Modeling supra-molecular helices: extension of the molecular surface recognition algorithm and application to the protein coat of the tobacco mosaic virus

Abstract Geometric matching of molecular surfaces appears to be essential for the formation of binary molecular complexes and of supra-molecular aggregates. The structure of a binary complex is characterized by the best geometric match, whereas the structure of an aggregate is characterized by the best combined match, i.e. the sum of all the internal matches in the system. We describe a method to identify and quantify the binary matches between molecules and then use them to form the supra-molecular helices and evaluate them. This method is applied to the single protein subunit of tobacco mosaic virus. It successfully predicts the structure of the helical protein coat of the virus and the structure of the disk that is formed as the initial step in the virus assembly process. It also predicts structural intermediates, between disk and helix, which explain how the disk can transform into a helix without dissociating into subunits.