Beta-sheet topology. A new system of nomenclature.

The topology of a protein beta-sheet, the relationship between the sequential ordering of strands and their connectedness in space, is an important and well studied feature of protein structures. The prevalent nomenclature for describing beta-sheet topologies is based on following a path through the sequence order of strands and noting their separation in space. Although powerful, this approach can be usefully complemented by a notation based on following a path through the connectedness of neighbouring strands and noting sequence separation. This leads in turn to a short hand expression of sheet topology, based on a method for describing the covalent structure of small molecules, which is able to express concisely the complex non-linear topological relationships of beta-sheets, including bifurcations and closed structures, in a clear and natural manner. Using this novel system of notation it is possible to follow simultaneously the sequence and hydrogen bonded connectedness of strands within the topology of a sheet.