Primary structure and sidechain interactions of PFL filamentous bacterial virus coat protein

Abstract

Two structural classes of filamentous bacterial viruses have been identified on the basis of their X-ray diffraction patterns. The class I structure¹ is found for the fd, If1 and IKe strains, while the class II structure² is found for the Pf1 and Xf strains. The two classes differ in the number of protein subunits per turn in the virus helix (4.5 units per turn for class I and 4.4 for class II, with ∼15 Å pitch), and in the fact that a periodic perturbation of the structure is observed for class I but not for class II. The major coat protein, which comprises about 99% of the virus coat, is largely α-helical^3,4 with a molecular weight of about 5,000 for all strains investigated². The sequence of the fd coat protein^4,5 is known. It is 50 residues long, with an acidic N-terminal region, a hydrophobic middle region and a basic C-terminal region. To facilitate the detailed analysis of the class II structure, and to investigate the possibility that the structural differences between class I and class II arise from differences in the coat protein, we have determined the sequence of Pf1 coat protein. This is the first system for which a molecular model of a structural protein has been described in sufficient detail to permit study of the bonding specificity between proteins. Since the α helix is a universal structure, study of the interactions between α helices can be of central importance in many unrelated systems. We have found that α helices are arranged in the virion so that hydrophobic sidechains on each protein subunit can fit into the space between sidechains on neighbouring subunits.