Chelator-Based Parameterization of the 12-6-4 Lennard-Jones Molecular Mechanics Potential for More Realistic Metal Ion–Protein Interactions
Paulius Kantakevičius, Calvin Mathiah, Linus O. Johannissen, Sam Hay
Abstract
coefficients were tested on a series of chelators: ethylenediaminetetraacetic acid, nitrilotriacetic acid, egtazic acid, and the EF1 loop peptides from the proteins lanmodulin and calmodulin. The new parameters show significant improvements in computed binding energies relative to existing force fields and produce coordination numbers and ion-oxygen distances that are in good agreement with experimental values. This parametrization method should be extensible to a range of other systems and could be readily adapted to tune properties other than binding energies.
Topics & Concepts
Molecular mechanicsMolecular dynamicsIonMetal ions in aqueous solutionNanotechnologyStatistical physicsComputational chemistryChemical physicsComputer scienceChemistryPhysicsMaterials scienceQuantum mechanicsProtein Structure and DynamicsMetal complexes synthesis and propertiesHemoglobin structure and function