Bacteriorhodopsin

Ann Hermone, Richard Jaffe (code ASC), Andreas Parusel, Andrew Pohorille and Michael Wilson

Abstract

Bacteriorhodopsin (BR) is a retinal protein molecule found in the photosynthetic system of a salt-marsh bacterium called Halobacterium salinarium. In its native form, the BR molecule is located in a cell membrane commonly called the purple membrane (PM). Within the bacterial cell, BR is critical to the survival of the organism in an oxygen-deficient environment, as the BR molecules function as light-driven proton pumps which transport protons across the cell membrane. This generates a proton gradient which in turn produces an electrochemical potential used by the organism to synthesize adenosine triphosphate (ATP). Effectively, BR is used by the bacterium to directly convert sunlight into chemical energy. The absorption of light also initiates a photocycle in the BR molecule which accompanies the transportation of protons. The characteristics and effects of this photocycle make it a potentially useful material for development as an optically sensitive film that is self-developing and erasable. A tremendous advantage of BR's organic nature is that it readily lends itself to genetic engineering, which allows the generation of genetic variants that may possess significantly different optical characteristics. We propose here to inititate an effort of quantum-level modeling and simulation that may allow different forms of BR to be rapidly developed, genetically tailored to optimize the optical characteristics for specific applications such as holographic data storage.

Statement of Problem and Its Importance

Holographic data storage techniques offer the possibility of storing digital or analog data within a 3-dimensional volume, rather than just on a surface such as with conventional magnetic or magneto-optic storage technology. In addition, data is written and read a block at a time rather than serially. Because of the volume effect, holographic storage in principle offers much higher storage densities and capacities than current storage systems. The parallel recording and readout capability of holographic data storage also promises significantly faster data transfer rates than can be obtained using the serial recording/readout employed with the current technology. Another potential advantage of holographic storage systems for the space environment may be decreased vulnerability to damage from gamma radiation since data bits are effectively distributed over a large volume of material rather than located at a single point. If a small region of the storage medium is damaged a decrease in signal-to-noise of a larger data block occurs, but specific data is not lost.

In terms of density, data stored holographically in a 1 mm thick optical medium can have an equivalent areal storage density of  100 bits/_m2, an increase of a factor of about 20 over the currently best DVD technology, and even more in comparison to magnetic hard disks. This translates into a total capacity of approximately 100 GBytes in a single 120 mm diameter disk (i.e. the size of a CD or DVD disk) of holographic material. The density and capacity numbers will scale approximately linearly with the thickness of the medium, so even higher capacities are possible several-mm thick materials. Because of this extraordinary potential, a great deal of research has gone into the general area of holographic data storage during the past decade. However, the single most problematic area obstructing the development of this technology is the availability of a holographic material with the appropriate characteristics for the application.

We believe that optical films fabricated with BR as the active chromophore have the potential to meet these demanding requirements. The active chromophore in BR, retinal, undergoes photochemical reaction from its fully-extended, lowest-energy form (trans) to one of several higher-energy cis isomers. Optical films incorporating BR in a polymeric matrix have already been demonstrated by Ames researchers and others, to allow the recording of extremely high resolution (>5000 lines/mm) holograms with reasonable diffraction efficiency ( 7-10that are optically erasable and can be re-written millions of times without film or material degradation. However, images or holograms recorded at room temperature in the natural form of BR (called wildtype BR) have a short lifetime (on the order of milliseconds to a few seconds) due to thermal relaxation of the excited molecular state back down to the ground molecular state. While appropriate for some optical processing applications, this is unacceptable for data storage applications, where the data must remain permanently recorded until actively erased.

Genetic engineering approaches have already been applied to BR as a means to alter the molecule's optical properties, primarily through the technique of site-specific mutagenesis. It is hoped that the thermal relaxation of the final molecular will be blocked in the genetically engineered BR without compromising the attractive photochemical propoerties that enable the hologram formation. In one example of genetically engineered BR, a variant known as D85N is created by substituting an asparagine residue for an aspartic acid at position 85 in the 248 amino acid polypeptide chain near the retinal part of the molecule. This variant shows dramatically different behavior in the sense that the excited molecular state formed by photon absorption in the red part of the visible spectrum is thermally stable and does not decay back down to the ground state. However, it is still optically erasable via the absorption of a blue photon, and is thus a good preliminary candidate for use in holographic data storage, although it does have some disadvantages such as low recording sensitivity.

Genetic engineering has resulted in significant advances in the utility of BR for holographic data storage applications, but this work has been pursued mainly by a trial-and-error approach. Given the complexity of the BR molecule, this type of approach has been quite slow. We propose to use a combined quantum chemistry-molecular simulation approach to guide the genetic engineering effort. We intened to use quantum chemistry methods to study photochemical pathways in retinal and use the results to determine the influence of the protein environment on the important photoisomerization mechanisms. When we have a better understanding of the changes taking place in BR upon photoabsorption and fluorescence, we will be able to determine how genetically engineered modifications fo the protein will alter the system. In particular, we will study ways of improving the optical performance of BR films. For example, we will seek to increase the thermal stability of the write states and enhance the quantum efficiency of the molecular transitions.

Impact of Proposed Research

The anticipated result of the proposed quantum mechanics-molecular modeling study of the BR molecule is a deeper understanding of changes it undergoes during the photocycle. This will enable us to evaluate the effects of specific genetic mutations on the photocycle and to identify genetic mutations that will modify the photocycle in a controlled fashion. Being able to simulate the molecular behavior of BR in different genetic configurations will allow us to guide the genetic engineering changes to be performed experimentally in the laboratory. This should permit the development of BR variants with superior optical characteristics for holography and other applications in a reduced time frame. It may also lead to the discovery of some genetic variants that might never be physically made without such prior modeling simulations.