Structural studies on an inhibitory antibody against Thermus aquaticus DNA polymerase suggest mode of inhibition

TP7, an antibody against Thermus aquaticus DNA polymerase I (TaqP), is usedas a thermolabile switch in 'hot start' variations of PCR to minimizenon-specific amplification events. Earlier studies have established thatTP7 binds to the polymerase domain of TaqP, competes with primer templatecomplex for binding and is a potent inhibitor of the polymerase activity ofTaqP. We report crystallographic determination of the structure of an Fabfragment of TP7 and computational docking of the structure with the knownthree-dimensional structure of the enzyme. Our observations stronglysuggest that the origin of inhibitory ability of TP7 is its binding toenzyme residues involved in DNA binding and polymerization mechanism.Although criteria unbiased by extant biochemical data have been used inidentification of a putative solution, the resulting complex offers aneminently plausible structural explanation of biochemical observations. Theresults presented are of general significance for interpretation of dockingexperiments and in design of small molecular inhibitors of TaqP, that arenot structurally similar to substrates, for use in PCR. Structural andfunctional similarities noted among DNA polymerases, and the fact thatseveral DNA polymerases are pharmacological targets, make discovery ofnon-substrate based inhibitors of additional importance.