Investigation of the diverse evolutionary developed mechanisms enabling bacteria to maintain homeostasis and to be resistant to heavy metals is crucial for the discovery of novel strategies for their isolation and subsequent elimination from contaminated environments. For example, the metalloregulatory proteins pbrR identified in Cupriavidus metallidurans and golB in Salmonella enterica are the only characterized natural metalloproteins with special affinities toward Pb(II) and Au(I), respectively, as they bind these metals with at least a 1000-fold selectivity.

We have used the multiscale computational modelling for studying these proteins, employing either conventional parametrization of metal cations or their cationic dummy models in which part of the mass and charge of the metal ion are fractioned in a number of rigidly fixed sites anchored to the metal center (Figure 1).

Molecular dynamics simulations substantiated how conformations amenable for the metal complexation through the specialized structural motifs are formed. In agreement with available experimental data, we found that these metal-binding proteins control their affinity toward metal cations by conformational changes that affect the distances between residues at the binding sites and their protonation states, thus being able to switch on the metal-sequestration or release-prone states in response to external stimuli.

 

 

Figure 1. Top: Lead-binding protein pbrR and its metal-binding tricysteine motif. Bottom: Simulation of lead binding. Simulation involving conventionally parametrized Pb(II) ion results in its early release in the water bulk (left), while the simulation including the cationic dummy model of the metal ion results in its coordination in the metal-binding motif (right).