A Novel Design Method for Protein-Like Molecules from the Perspective of Sheaf Theory

Abstract

Proteins perform a variety of functions in living organisms and their functions are largely determined by their shape. In this paper, we propose a novel mathematical method for designing protein-like molecules of a given shape. In the mathematical model, molecules are represented as loops of n -simplices (2-simplices are triangles and 3-simplices are tetrahedra). We design a new molecule of a given shape by patching together a set of smaller molecules that cover the shape. The covering set of small molecules is defined using a binary relation between sets of molecules. A new molecule is then obtained as a sum of the smaller molecules, where addition of molecules is defined using transformations acting on a set of ( n + 1)-dimensional cones. Due to page limitations, only the two-dimensional case ( i.e. , loops of triangles) is considered. No prior knowledge of Sheaf Theory, Category Theory, or Protein Science is required. The author hopes that this paper will encourage further collaboration between Mathematics and Protein Science.