Visualizing Movements of Protein Tunnels in Molecular Dynamics Simulations

Abstract

Analysis and visualization of molecules and their structural features help biochemists and biologists to better understand protein behavior. Studying these structures in molecular dynamics simulations enhances this understanding. In this paper we introduce three approaches for animating specific inner pathways composed of an empty space between atoms, called tunnels. These tunnels facilitate the transport of small molecules, water solvent and ions in many proteins. They help researchers understand the structure-function relationships of proteins and the knowledge of tunnel properties improves the design of new inhibitors. Our methods are derived from selected tunnel representations when each stresses some of the important tunnel properties-width, shape, mapping of physico-chemical properties, etc. Our methods provide smooth animation of the movement of tunnels as they change their length and shape throughout the simulation.