Figure 1. Schematic, heuristic model of a protein motor performing vectorial translocation along the ssDNA. The protein has two effective DNA-binding sites, s1 and s2. The protein also has structural and functional asymmetry. The enzyme–DNA complex goes through a cycle of different conformational and binding states in response to the binding of NTP (black circle), its hydrolysis, and release of the NTP hydrolysis product (grey circle). The NTP hydrolysis is coupled to the protein structure changes synchronized with the changes of the affinities of the ssDNA-binding sites. As a result, with each cycle of NTP binding and hydrolysis, the protein performs unidirectional translocation on the DNA lattice.

Figure 2. An outline of the active, rolling model of the DNA unwinding and mechanical translocation proposed for the Escherichia coli Rep helicase. In the presence of ATP, the Rep dimer, associated with the 3¢ ssDNA arm of the DNA fork, acquires functional and structural asymmetry, with one subunit having a high affinity for the ss and the other for the dsDNA conformation. As a result, the dimer invades the duplex part of the fork. Unwinding and hydrolysis of ATP returns the protein–DNA complex to the initial state, but with a different subunit now engaged in interactions with the ssDNA. The reaction results in net translocation of the Rep dimer on the ssDNA in the 3¢ 5¢ direction (Lohman and Bjornson, 1996).

Figure 3. Current model of the Escherichia coli DnaB hexamer bound to a replication fork DNA substrate. The hexamer, bound to the 5¢ arm of the fork, is oriented towards the dsDNA with the large domain of each protomer as the ssDNA passes through the cross channel. The ATP binding sites (black circles) are adjacent to the strong ssDNA-binding subsite that is near the small 12 kDa domain of each protomer (Jezewska et al., 1998). The arrow indicates the direction of the helicase translocation.

Figure 4. Schematic representation of a DNA polymerase, based on the structure of the Escherichia coli pol I Klenow fragment, in the complex with template-primer DNA (Joyce and Steitz, 1994).