Development of Accurate Force Fields for Mg2+ and Triphosphate Interactions in ATP·Mg2+ and GTP·Mg2+ Complexes.

Abstract

In cells, adenosine triphosphate (ATP) and guanosine triphosphate (GTP) molecules typically form tricoordinated or bicoordinated ATP·Mg²⁺ or GTP·Mg²⁺ complexes with Mg²⁺ ions and bind to proteins, participating in and regulating many important cellular functions. The accuracy of their force field parameters plays a crucial role in studying the function-related conformations of ATP·Mg²⁺ or GTP·Mg²⁺ using molecular dynamics (MD) simulations. The parameters developed based on the methyl triphosphate model in existing AMBER force fields cannot accurately describe the conformational distribution of tricoordinated or bicoordinated ATP·Mg²⁺ or GTP·Mg²⁺ complexes in solution. In this study, we develop force field parameters for the triphosphate group based on the new ribosyl triphosphate model, considering the dihedral coupling effect, accurate van der Waals (vdW) interactions, and the influence of strongly polarized charges on conformational balance. The new force fields can accurately describe the conformational balance of tricoordinated and bicoordinated ATP·Mg²⁺ or GTP·Mg²⁺ conformations in solution and can be applied to simulate biological systems containing ATP·Mg²⁺ or GTP·Mg²⁺ complexes.