MODELING SUPRA-MOLECULAR HELICES - EXTENSION OF THE MOLECULAR-SURFACERECOGNITION ALGORITHM AND APPLICATION TO THE PROTEIN COAT OF THE TOBACCO MOSAIC-VIRUS

Geometric matching of molecular surfaces appears to be essential for t he formation of binary molecular complexes and of supra-molecular aggr egates. The structure of a binary complex is characterized by the best geometric match, whereas the structure of an aggregate is characteriz ed by the best combined match, i.e. the sum of all the internal matche s in the system. We describe a method to identify and quantify the bin ary matches between molecules and then use them to form the supra-mole cular 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 o f the disk that is formed as the initial step in the virus assembly pr ocess. It also predicts structural intermediates, between disk and hel ix, which explain how the disk can transform into a helix without diss ociating into subunits. (C) 1997 Academic Press Limited.