Simulated Mechanical and Electrical Properties of Three-Dimensional Protein Lattices

Abstract

The chief goal in the field of nanomaterials is to create macroscopic structures whose properties are precisely engineered at the nanoscale. Protein-based lattices are promising candidates for this goal since proteins naturally self-assemble and play a huge variety of functional roles in their native environment. We use molecular dynamics simulations to characterize the mechanical and electrical properties of several three-dimensional lattices designed from protein subunits. Simulations of infinite lattices are achieved by constructing a “unit cell” structure and applying periodic boundary conditions across all faces of the cell to tile it in 3-D space, allowing for explicit interactions between the structure and its periodic images. Each unit cell consists of a mechanically robust rod-like protein belonging to the Beta-Solenoid protein family covalently bonded to a symmetric multi-mer; in this study, tetramers and dodecomers were used to construct tetrahedrally coordinated lattices, analogous to the zinc-blende crystal structure. Once these structures have been relaxed through energy minimization and constrained equilibration, the structure is strained by applying a prescribed deformation to the unit cell and the atoms it contains. We then analyze the resultant stress and polarization produced by this strain and extract the corresponding elastic and piezoelectric moduli, respectively. These material properties are useful measures of the viability of these protein lattice structures as functional biomaterials.