Paper Citing NAMD - Abstract
He, Jia; Wu, Ming; Feng, Xizeng; Shao, Xueguang; Cai, Wensheng
Immobilization of papain on nanoporous silica
RSC ADVANCES, 4:13304-13312, 2014
Immobilization of enzymes has attracted much attention in nanoscience and nanotechnology. However, the mechanisms of recognition and immobilization are still poorly understood at atomic resolution. In this study, we report that a newly synthetized single-crystal-like, nanoporous silica particle possesses a high adsorption capacity for the immobilization of papain. The immobilized enzyme could be used in the degradation of proteins, such as bull serum albumin. Moreover, the adsorption mechanism of papain on the silica surface was investigated by employing docking, classical atomistic molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area calculations. Ten independent simulations starting from two representative initial orientations of papain toward the solid surface were performed, resulting in four representative adsorption modes. The calculated relative binding free energies of the four different modes show that the one with the binding patch primarily consisting of an alpha-helix (ASP108-TYR116), beta-sheet (GLN73, ALA76, GLN77), and turn (ARG59) is most energetically favored. Further analysis of the most favored immobilization mode demonstrates that, after initial binding to the silica, the papain optimized its conformation to allow more atoms to contact with the surface. Electrostatic and van der Waals interactions drove the adsorption in a cooperative fashion, wherein van der Waals contributions are the primary component of the binding free energy in the most energetically favored adsorption mode. Besides, the global structure of the papain was preserved in the course of adsorption. Slight structural rearrangements at the entrance of the active site were observed, which increase the accessibility of the active site to solvent and presumably to substrates, and thus could facilitate productive binding between substrates and papain.
