Part I. Bacteriorhodopsin-related materials work for molecular electronics. Part II. Volumetric optical memory based on the branched photocycle of bacteriorhodopsin. Part III. The role of calcium in the bacteriorhodopsin binding site

Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)




Robert R. Birge


Dried films, Calcium binding, Chromophores, Optical memory, Bacteriorhodopsin

Subject Categories



Part I. A protocol for the routine isolation and purification of purple membrane sheets containing the integral membrane protein, bacteriorhodopsin, was developed based upon modifications of protocols already in the literature. This simplified protocol is geared toward the facile isolation of protein for use in molecular electronic devices. Methods for the incorporation of bacteriorhodopsin into various polymeric supports were also developed, primarily in the form of dried films and hydrated cubes. This work also represents the first reported production of dried films of the deionized protein, or blue membrane.

Part II. An architecture for a volumetric optical memory based on the branched-photocycle of bacteriorhodopsin is presented. The branching reaction circumvents problems associated with destructive reading and writing processes and allows access to a stable, long-lived state, separated both temporally and energetically from the main photocycle, thereby making long-term data storage possible. The state, denoted as Q, can only be accessed by exposing the protein to two different wavelengths of light in the proper sequence, with the appropriate temporal separation (roughly 2 ms between the light pulses). The Q-state (assigned as a binary one) is transparent to both writing and reading processes, making them rigorously non-destructive. Bacteriorhodopsin in its resting state is assigned as a binary zero. A differential absorption reading process is used to determine the state of each volumetric binary element. Preliminary results are reported.

Part III. The nature of the chromophore binding site of light-adapted bacteriorhodopsin is analyzed by using all-valence electron MNDO and MNDO-PSDCI molecular orbital theory to interpret previously reported linear and nonlinear optical spectroscopic measurements. It is concluded that the unique two-photon properties of the chromophore are due in part to the electrostatic field associated with a Ca$\sp{2+}$ ion near the chromophore. Four amino acids and three water molecules contribute significantly to the assigned chromophore adjacent calcium binding site, and two conformational minima are predicted. The cation binding site described is identified as the second high affinity binding site for calcium, and the chromophore binding site is, to a first approximation, positively charged.


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