Molecular interstitial skeleton

Abstract

Abstract The three-dimensional structures of protein molecules, as determined by X-ray crystallography, have been shown to possess packing defects or interior cavities of various sizes. These packing defects have been considered as a possible explanation for how small molecules, such as water and molecular oxygen, gain access to protein interiors. Most previous computational methods for analyzing packing defects use a fixed probe sphere radius or a fixed cube width, and so are limited with regard to the size of the packing defects that they find. Most methods also concentrate on identifying cavities, rather than on finding the tunnels that connect the cavities. The method presented here identifies packing defects of all sizes, and it also delineates the tunnels connecting them to each other and to the protein exterior. In particular, the radius of each tunnel at its narrowest point is determined.