ANALYTICAL SHAPE COMPUTATION OF MACROMOLECULES - II - INACCESSIBLE CAVITIES IN PROTEINS

The structures of proteins are well-packed, yet they contain numerous cavities which play key roles in accommodating small molecules, or ena bling conformational changes. From high-resolution structures it is po ssible to identify these cavities. We have developed a precise algorit hm based on alpha shapes for measuring space-filling-based molecular m odels (such as van der Waals, solvent accessible, and molecular surfac e descriptions). We applied this method for accurate computation of th e surface area and volume of cavities in several proteins. In addition , all of the atoms/residues Lining the cavities are identified, We use this method to study the structure and the stability of proteins, as well as to locate cavities that could contain structural water molecul es in the proton transport pathway in the membrane protein bacteriorho dopsin. (C) 1998 Wiley-Liss,Inc.