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Molecular Machine Operations

So far we have modeled a molecular machine jiggling at equilibrium, and we found that it can be represented by a sphere in Y space. Now let's investigate what happens when the machine operates. Recall our four example machines. For DNA an operation means base-pairing or hybridization, for a genetic recognizer like EcoRI it means locating a binding site, for rhodopsin it means switching to bathorhodopsin, and for muscle it means contracting. We say that ``information is gained'' when a machine changes from an indeterminate state to a more determined state. Decreases in thermal motion corresponding to machine operations have been observed in many molecular machines [Porter et al., 1983,Petsko & Ringe, 1984]. In each case, a corresponding energy decrease allows a specific action to be taken. Thus, rhodopsin dissipates the energy of a photon to change states [Warshel, 1976,Birge & Hubbard, 1980,Huber & Bennett, Jr., 1983] and actomyosin dissipates the energy of a hydrolyzed ATP molecule to generate motion [McClare, 1971,Highsmith & Jardetzky, 1983]. When DNA becomes double-stranded [Britten & Kohne, 1968], or when genetic recognizers stick to their binding sites [Weber & Steitz, 1984a,Weber & Steitz, 1984b,Rosenberg et al., 1987a], their range of motion becomes restricted by a lower potential energy.

We only need to consider two energetic states of the machine [Rosenberg et al., 1987a]. Before an operation, a machine has some specific amount of energy, while afterwards it has a smaller amount. How the machine attains the activated before state (i.e., ``priming'') is outside the scope of our considerations, though we may note that a photon does this for rhodopsin [Birge & Hubbard, 1980], and ATP hydrolysis does it for actomyosin [Highsmith & Jardetzky, 1983]. Even large (but rare) thermal fluctuations can cause this priming, since they can free repressors and other proteins like EcoRI from their binding sites [Weber & Steitz, 1984a]. Likewise, DNA strands may be separated artificially by heat and chemical denaturants, or naturally by helicases using ATP, while bases incorporated into growing nucleic-acid chains are already separate.