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Biological Nanotechnology
Andrew Pohorille, Michael New, Michael Wilson and Christophe Chipot Planetary Biology Branch, NASA Ames Research Center and Department of Pharmaceutical Chemistry, University of California San Francisco
Nanotechnology offers the prospect of designing and building novel materials and devices at the atomic level. A long-term goal of this field is to devise nanomachines that will be able to store, retrieve and replicate programs accurately, acquire raw materials, assemble them according to their programming, and obtain or generate the energy needed to carry out these elementary processes. Such capabilities are necessary before a nanomachine can ultimately replicate itself. Much of the current work in the design of nanomachines has utilized mechanical analogies in an attempt to duplicate macroscopic mechanisms, such as gears and rods, on a microscopic scale.
An alternative paradigm to the `mechanical engineering' approach to nanomachines is provided by biological systems. At the cellular level, information is stored by sequences of nucleic acids, which constitute the programs for the key functions of the organism. With the aid of appropriate enzymes, the specific sequence of nucleic acids is replicated, and, when necessary, repaired, with an error rate of only 10[SUP]-6[/SUP]. Other enzymes enhance the rates of chemical reactions in cells by several orders of magnitude. These reactions allow for building long biopolymers and operating the cellular machinery in an accurate and highly controlled manner. The energy necessary to drive these chemical reactions is captured from the environment by specialized assemblies of proteins. One broad class of energy-capturing proteins converts light energy into chemical energy, in the form of proton gradients across membranes. Since light energy can easily be distributed over large areas, we can envision large 2-dimensional arrays of nonomachines, each including a set of proton pumps for its power supply. However, naturally occuring light-driven proton pumps, such as bacteriorhodopsin, are complex and involve many, sometimes poorly-understood, stages. We propose to study the design of a simple, light-driven proton pump using state-of-the-art molecular modeling.
There are two basic components to a simple light-driven proton pump: a source of photo-generated protons and a `gate-keeper', which prevents these protons from re-binding to their source. Deamer has shown that polycyclic aromatic hydrocarbons, incorporated into membranes, release protons when they are illuminated. Our work will, therefore, focus on the design of the `gate-keeper.' Our initial approach involves a pair of proton acceptors, coupled to each other by a transient water bridge, and supported in the membrane by a small bundle of peptide helices. Upon illumination, the proton source transfers its proton to the first acceptor of the gate-keeper. While the reverse reaction is highly probable, irreversibility is ensured by a nonvanishing probability that the proton will be transferred to the second acceptor across a transient water bridge. Back transfer of the proton to the first acceptor, and thence to the proton source, is impeded by the free energy required to move the proton uphill towards the proton source, as well as by the disruption of the water bridge resulting from the change in the hydration of the two acceptors.
As a prototypical water-bridged proton transfer system, we will study the transfer of a proton across a water bridge from a formic acid to a formate anion. With a pK[SUB]a[/SUB] of 3.7, formic acid is a good model for the acidic glutamic and aspartic amino acids, which are good candidates for gate-keeper proton acceptors in the final system. Bilayers of glycerol-1-monooleate (GMO) will be used as models of biomembranes. Studies will be performed to determine the geometric constraints on the proton transfer as well as to elucidate the role of the environment on the proton transfer energetics. Based on the established principles, a prototypical peptide proton pump can be readily constructed and tested by experimentalists. Once it is successfully demonstrated that the pump performs its functions, it can be further optimized for efficiency and regulatory precision.
Beyond this application of biological principles to nanotechnology, we will work on designing small, peptide enzymes supported by membranes. Using membranes as the supporting material would allow for the reduction in the size of enzymes and aligning them in two-dimensional arrays. This, in turn, can prove very useful in synthesis of different types of polymers. Furthermore, using membrane-supported enzymes in combination with proton pumps and membrane-bound peptide channels could lead to a simple synthetic system entirely driven by light (with no other source of energy needed).
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