Accurate Description of Nitrogenous Base Flexibility in Classical Molecular Dynamics Simulations of Nucleotides Bound to Proteins

Proteins can induce significant distortions in planar cyclic compounds upon binding, in particular in nucleotide-enzyme complexes. An accurate representation of the ring flexibility is thus desirable when modeling these systems through classical force fields, especially when deformations are supposed to be involved in the catalytic mechanism. In this study, we use a newly developed general procedure to determine sets of dihedral parameters for planar cycles that accurately reproduce their out-of-plane normal modes as determined at the quantum mechanical (QM) level. The optimization allows the deviation from reference data to be reduced for the pyrimidine bases to values comparable to the accuracy of the QM data. Furthermore, the influence of the description of ring flexibility in protein-ligand interactions is assessed through molecular dynamics simulations of the complex between uridine and the pyrimidine-specific nucleoside hydrolase YeiK using the AMBER force field. The differences in ligand-protein interactions emerging from different parameter sets are also discussed with respect to existing biochemical data.