The Role of Cavities in Biological Structures

Abstract

We investigate the significance of cavities within biological structures, ranging from single proteins to large complexes, such as viruses and even protein clusters composed of intrinsically disordered proteins. Utilizing our SPACEBALL algorithm, we detect empty spaces within these structures and quantify their volumes. This enables us to elucidate the impact of cavities on the properties of the given structures. Finally, we discuss how the presence of cavities in protein clusters facilitates the assessment of their hydration levels within a coarse-grained implicit solvent approach. Our discussion aims to demonstrate that the functions of various proteins originate from their specific tertiary structures containing cavities. topics: cavities in biological structures, molecular dynamics simulations, viruses, simulations of gluten