How round is a protein? Exploring protein structures for globularity using conformal mapping.

We present a new algorithm that automatically computes a measure of the geometric difference between the surface of a protein and a round sphere. The algorithm takes as input two triangulated genus zero surfaces representing the protein and the round sphere, respectively, and constructs a discrete conformal map f between these surfaces. The conformal map is chosen to minimize a symmetric elastic energy E S (f) that measures the distance of f from an isometry. We illustrate our approach on a set of basic sample problems and then on a dataset of diverse protein structures. We show first that E S (f) is able to quantify the roundness of the Platonic solids and that for these surfaces it replicates well traditional measures of roundness such as the sphericity. We then demonstrate that the symmetric elastic energy E S (f) captures both global and local differences between two surfaces, showing that our method identifies the presence of protruding regions in protein structures and quantifies how these regions make the shape of a protein deviate from globularity. Based on these results, we show that E S (f) serves as a probe of the limits of the application of conformal mapping to parametrize protein shapes. We identify limitations of the method and discuss its extension to achieving automatic registration of protein structures based on their surface geometry

Examples, Counterexamples, and Enumeration Results for Foldings and Unfoldings between Polygons and Polytopes

We investigate how to make the surface of a convex polyhedron (a polytope) by folding up a polygon and gluing its perimeter shut, and the reverse process of cutting open a polytope and unfolding it to a polygon. We explore basic enumeration questions in both directions: Given a polygon, how many foldings are there? Given a polytope, how many unfoldings are there to simple polygons? Throughout we give special attention to convex polygons, and to regular polygons. We show that every convex polygon folds to an infinite number of distinct polytopes, but that their number of combinatorially distinct gluings is polynomial. There are, however, simple polygons with an exponential number of distinct gluings. In the reverse direction, we show that there are polytopes with an exponential number of distinct cuttings that lead to simple unfoldings. We establish necessary conditions for a polytope to have convex unfoldings, implying, for example, that among the Platonic solids, only the tetrahedron has a convex unfolding. We provide an inventory of the polytopes that may unfold to regular polygons, showing that, for n>6, there is essentially only one class of such polytopes.Comment: 54 pages, 33 figure