Atomistic investigation on non-covalent binding interaction in biomolecular systems

Abstract

In recent decades, personalized medicine has been extensively investigated with the state-of-the-art technology, and the specificity/stability issue between protein and nucleic acid has been of critical importance. To understand noncovalent interaction which plays a major role in stabilizing biomolecular structures, we developed our systematic framework based on grid-based mean-field type quantum mechanics/molecular mechanics (QM/MM) coupling protocol. By utilizing our method, we delved into the aromatic-aromatic interaction to be changed in aqueous solution. In addition, we analyzed recognition/binding processes for DNA-bound TALEN protein, which has been spotlighted by genome editing techniques, at the atomic/molecular level based on large-scale molecular dynamics simulation. We expect that this study could shed light on understanding specific binding principles of biomolecules and proposing an effective therapeutic drug specifically binding to various targets.