Competition between protein ligands and cytoplasmic inorganic anions for the metal cation: a DFT/CDM study

Many of the essential metalloproteins are located in the cell, whose cytoplasmic fluid contains several small inorganic anions, such as Cl-, NO2-, NO3-, H2PO4-, and SO4(2-), that play an indispensable role in determining the cell's volume, regulating the cell's pH, signal transduction, muscle contraction, as well as cell growth and metabolism. However, the physical principles governing the competition between these abundant, intracellular anions and protein or nucleic acid residues in binding to cytoplasmic metal cations such as Na+, K+, Mg2+, and Ca2+ are not well understood; hence, we have delineated the physicochemical basis for this competition using density functional theory in conjunction with the continuum dielectric method. The results show that the metal cation can bind to its target protein against a high background concentration of inorganic anions because (i) desolvating a negatively charged Asp/Glu carboxylate in a protein cavity costs much less than desolvating an inorganic anion in aqueous solution and (ii) the metal-binding site acts as a polydentate ligand that uses all its ligating entities to bind the metal cation either directly or indirectly. The results also show that the absolute hydration free energy of the "alien" anion as well as the net charge and relative solvent exposure of the metal-binding protein cavity are the key factors governing the competition between protein and inorganic ligands for a given cytoplasmic metal cation. Increasing the net negative charge of the protein cavity, while decreasing the number of available amide groups for metal binding, protects the metal-bound ligands from being dislodged by cellular anions, thus revealing a "protective" role for carboxylate groups in a protein cavity, in addition to their role in high affinity metal-binding.