Many-body effect determines the selectivity for Ca ²⁺ and Mg ²⁺ in proteins

Abstract

Calcium ion is a versatile messenger in many cell-signaling processes. To achieve their functions, calcium-binding proteins selectively bind Ca against a background of competing ions such as Mg The high specificity of calcium-binding proteins has been intriguing since Mg has a higher charge density than Ca and is expected to bind more tightly to the carboxylate groups in calcium-binding pockets. Here, we showed that the specificity for Ca is dictated by the many-body polarization effect, which is an energetic cost arising from the dense packing of multiple residues around the metal ion. Since polarization has stronger distance dependence compared with permanent electrostatics, the cost associated with the smaller Mg is much higher than that with Ca and outweighs the electrostatic attraction favorable for Mg With the AMOEBA (atomic multipole optimized energetics for biomolecular simulation) polarizable force field, our simulations captured the relative binding free energy between Ca and Mg for proteins with various types of binding pockets and explained the nonmonotonic size dependence of the binding free energy in EF-hand proteins. Without electronic polarization, the smaller ions are always favored over larger ions and the relative binding free energy is roughly proportional to the net charge of the pocket. The many-body effect depends on both the number and the arrangement of charged residues. Fine-tuning of the ion selectivity could be achieved by combining the many-body effect and geometric constraint.

Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE

“…Thirdly, Mg 2+ is known to exhibit a lower first stability constant for replacement of water in the aqueous ion by a ligand compared to other divalent transition metal ions in the Irving-Williams series 31,32 . A recent MD simulation study using a polarizable force field provides insights on Mg's low affinity towards many Ca-preferred highly charged metal binding sites 33 . Crystallographically, Mg 2+ is much lighter than the other multivalent cations studied in this work, so Mg 2+ binding with low occupancy would not be readily detected.…”

Structural determinants of calcium binding beyond the EF-hand binding site: a study of alpha parvalbumins

“…One of our goals was to elucidate the thermodynamic factors governing the variations in affinity among variants of αPV. Free energy techniques including thermodynamic integration, umbrella sampling and adaptive biasing force have been used for rigorous estimates of Ca 2+ affinity for a variety of Ca 2+ -binding proteins [48,26].…”

“…The experimentally-determined affinity difference of ≈ 10 kcal/mol in large part can be rationalized by the considerably higher desolvation cost for Mg 2+ relative to Ca 2+ and to a lesser extent by the reduced number of protein oxygens bound by Mg 2+ [22], as was confirmed by our MSA calculations. Additional factors, however, though can further tune the observed affinity differences for these ions, including the energetic cost of distorting the EF-hand to accommodate the smaller Mg 2+ ion over Ca 2+ [37], polarizability [69,70] and many-body polarization effects [26], which depend on the number and the arrangement of charged residues.…”

“…Other algorithms that account for the geometric configuration of Ca 2+ chelating ligands to achieve optimal coordination geometries have further improved EF-hand prediction [25] and have helped to rationalize selectivity against other ions like Mg 2+ [26]. Molecular dynamics (MD) simulations [27] have facilitated detailed analyses of Ca 2+ binding in intact proteins, using force fields fit to quantum chemical calculations of metal oxygen interactions [28].…”

Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking

“…All homology models were refined using the 2018 AMOEBA force field (20,41) with Generalized Kirkwood implicit solvent (23). The input homology models were first locally optimized using the L-BFGS algorithm available in FFX that is accelerated using OpenMM on GPUs to an RMS gradient convergence criterion of 0.8 kcal/mol/Å.…”