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Examples of Molecular Machines

In Jacob's hierarchy of physical, chemical, biological and social objects [Jacob, 1977], molecular machines lie just inside the domain of biology, because they perform specific functions for living systems. Molecular biologists continuously unveil lovely examples of molecular machines [Porter et al., 1983,Alberts, 1984,McClarin et al., 1986,Watson et al., 1987,Vyas et al., 1988] and many people have pointed out the technological advantages of building these devices ourselves [Feynman, 1961,McClare, 1971,Drexler, 1981,Carter, 1984,Haddon & Lamola, 1985,,Conrad, 1986,Drexler, 1986,Arrhenius et al., 1986,Hong, 1986,Hopfield et al., 1988]. If we were to consider only one kind of molecular machine at a time, we would miss the general features common to all molecular machines. Therefore, throughout this paper we will refer to the following four molecular machines.

1.

The genetic material deoxyribonucleic acid (DNA) can act like a simple molecular machine. If DNA is sheared into a heterogeneous population of 400 base-pair long fragments and then heated (or denatured by other means), the double stranded structure is ``melted'' into separate single strands. When the solution is slowly cooled, many of the single strands bind to a complementary strand and reform the double helix (Fig. 2a) [Britten & Kohne, 1968].

  

Figure 2: Operations of Two Molecular Machines.

A. Single-stranded DNA will hybridize to become a double-stranded helix.
B. EcoRI will scan along a DNA molecule and then bind specifically to the sequence 5' GAATTC 3'.

Two characteristics make this reaction machine-like. First, a priming step (denaturation) brings the molecules into a high energy state. Second, the molecules dissipate the energy and anneal to one another in a reasonably precise way by using the complementarity between bases [Watson & Crick, 1953]. This ``hybridization'' reaction can be made so specific that it is widely used as a technique in molecular biology [Britten & Kohne, 1968,Maniatis et al., 1982,Gibbs et al., 1989]. Base complementarity is also essential to all living things because it is the basis of nucleic-acid replication. For this reason, the degree of base-pairing precision is important in evolution.

2.

The restriction enzyme EcoRI is a protein which cuts duplex DNA between G and A in the sequence 5' GAATTC 3'[Smith, 1979,McClarin et al., 1986,Rosenberg et al., 1987b]. A single molecule of EcoRI performs three machine-like operations [Rosenberg et al., 1987a]. First, it can bind non-specifically to a DNA double helix. Second, after sliding along the DNA until it reaches GAATTC, it will bind specifically to that pattern. Third, it cuts the DNA. In the absence of magnesium, binding is still specific but cutting does not occur, so binding can be distinguished from cutting experimentally. We will focus on the binding operation (Fig. 2b). As with DNA, two characteristics make this reaction machine-like. First, there is a priming operation in which the non-specific binding to DNA places EcoRI into a ``high'' energy state relative to its energy when it is bound specifically. Second, the transition from non-specific to specific binding dissipates this energy so that EcoRI is located precisely on a GAATTC sequence. Without a dissipation associated with the specific binding, EcoRI would quickly move away from its binding site. After this local dissipation, the molecule is obliged to remain in place until it has cut the DNA, or a sufficiently large thermal fluctuation kicks it off again.

In vivo cellular DNA is protected from EcoRI by the actions of another enzyme called the modification methylase. This enzyme attaches a methyl group to the second A in the sequence GAATTC, so that EcoRI can no longer cut the sequence. In contrast, invading foreign DNAs are liable to be destroyed because they are unmethylated. The methylase is precise, attaching the methyl only to GAATTC and not to any of the sequences, such as CAATTC, that differ by only one base from GAATTC [Dugaiczyk et al., 1974]. So in vivo EcoRI is exposed to many hexamer sequences that are almost an EcoRI site, yet under optimal conditions [Polisky et al., 1975,Woodhead et al., 1981,Pingoud, 1985] it only cuts at GAATTC. How a single molecule of EcoRI can achieve this extraordinary precision has not been understood [Rosenberg et al., 1987a,Needels et al., 1989,Thielking et al., 1990].

3.

The retina contains a protein called rhodopsin which detects single photons of light [Lewis & Priore, 1988,Wessling-Resnick et al., 1987]. Upon capturing a photon, rhodopsin becomes excited and then dissipates the energy. Most of the time this converts rhodopsin into bathorhodopsin. A chemical cascade then amplifies the bathorhodopsin ``signal'' 400,000 times, leading to a nerve impulse. Because of this enhancement we can see single photons of light.

Why doesn't rhodopsin merely ``use the energy'' to convert directly into bathorhodopsin? This transformation is not as easy as it first appears, since the high energy state is a chemical transition state from which it is possible to go backwards to rhodopsin, rather than forwards to bathorhodopsin. Rhodopsin must make a ``decision'' about what to do.

4.

Little is known about the exact molecular mechanism of muscles [Huxley, 1969,McClare, 1971,Highsmith & Jardetzky, 1983,Trayer & Trayer, 1988]. However, we know that the interaction of the proteins myosin and actin consumes the energy molecule adenosine triphosphate (ATP). We may therefore imagine that the hydrolysis of an ATP molecule primes the actomyosin complex into a high energy state so that as the energy is dissipated a force is generated. As with rhodopsin, the activated actomyosin complex must ``choose'' whether to go forwards or backwards.