On the Structure of the Scaffolding Core of Bacteriophage T4 and Its Role in Head Length Determination Bonnie Berger 1 Mathematics Department and Laboratory for Computer Science, Room 2-389, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and Peter W. Shor AT&T Laboratories, Florham Park, New Jersey 07932 Received June 5, 1996 and in revised form November 20, 1997 The scaffolding core in bacteriophages is a tempo- rary structure that plays a major role in determin- ing the shape of the protein shell that encapsulates the viral DNA. In the currently accepted structure for the scaffolding core in bacteriophage T4, there is a symmetry mismatch between the protein shell, which has fivefold symmetry, and the scaffolding core, which is believed to consist of six helical chains. Alternate structures for the scaffolding core in T4 are investigated. Starting with the hypothesis that the shell and a 10-helix core would have match- ing symmetry, a Vernier mechanism is proposed that explains the previously unexplained behavior of the length determination process in giant head mutants of T4. Other possible Vernier mechanisms for core structures containing six and eight helices are also explored.  1998 Academic Press Key Words: bacteriophage T4; scaffolding proteins; self-assembly; morphogenesis; Vernier mechanism. INTRODUCTION Bacteriophage T4 is one of the most extensively studied viruses. It consists of a head and a tail which form separately and then join together. The head is a protein shell containing the viral DNA. Like many viruses, T4 has a shell that is essentially icosahedral. However, the T4 head is atypical in that it is elongated along a fivefold symmetry axis by the insertion of extra hexamers (Moody, 1965; Aebi et al., 1974; Branton and Klug, 1975; Baschong et al., 1988). Despite extensive study, the mechanism for the shape determination of this T4 protein shell is still quite poorly understood. Part of the difficulty is the relative complexity of the morpho- genetic mechanism of T4. The shape-determining mech- anism of the T4 head appears to involve approximately 10 proteins, including 3 proteins (2 coat proteins gp23 and gp24 and the portal protein gp20) which remain in the mature virus coat, and approximately 7 proteins (gp22, gp21, IPI, IPII, IPIII, gp67, and gp68), which are temporarily incorporated into an internal scaffolding core that is subsequently destroyed during the matura- tion process (Kellenberger, 1990). The focus of this paper is on the structure of the scaffolding core of T4 and its possible role in the length determination of the shell. The structure of the T4 scaffolding core was first studied by Paulson and Laemmli (1977), who con- cluded that the scaffolding core contains six helical chains wrapped around a hollow core. These chains are believed to be composed of the protein gp22, a predominant component of the core which comprises 38% of the mass of the core according to current estimates of molecular masses and copy numbers for the core proteins (Black et al., 1995). The protein gp22 will spontaneously polymerize into long fila- ments (van Driel, 1980b) and is thus a good candi- date for the principal component of these helices. These filaments are approximately 95 Å wide and 25 Å thick, with subunits spaced approximately 15 Å apart along the filaments; the gp22 molecules them- selves have dimensions approximately 15  25  95 Å (van Driel, 1980a; Engel and van Driel, 1981; Engel et al., 1982; Mesyanzhinov et al., 1990). A core consisting of six helical chains is surprising, because it implies a symmetry mismatch between the virus shell, which has 5-fold rotational symme- try, and the scaffolding core, which could have 3-fold or 6-fold symmetry but not 5-fold symmetry. While 1 To whom all correspondence should be addressed. JOURNAL OF STRUCTURAL BIOLOGY 121, 285–294 (1998) ARTICLE NO. SB973942 285 1047-8477/98 $25.00 Copyright  1998 by Academic Press All rights of reproduction in any form reserved.