James M. HogleDepartment of Biological Chemistry & Molecular Pharmacology
Harvard Medical School
Building C2, Room 122
240 Longwood Avenue, Boston, MA 02115
Our research program currently has four major areas of focus: 1) Structural and biochemical characterization of the cell entry pathway of polio and related viruses. 2) Structural characterization of RNA protein complexes involved in viral replication and translation. 3) Structural characterization of components of the Herpes virus replication complex. 4) Development of tools for structure-based drug design.
1) Structural and biochemical dissection of the cell entry pathway of polio and related picornaviruses. Because nonenveloped viruses such as poliovirus lack an outer membrane they cannot use membrane fusion to gain entry to the cell and must instead provide a mechanism for translocation of either the viral genome or the entire viral nucleocapsid across the cell membrane. The mechanisms responsible for this translocation process are poorly understood. Previous studies have shown that attachment of poliovirus to its receptor leads to conformational changes that result in the insertion of normal internal viral protein sequences in the membrane and the production of channels. This has led to a working model in which the channels are proposed to form translocation pores that allow the RNA to be moved across the cell membrane to initiate infection. This project includes a combination of x-ray crystallographic and electron microscopic characterization of the structures of virus receptor complexes and cell entry intermediates in solution. We have also developed a liposome-based system for biochemical and structural characterization of the entry pathway in the context of membranes and have initiated structural studies of the virus-receptor-liposome and entry-intermediate-liposome complexes by electron cryomicroscopy. The structural studies are being complemented with optical microscopic analysis of virus entry, including real-time, live-cell studies in collaboration with Xiaowei Zhuang in the Chemistry department, aimed at determining where virus uncoating and RNA translocation take place during cell entry.
2) Structural characterization of RNA-protein interactions that regulate translation and replication of viral genomes. In collaboration with Lee Gehrke we have recently solved the structure of an complex of a fragment of the capsid protein of AMV with a fragment of the 3’UTR of Alfalfa Mosaic Virus which reveals a stunning peptide-dependent tertiary fold of the RNA that explains the requirement of capsid protein for RNA replication in AMV. We are currently developing expression systems to allow us to address similar RNA protein interactions known to be important for a switch between translation and replication of poliovirus RNA, and for priming and initiation of poliovirus RNA replication.
3) In collaboration with Don Coen we have initiated a program of structural studies of proteins essential for replication in herpes viruses. The DNA replication in herpes viruses includes at least seven proteins, and our ultimate goal in this collaboration is to develop a picture of the complete replication complex. Our initial focus has been on the interaction between the DNA polymerase of HSV1 and an accessory protein, UL42, which is required for processive DNA synthesis. We have solved the structure of a complex between UL42 and the minimal C-terminal domain of the polymerase, and have recently solved the structure of the homologous protein UL44 from cytomegalovirus with and without the C-terminal peptide from the CMV polymerase. These structures reveal a stunning similarity of the monomers of the processivity factors to monomers of eukaryotic and prokaryotic processivity factors. However, instead of associating to form torroidal trimeric clamps that are topologically tethered to DN A like the eukaryotic processivity factor PCNA the herpes processivity factors either bind DNA as a monomer UL42 or as a tail-tail dimer UL44 that we call a ‘C-clamp’. Based on unusual concentration of basic residues on the prutative DNA binding faces of the UL42 monomer and the UL44 dimer and on biochemical studies in the Coen laboratory we have proposed that these proteins confer processivity by electrostatic tethering UL42 or by a combination of electrostatic and topological thethering UL44.
4) Our interest in virus structures has naturally led us to investigate methods for using the structures to design antiviral. We are currently developing methods in which the structures are used to develop templates for structurally-biased combinatorial libraries, and the libraries are screened for ligands with antiviral activity.
Belnap, D. M., D. J. Filman, B. L. Trus, N. Cheng, F. P. Booy, J. F. Conway, S. Curry, C. N. Hiremath, S. K. Tsang, A. C. Steven, and J. M. Hogle (2000). Molecular tectonic model of virus structural transitions: the putative cell entry states of poliovirus. J Virol 74:1342-54.
Belnap, D. M., B. M. McDermott, Jr., D. J. Filman, N. Cheng, B. L. Trus, H. J. Zuccola, V. R. Racaniello, J. M. Hogle, and A. C. Steven (2000). Three-dimensional structure of poliovirus receptor bound to poliovirus. Proc Natl Acad Sci U S A 97:73-8.
Zuccola, H. J., D. J. Filman, D. M. Coen, and J. M. Hogle (2000). The crystal structure of an unusual processivity factor, herpes simplex virus UL42, bound to the C terminus of its cognate polymerase. Mol Cell 5:267-78.
Tsang, S.K., J. Cheh, L. Isaacs, D. Joseph-McCarthy, S.-K. Choi, D.C. Pevear, G.M. Whitesides, and J.M. Hogle (2001). A structurally-biased combinatorial approach for discovering new anti-picornaviral compounds. Chemistry and Biology, 8:33-45.
Hogle, J.M. (2002). Poliovirus cell entry: Common structural themes in viral cell entry pathways. Annu Rev Microbiol 56:677-702.
Appleton, B.A., Loregian, A., Filman, D.J., Coen, D.M., and Hogle, J.M. (2004). The cytomegalovirus DNA polymerase subunit UL44 forms a C clamp-shaped dimer. Molecular Cell 15: 233-44.
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