Biomolecular Electronics: An Introduction via Photosensitive Proteins (1998)

1. Introduction.- A. Biophotonic Processes.- B. Bioelectric Phenomena.- C. Molecular Electronics.- D. Biomolecular Electronics.- E. Biomolecular Computing: An Overview of What Needs to Be Done.- 2. The Distinguished Family of Rhodopsins..- A. Visual Rhodopsin (VR) in Vertebrates.- 1. General Structure of Rhodopsins.- 2. The Photochemical Process in VR is Irreversible.- 3. Photoinduced VR Intermediates.- 4. Electrogenic VR Intermediates.- 5. Electrical Signals from the Retina.- 6. A Brief Look at Visual Pathways and Mechanisms.- 7. Measurement of Early and Late Receptor Potentials.- 8. VR Response to an Electric Field (Electrochromism).- 9. The Boundary Between Photochromism and Photoisomerism in Rhodopsins.- 10. The Influence of Ions on VR Spectra (Ionochromism).- 11. Rhodopsin in Fish Eyes.- B. Rhodopsins in Invertebrates and Microorganisms.- 1. Some Natural Examples of Rhodopsin-based Photopigments.- 2. Retinochrome: A Photoisomerizing Enzyme.- 3. Retinal-binding Proteins.- 4. Rhodopsins for Use in Detecting UV Light.- 5. Chlamyrhodopsin: A Recently Discovered Photopigment.- C. Bacterial Rhodopsin Isolated from Halobacteria.- 1. Discovery of a New Proton Pump.- 2. The Story of Discovery Unfolds.- 3. Biosynthesis of Purple Membranes.- 4. Purple Membranes: Two-dimensional Crystals.- 5. Halobacteria: A Riddle for Biological Evolution.- D. Modification of Rhodopsins.- 3. The Unique Properties of Bacteriorhodopdins (BR) as Energy Converters.- A. Wild-type Bacteriorhodopsin (BR).- 1. Chemical and Physical Properties of BR.- 2. The Photochemical Process of BR is Reversible!.- 3. Photocycle Intermediates.- 4. The Effects of Various Parameters on the BR Photocycle.- 5. Photochromic Properties.- 6. Photoelectric Properties.- 7. Electrochromic Properties.- 8. BR Viewed as a Black Box Energy Converter.- B. BR Variants.- 1. Random Mutagenesis.- 2. Site-specific Mutagenesis.- 3. How Many Strains of Halobacteria Have Been Found?.- 4. Photochromic Properties of BR Variants.- C. BR Analogs.- 1. Apomembranes.- 2. Artificial Retinal-Proteins.- 3. Photochemistry of BR Analogs.- 4. Analogs with Infrared Absorption.- 5. Analogs with Ultraviolet Absorption.- D. BR Monolayers and BR Films.- 1. BR Solubilization.- 2. BR Films.- 3. BR Aggregates.- 4. The Possibility of a Three Dimensional BR Crystal.- E. Halorhodopsin Acting as a Chloride Ion Pump.- F. The Discovery of Sensory Rhodopsins (SR).- 1. SR-I- An Attractant Receptor for Orange-red Light.- 2. SR-II- A Repellent Receptor for Blue-green Light.- G. Phototaxis of Phoborhodopsins.- 1. Phoborhodopsins Isolated from Halobacteria.- 2. Pharaonis Phoborhodopsin.- H. Yellow Protein Isolated from a Halophile.- I. A Summary of Properties of BR and BR Variants.- J. From Electronics to Bioelectronics.- 4. Photosensitive Materials for Use as Optical Memory.- A. Photographic Films.- 1. 150 Years of Photography.- 2. The End of Halogen-Silver Films?.- B. Photochromic Materials.- 1. 35 Years of Photochromic Materials Research.- 2. The Physics and Chemistry of Photochromic Processes.- 3. Organic and Inorganic Photochromic Materials.- 4. Is There a Future for Photochromic Materials?.- C. Construction of Layered Purple Membranes.- 1. Air-dried Layers on Supports.- 2. Layers with Oriented Purple Membrane.- 3. Purple Membranes in a Polymeric Matrix.- D. Biochrome: A BR-based Photochromic Film.- 1. The Discovery of Biochromic Films.- 2. Optical Characteristics.- 3. Holographic Properties.- E. BR Analogs for New Photochromic Films.- 1. Properties of BR Analogs.- 2. 4-keto BR Films.- 3. 4-keto BR: A Potentially Useful Anomaly.- F. More Photosensitive Materials.- 1. Chlorophyll Photographic Films.- 2. Visual Rhodopsin Photographic Films.- 3. Photographic Films with Enzymes.- 4. Other Types of Photochromic Materials in Nature.- 5. BR as Optolectronic Materials.- A. Molecular Computing Elements.- B. Ultrafast Electro-optical Detectors.- C. Biosensors.- D. Photosensitive Hybrids of Purple Membrane with Mitochondria and Nonphotosynthetic Bacteria.- E. Position-sensitive Detectors.- F. Photovoltaic Devices.- G. 3-D memory in BR.- 6. Applications of Biochrome and Similar Films.- A. Optical Memory.- B. Can Bacteriorhodopsin-based Compact Disks Exist?.- C. The Generation of the Second Harmonic of Laser Radiation.- D. Increasing the Contrast of a Photostat copy.- E. Polarization Holography.- F. Real Time Holography.- G. Holographic Connections for Optical Communication.- H. Biomedical Applications.- I. Military Use.- J. Light Testers.- K. From Toys to Computers.- 7. Conclusion.- A. Proteins in Bioelectronics.- B. The Truth and Science Fiction of Biocomputers.- 8. References.- 9. Glossary and abbreviations.- 10. Appendix.