Using Molecular Dynamics Simulations to Compare the Stability of Lysenin Structures Obtained through X-ray Crystallography and Single-Particle Cryo-Electron Microscopy

Abstract

Single-particle cryo-electron microscopy is being used more frequently to determine the atomic structure of macromolecules. Recent advances in technology have greatly improved the quality of structures obtained with this method, which is now comparable to x-ray crystallography in terms of resolution. Lysenin is a member of the aerolysin family of pore-forming toxins. Recently, both x-ray crystallography and cryo-EM structures of the lysenin pore have been published. We have used molecular dynamics simulations to analyze and compare both structures. In addition to the wild-type structures, we also analyzed two different experimentally studied lysenin mutants. Both mutants showed a reduction in the fixed negative charge on the pore wall, resulting in reduced pore size and functional activity compared to the wild-type pore. The simulation setup involved a nonameric lysenin pore, which was embedded in a membrane bilayer composed of POPC lipids. This protein-membrane complex was solvated in a water box and equilibrated to determine the stability and fluctuations of different regions of the protein. The two structures obtained from different techniques were initially modeled in their wild-type forms. The differential behavior of both structures, due to the mutation of functionally important residues, was then compared. This research sheds light on the structure-function relationship in lysenin and also investigates the relative reliability of the cryo-EM and crystal structures.