Magnesium-cationic Dummy Atom Molecules Enhance Representation of DNA Polymerase β in Molecular Dynamics Simulations: Improved Accuracy in Studies of Structural Features and Mutational Effects

Abstract

SummaryHuman DNA polymerase β (pol β) fills gaps in DNA as part of base excision DNA repair. Due to its small size it is a convenient model enzyme for other DNA polymerases. Its active site contains two Mg 2+ ions, of which one binds an incoming dNTP and one catalyzes its condensation with the DNA primer strand. Simulating such binuclear metalloenzymes accurately but computationally efficiently is a challenging task. Here, we present a magnesium-cationic dummy atom approach that can easily be implemented in molecular mechanical force fields such as the ENZYMIX or the AMBER force fields. All properties investigated in this paper, that is, structure and energetics of both Michaelis complexes and transition state (TS) complexes were represented more accurately using the magnesium-cationic dummy atom model than using the traditional one-atom representation for Mg 2+ ions. The improved agreement between calculated free energies of binding of TS models to different pol β variants and the experimentally determined activation free energies indicates that this model will be useful in studying mutational effects on catalytic efficiency and fidelity of DNA polymerases. The model should also have broad applicability to the modeling of other magnesiumcontaining proteins.

Accommodation of an N-(Deoxyguanosin-8-yl)-2-acetylaminofluorene Adduct in the Active Site of Human DNA Polymerase ι: Hoogsteen or Watson−Crick Base Pairing?

“…Our simulations support this insofar as no simulation showed perfect octahedral coordination of both Mg 2+ ions simultaneously at any time. However, current force field issues concerning proper treatment of Mg 2+ ions is still a frontier issue (88). In this connection, simulations of large systems such as in the present work are necessarily subject to current approximations in the state of the art including force field and sampling considerations (89).…”

Communications: Electron polarization critically stabilizes the Mg2+ complex in the catalytic core domain of HIV-1 integrase

“…Different solutions have been developed to model Magnesium ions in protein dynamics. One of attractive strategies was presented by Warshel, 21 in which the metal was described by additional off-center charges bonded to the metal. Moreover, conventional force fields ͑FFs͒ employed in MD simulation do not include polarization effect explicitly, so simulations based on conventional FF have their limitations.…”

“…22,23 Recent works by Warshel and co-workers have demonstrated the importance to account for the polarizability of protein in pKa calculations 24 and solvation energy calculation with Mg complexes. 21 Although polarizable FFs can in principle incorporate polarization effect, its practical application is much more complicated than that of the standard FF. To gain both accuracy and efficiency, polarized protein-specific charge ͑PPC͒ 25 has recently been developed based on linear scaling quantum fragmentation approach ͑MFCC͒.…”

Structural Studies of Trypanosoma brucei RNA Editing Ligases and Their Binding Partner Proteins

“…We used the XLEAP module of AMBER to build the Mg 2+ cationic dummy model and adopted the force field parameters from Oelschlaeger et al 24 Modeling the Unbound OB Domain of Interaction Partner A1. The structure of the C-terminal OB-folded domain of KREPA1 (termed A1 OB , residues 627−762) was recently determined at 2.65 Å resolution (PDB entry 4DK6) as a homodimer in complex with a nanobody.…”