Theoretical and applied studies of rhodopsin and bacteriorhodopsin
Date of Award
Doctor of Philosophy (PhD)
Robert R. Birge
Retinal, Holographic memory, Rhodopsin, Bacteriorhodopsin
Biochemistry, Biophysics, and Structural Biology | Biophysics | Chemistry | Life Sciences | Physical Sciences and Mathematics
Part I . The conformational and electronic properties of the 12-s-cis and 12-s-trans conformers of 11-cis retinal are analyzed. Our models confirm that the 12-s-cis isomer is more stable in vacuum and the 12-s-trans conformer is more stable in polar and nonpolar solvent environments due to dispersive and electrostatic interactions. Electronic analysis indicates that the features in the absorption spectrum are due to a complex set of overlapping transitions. Assignments are made for all four band systems.
Ground- and excited-state surfaces connecting rhodopsin and bathorhodopsin along the [Special characters omitted.] dihedral reaction path are partially adiabatically mapped. Forward and reverse photochemistry is simulated via molecular dynamics. The activated complex is reached in ∼375 fs following excitation. Best results for quantum yields and product formation times are obtained by including both dynamic and phased (partitioned) nonadiabatic coupling: [Special characters omitted.] ps; [Special characters omitted.] ps. The lower quantum yield of the B [arrow right] R isomerization is due to a sign change in the nonadiabatic coupling term at [Special characters omitted.] = 92° and to the rapid arrival of the trajectory into the activated complex which prevents equilibration of the excited state and lowers the dynamic coupling term. The [Special characters omitted.] excited singlet state spectrum is calculated as a function of time following excitation of rhodopsin.
A model of thermal noise in rods is proposed whereby thermal isomerization occurs when the retinal Schiff base is unprotonated. This model accounts for the low activation energy of 23-27 kcal mol -1 and is supported by both molecular models and experimental measurements.
Part II . A prototype holographic memory is described which demonstrates simultaneous storage and retrieval of ten holographic images in the same volume of a bacteriorhodopsin(BR)/polyvinylalcohol(PVA) film. The suitability of BR as a volume holographic memory medium is discussed.
Photochemistry in dried PVA films of the blue membrane form of BR is demonstrated. As in solution, blue[Lef-right arrow]pink interconversion occurs, but with much lower quantum yield. Additionally, a species absorbing maximally at 450 nm appears as a photoproduct of blue membrane.
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Tallent, Jack R., "Theoretical and applied studies of rhodopsin and bacteriorhodopsin" (1999). Chemistry - Dissertations. Paper 100.