in silico studies to understand structure/function of exopolyphosphatase from Escherichia coli

BOETSCH, C; LISA, AT; BEASSONI, PR

Puerto Varas

Congreso; XII PABMB congress; 2013

Escherichia coli exopolyphosphatase (PPX) hydrolyzes polyphosphate (polyP) in a proccesive way to yield PolyP(n-1) and orthophosphatePi. Putative catalytic residues and the Mg2+ binding pocket were suggested, by the interaction mode PolyP is not very clear. Based on sulfate ions present in the crystal and electrostatic potential a putative region to bind long chain of PolyP was described1,4. Here, we made an evolutionary trace3 study in order to analyze possible binding sites for polyP. The results shown here let us to propose several sites where polyP may interact and reach the active site. Both active site and an electropositive channel contain well conserved residues consistent with those predicted in1,4. Possible new sites located in the N-termini where found, one of them is consistent with the one described in1, and the other with described in4. One of the sites described in1 is poorly conserved. To characterize the binding of polyP to these sites we pretend to perform molecular dynamics. Considering the lack of parameters available for this ligand, in first place we optimized a chain of 4 residues of polyP using quantum mechanics (QM) and optimize the parameters of the molecule, so the molecular mechanics (MM) energy profile resembles those calculated by QM. Unbinding studies will be carried out in order to understand in which way polyP interact with PPX, and we will correlate the theoretical studies experimentally, in quasiprocesive studies2.