Assistant Professor

Ph.D., University of Illinois at Chicago, 1996
Postdoctoral Fellow, University of Texas, Southwestern Medical Center, 1996-1999
Purdue University, 1999-2005

Program Affiliation: Molecular Biology & Genetics | Microbiology

Research Groups Affiliation: Biochemistry | Microbiology

Phone: 812/856-3686
Fax: 812/855-6705
Email Tuli

Alphavirus Structure and Assembly

My lab is focused on examining molecular interactions required for efficient assembly and release of infectious virus particles.  We work with alphaviruses which are enveloped, positive-strand RNA viruses that are transmitted to a variety of hosts by mosquitoes.  Their life cycle is comprised of receptor mediated host-cell infection, viral-host membrane fusion, genome replication, virus assembly and budding.  Efficient budding is fundamental for successful and continual virus infection. 

Alphavirus virions are icosahedral and have an external diameter of ~700-Å.  The virus surface consists of 80 spikes, each a trimer of the E1-E2 glycoprotein heterodimers.  Internal to the spikes is the lipid bilayer and then a nucleocapsid core which is comprised of 240 copies of the capsid protein and a single copy of the genomic RNA.  E2 is the only protein that is present at the virus surface, in the lipid bilayer and in the nucleocapsid core, suggesting it has multiple structural and functional roles in the virus lifecycle. 

Left:  Cryo-EM image of purified Sindbis particles flash frozen in vitreous ice.  Middle:  Structure of Sindbis virus at 20 Å resolution determined by cryo-EM and 3D image reconstruction techniques.  Right:  Cross section of Sindbis virus at 11 Å resolution with the glycoproteins (E1 and E2), the lipid bilayer, and the capsid protein (NCP) all identified (Zhang, Mukhopadhyay et al., 2002).

Assembly of alphavirus particles is a two-step process, neither of which has been well characterized either in vivo or in vitro.  One step consists of the E1 and E2 glycoproteins being translated, heterodimerizing in the ER and subsequently being transported to the plasma membrane as trimers of heterodimers.  The second step involves the assembly of cytosolic nucleocapsid cores (capsid protein and viral genome) and their migration to the plasma membrane.  Budding of alphavirus particles is an ordered process requiring that the C-terminus of the integral membrane E2 glycoprotein first bind to a "pocket" of the capsid protein in cytoplasmic nucleocapsid cores. 

In order to understand the molecular mechanisms at the different stages of the virus life cycle, my group will employ structure-function studies using a combinatorial approach of genetics, biochemistry and structure determination.  Our primary tool for structure determination is cryo electron microscopy which has become a powerful tool for determining three-dimensional structures of specimens that are too heterogeneous, too large, or too transient for conventional X-ray crystallographic methods.  Rapid freezing of samples can trap viral intermediates and their real-time structures can be determined. 

Goicochea NL, De M, Rotello VM, Mukhopadhyay S, Dragnea B. (2007) Core-like particles of an enveloped animal virus can self-assemble efficiently on artificial templates. Nano Lett. 7(8):2281-90.

Mukhopadhyay, S., Zhang, W., Gabler, S., Chipman, P. R., Strauss, E. G., Strauss, J. H., Baker, T. S., Kuhn, R. J., and Rossmann, M. G. (2006) Mapping the Structure and Function of the E1 and E2 Glycoproteins in Alphaviruses, Structure 14(1):63-73.

Mukhopadhyay, S., Kuhn, R. J., and Rossmann, M. G. (2005) Structural Perspective of Flavivirus Lifecycle, Nat. Rev. Microbiol. 3(1):13-22.

Mukhopadhyay, S., Kim, B. S., Chipman, P. R., Rossmann, M. G., and Kuhn, R. J. (2003) Structure of West Nile Virus, Science 302(5643):248.

Zhang, W*, Mukhopadhyay, S.*, Pletnev, S. V., Baker, T. S., Kuhn, R. J., and Rossmann, M. G. (2002) Placement of the Structural Proteins in Sindbis Virus, J Virol.  67(22):11645-58. *equal authorship

Mukhopadhyay, S., Chipman, P. R., Hong, E., Kuhn, R. J., and Rossmann, M. G. (2002) In vitro-assembled alphavirus core-like particles maintain a structure similar to that of nucleocapsid cores in mature virus, J Virol.  67(21):11128-32.

Pletnev, S., Zhang, W., Mukhopadhyay, S., Fisher, B., Hernandez, R., Brown, D. T., Baker, T. S., Rossmann, M. G., and Kuhn, R. J. (2001) Location and Characterization of the Carbohydrate Residues of Sindbis Virus, Cell  105(1): 127-136.