Prospects for octopus rhodopsin utilization in optical and quantum computation

Physics of Particles and Nuclei Letters

Volumn 4, Issue 2, 2007, Pages 189-196

  Sivozhelezov, V ^a   Nicolini, C ^a,b  

^a Fondazione ELBA Rome   (Italy)

^b UNIVERSITY OF GENOA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 34147124962     PISSN: 15474771     EISSN: None     Source Type: Journal    
DOI: 10.1134/S1547477107020227     Document Type: Article

References (31)

1. US Government Advanced Research and Development Activity, QIST Quantum Computing Roadmap Overview (2004), p. 12; http://qist.lanl.gov (2004).
2. L. M. Duan and H. J. Kimble, "Scalable Photonic Quantum Computation through Cavity-Assisted Interactions," Phys. Rev. Lett. 92, 127 902 (2004).
3. G. D. Field, A. P. Sampath, and F. Rieke, "Retinal Processing near Absolute Threshold: From Behavior to Mechanism," Annu. Rev. Physiol. 67, 491-514 (2005).
4. N. Shashar and T. W. Cronin, "Polarization Contrast Vision in Octopus," J. Exp. Biol 199, 999-1004 (1996).
5. A. Davies et al., "Three-Dimensional Structure of an Invertebrate Rhodopsin and Basis for Ordered Alignment in the Photoreceptor Membrane," J. Mol. Biol. 314, 455-463 (2001).
6. T. Hirai and S. Subramaniam, "Structural Insights into the Mechanism of Proton Pumping by Bacteriorhodopsin," FEBS Lett. 545, 2-8 (2003).
7. T. Fischer and N. A. Hampp, "Encapsulation of Purple Membrane Patches into Polymeric Nanofibers by Electrospinning," IEEE Trans. Nanobiosci. 3, 118-120 (2004).
8. J. L. Faulon, K. Sale, and M. Young, "Exploring the Conformational Space of Membrane Protein Folds Matching Distance Constraints," Protein Sci. 12, 1750-1761 (2003).
9. K. Bryl, "Visual and Archaeal Rhodopsins: Similarities, Differences, and Controversy," Cell. Mol. Biol. Lett. 8, 285-296 (2003).
10. I. M. Pepe and C. Cugnoli, "Retinal Photoisomerase: Role in Invertebrate Visual Cells," J. Photochem. Photobiol. B 13, 5-17 (1992).
11. G. Pollastri and A. McLysaght, "Porter: A New, Accurate Server for Protein Secondary Structure Prediction," Bioinformatics (2004).
12. J. Wang et al., "Development and Testing of a General Amber Force Field," J. Comput. Chem. 25, 1157-1174 (2004).
13. T. Madej, J. F. Gibrat, and S. H. Bryant, "Threading a Database of Protein Cores," Proteins 23, 356-369 (1995).
14. S. U. Miedlich et al., "Homology Modeling of the Transmembrane Domain of the Human Calcium Sensing Receptor and Localization of an Allosteric Binding Site," J. Biol. Chem. 279, 7254-7263 (2004).
15. I. D. Pogozheva, A. L. Lomize, and H. I. Mosberg, "The Transmembrane 7-Alpha-Bundle of Rhodopsin: Distance Geometry Calculations with Hydrogen Bonding Constraints," Biophys. J. 72, 1963-1985 (1997).
16. R. J. Trabanino et al., "First Principles Predictions of the Structure and Function of G-Protein-Coupled Receptors: Validation for Bovine Rhodopsin," Biophys. J. 86, 1904-1921 (2004).
17. J. Nathans, "Rhodopsin: Structure, Function, and Genetics," Biochemistry 31, 4923-4931 (1992).
18. M. Nakagawa et al., "How Vertebrate and Invertebrate Visual Pigments Differ in Their Mechanism of Photoactivation," Proc. Nat. Acad. Sci. USA 96, 6189-6192 (1999).
19. A. Terakita et al., "Counterion Displacement in the Molecular Evolution of the Rhodopsin Family," Nat. Struct. Mol. Biol. 11, 284-289 (2004).
20. Y. Yamazak et al., "Interaction of Tryptophan-182 with the Retinal 9-Methyl Group in the L Intermediate of Bacteriorhodopsin," Biochemistry 34, 577-582 (1995).
21. B. Isralewitz, S. Izrailev, and K. Schulten, "Binding Pathway of Retinal to Bacterioopsin: A Prediction by Molecular Dynamics Simulations," Biophys. J. 73, 2972-2979 (1997).
22. S. Rouhani et al., "Crystal Structure of the D85S Mutant of Bacteriorhodopsin: Model of an O-Like Photocycle Intermediate," J. Mol. Biol. 313, 615-628 (2001).
23. E. S. Imasheva et al., "Exploring the Function of Tyr83 in Bacteriorhodopsin: Features of the Y83F and Y83N Mutants," Biochemistry 40, 13 320-13 330 (2001).
24. J. Klein-Seetharaman et al., "Differential Dynamics in the G-Protein-Coupled Receptor Rhodopsin Revealed by Solution NMR," Proc. Nat. Acad. Sci. USA 101, 3409-3413 (2004).
25. Y. Koutalos et al., "Regeneration of Bovine and Octopus Opsins In situ with Natural and Artificial Retinals," Biochemistry 28, 2732-2739 (1989).
26. H. Tsukamoto, A. Terakita, and Y. Shichida, "A Rhodopsin Exhibiting Binding Ability to Agonist All-Trans-Retinal," Proc. Nat. Acad. Sci. USA 102, 6303-6309 (2005).
27. S. A. Schadel et al., "Ligand Channeling within a G-Protein-Coupled Receptor. The Entry and Exit of Retinals in Native Opsin," J. Biol. Chem. 278, 24896-24903 (2003).
28. A. Terakita, R. Hara, and T. Hara, "Retinal-Binding Protein As a Shuttle for Retinal in the Rhodopsin-Retinochrome System of the Squid Visual Cells," Vision Res. 29, 639-652 (1989).
29. I. M. Pepe, C. Cugnoli, and J. Schwemer, "Rhodopsin Reconstitution in Bleached Rod Outer Segment Membranes in the Presence of a Retinal-Binding Protein from the Honeybee," FEBS Lett. 268, 177-179 (1990).
30. A. Lewis et al., "Optical Computation with Negative Light Intensity with a Plastic Bacteriorhodopsin Film," Science 275, 1462-1464 (1997).
31. C. Nikolini et al., "Towards Light-Addressable Transducer Bacteriorhodopsin Based," Nanotecnology 9, 223-227 (1998).