Structural Basis for Arsenate-Phosphate Discrimination

Abstract

In Nature arsenate can in principle replace phosphate in its role as a key biological molecule (e.g. as in ATP) but arsenate analogues are less stable with respect to hydrolysis and reduction. Yet bacterial adoption of arsenic has been described and although the precise nature of the arsenic species is undetermined, it is possible that arsenate is incorporated as direct substitution for phosphate in cellular macromolecules. Several phosphate-binding proteins are able to selectively bind phosphate over arsenate despite their chemical similarities. We take advantage of this chemical similarity to elucidate arsenate-phosphate discrimination and to probe our understanding of phosphate-binding mechanisms in general. Specifically we consider a highly flexible synthetic hexapeptide capable of irreversibly binding phosphate as well as a number of highly selective phosphate binding proteins, including those with the evolutionarily conserved sequence known as a P-loop. A major challenge in structural analysis is that automatic ligand search methods are deemed to fail in detecting phosphate-binding sites in small and disordered phosphate-binding peptides. We use the Generalized Amber Force Field (GAFF) and extend it to include arsenate. Our ability to explore and explain experimental results using a combination of DFT, MD, and MCMC techniques are demonstrated in their ability to distinguish between the chemically close phosphate and arsenate ligands. Using a number computational techniques, we explore the large number of potential interactions that may be exploited to explain and control the specificity and selectivity of binding.