Ab initio simulations of Protein Surface Interactions mediated by Water

Abstract

Recent combinatorial biotechnologies have shown that the molecular recognition capability of proteins can be specifically oriented toward inorganic surfaces. However, at present the principles regulating protein-surface interactions are poorly understood. What features of the surface and of the proteins determine which protein is able to bind to a given surface and how? In addition, the exact role of water in the process of protein-surface interaction is unknown. The comprehension of such mechanisms would foster several technological applications based on the rational design of protein/surface interactions, ranging from biomaterials to nanobioelectronics. To unravel the mechanisms of interaction between a surface and a protein, including the role played by water, PSIWat will give a first-principle description of the interaction between a prototype protein molecule and a gold surface, by explicitly taking into account the hydration layer surrounding the molecule and the surface. In particular, we will perform ab initio molecular dynamics (AIMD) simulations at finite temperature, using plane-wave Density Functional Theory. Such calculations represent a huge computational effort, due to the size of the studied systems (hundreds of atoms, thousands of electrons) and the need for meaningful statistics (hundreds of thousands of molecular dynamics steps). This computational grand-challenge requires extreme supercomputing resources, such as those made available by DECI. The results of our AIMD simulations will also be a fundamental computational benchmark for the production and testing of classical force-field parameters. These force-fields will allow performing reliable classical MD simulations of these systems at routine computational costs.