Modeling Ion Selectivity in EF-hand Proteins - Project Summary/Abstract Metal ions play crucial roles in numerous vital biological processes, encompassing muscle contraction, respiration, photosynthesis, signal transduction, enzyme catalysis, and hormone secretion. It is estimated that approximately 40% of proteins rely on metal ions for their functionality. Among the roughly two dozen biologically available metal ions, precise ion selection is paramount, as incorrect ion binding can lead to reduced efficiency and toxicity. However, our understanding of ion selectivity in many proteins remains limited. Molecular dynamics (MD) simulations have emerged as an important tool in biochemistry research, offering atomic-level insights into the fundamental mechanisms governing biomolecular function. However, accurate force field models are imperative for meaningful MD simulation results. Modeling metal ion-ligand interactions is challenging due to the involvement of polarization and charge transfer effects. A key goal of this proposal is to establish a multiscale modeling strategy to simulate ion selectivity in proteins. The Li research group has developed novel force fields that efficiently and accurately capture the polarization and charge transfer effects in protein-ion systems. By utilizing these force fields, which are parameterized from high-level quantum mechanical calculations, MD simulations will be conducted to provide structural and dynamic insights into protein-ion interactions. Furthermore, free energy simulations will be employed to unveil thermodynamic insights and identify key residues and factors influencing ion binding affinity. Enhanced-sampling simulations will also be employed to extract kinetic properties of ion binding. These simulation results will be compared with existing experimental data or results obtained through collaboration with experimental researchers, with the fundamental factors dictating ion selectivity will be analyzed based on a comprehensive perspective. Ultimately, our proposal's central objective is to apply this modeling strategy to investigate ion selectivity in EF-hand containing proteins, which are widespread in various organisms and display remarkable and distinctive ion selectivity profiles. EF-hand motifs exhibit the capacity to bind to diverse metal ions with varying affinities. However, the mechanisms governing this selectivity remain incompletely understood. We will focus on four EF-hand containing proteins: Calmodulin (CaM), Lanmodulin (LanM), Troponin C (TnC), and Lanthanide binding tags (LBT), exploring their interactions with various metal ions. Our research will elucidate the roles of ions, ligands, protein conformational dynamics, and solvents in determining ion selectivity. The insights gained regarding how these proteins regulate ion selectivity will facilitate the design of proteins with tailored ion selectivity and have implications for relevant drug design efforts.
