness in proteins and DNA
* Introduces metal and lipid binding proteins and DNA-protein interactions
* Explains the principles involved in understanding secondary and quaternary structure
* Includes coverage of protein-metal, protein-nucleic acid, and protein-lipid interactions