Functional Roles of a Novel Structural Element Involving the Na+−π Interaction Present in the Catalytic Site of T1 Lipase Revealed by Molecular Dynamics Simulations

Abstract

The interaction between a cation and an aromatic ring, i.e., the cation-π interaction, is one of the strongest noncovalent forces. Metal cations such as Na+ and K+ can also participate in the cation-π interactions, and are known to yield significant stabilization energy. However, in biological systems, few structures containing metal-π coordination have been determined, preventing understanding of its biological roles. Recently, we have determined the crystal structure of a thermoalkalophilic lipase where a Na+ is coordinated to a phenylalanine (Phe) in its catalytic site. To elucidate the functional roles of the Na+−Phe complex, we performed molecular dynamics (MD) simulations of the system. Note that the current force fields cannot correctly estimate the metal-π interaction energy, requiring quantum mechanical calculations. However, their huge computational costs prohibit long-time MD simulations. Accordingly, we developed a novel scheme to calculate the interaction energy with an accuracy comparable to that of advanced ab initio calculations at the CCSD(T) levels, and with computational costs comparable to those of force field calculations.A comparison of the MD simulations in the presence/absence of the accurate description revealed that a significantly large enthalpy gain in Na+−Phe substantially stabilizes the catalytic site. Thereby, the cation−π interaction in the lipase establishes a remarkably stable core structure by combining a hydrophobic aromatic ring and hydrophilic residues, of which the latter form the catalytic triad, thus contributing to large structural changes from the complex with ligands to the free form of the lipase. Thus, we have elucidated the detailed functional roles of Na+−π complex with use of our presented scheme, which is currently the only way to perform long-time MD simulations with reasonable computational costs.