Structural Instability of the Active Site of T1 Lipase where Na +-π Interaction is Replaced with Water-π Complex

Abstract

The cation-π interaction is one of the strongest noncovalent forces. However, its biological role has been unknown, since few structures containing cation-π interaction have been determined in biological systems. Matsumura, et al. determined the crystal strcture of T1 lipase and found interactions between Na+ and the aromatic ring of Phe16 in the active site. However, this Na+-π interaction remained to be discussed whether it really exists or not. To investigate structural stability of Na+-Phe interactions, we performed molecular dynamics (MD) simulations of T1 lipase.It is well known that the current conventional force fields cannot estimate the cation-π interaction correctly, whereas ab initio calculations require huge computational costs for the MD simulations. Accordingly, we developed a novel scheme to calculate the interaction energy with a high accuracy compared with the CCSD(T) level, and with a low calculation cost compared with the force field calculations. The result of our calculations definitely showed that the large enthalpy gain of the Na+-π interaction was required to preserve the catalytic core structure. Since experimental approaches could not dismiss the possible presence of water instead of Na+ in the active site of T1 lipase, we also examined the effects of water by performing MD simulations. Our analyses revealed that the water-π complex was unstable and led to the collapse of the coordinated structure of the active site. Thus, we concluded that the possible presence of water may be excluded. Our novel scheme is currently the only way to perform long-time MD simulations involving cation-π interactions with reasonable computational cost and with high accuracy. Based on this analysis, we propose a novel structural and functional element indentified in the active site of T1 lipase.