Research

Projects:
HIV
TRIMs

Our long-term goal is to understand how proteins interact with each other and how these interactions underlie biological processes. We are particularly interested in molecular and structural switches that control how proteins form and transform high-order quaternary interactions — that is, the structure and dynamics of macromolecular assemblies. Our primary techniques are biochemistry, x-ray crystallography, and electron microscopy. Through collaborators, we complement our biochemical and biophysical approach with cell biology and virology experiments. In this way, we obtain a comprehensive understanding of the biological systems we are studying.

 

HIV Assembly and Maturation

Geometric and molecular models of the HIV capsid

Geometric and molecular models
of the mature HIV capsid

HIV and other orthoretroviruses are membrane-enveloped viruses that adopt two distinct morphological states in the course of their replication.  These viruses initially assemble in an immature, non-infectious form, wherein the viral genome is encased within a spherical capsid shell composed of the viral Gag protein.  To become infectious, the immature virus undergoes a morphological change into the mature form, wherein the genome is now packaged within a cone-shaped mature capsid composed of the CA protein.  This process, termed “maturation,” prepares the genome for delivery into host cells and a new round of replication.  Maturation is triggered by proteolytic processing of Gag into CA (and other mature proteins), and is a proven target for inhibition of HIV/AIDS in the clinic.

Working with Mark Yeager (UVa Dept. of Molecular Physiology and Biological Physics), we solved x-ray structures of the mature capsid building blocks — the hexameric and pentameric forms of the CA protein — and computed a molecular model for the full capsid.  We are currently working on the structure of the immature Gag shell.  Ultimately, we hope to integrate the structures with information derived from biochemical reconstitution experiments, in order to obtain a high-definition 3D movie of the molecular transformations that drive HIV maturation. Other projects in this area have the broad goal of understanding how host proteins, such as cyclophilins, nucleoporins, and TRIMs, recognize the capsid in order to positively or negatively regulate specific steps in the HIV-1 life cycle.

Tripartite Motif Proteins

Trim primary sequence diagram

Domain organization of TRIM proteins

We have a number of projects in the lab to investigate the structure and function of cellular proteins that comprise the TRIM/RBCC family (about 100 different human proteins identified so far).  TRIM proteins are RING-domain E3 ubiquitin ligases that regulate many different cellular processes and pathways.  They appear to have particularly important roles in anti-viral defense, activation of the cellular innate immune response, inflammation, and the development of cancer. TRIMs are modular proteins with an N-terminal RING domain, followed by one or two B-box domains, a coiled-coil domain, and a C-terminal domain.  The RING/B-box/coiled-coil (RBCC) or tripartite motif mediates formation of high-order assemblies.  Our broad goal is to understand how TRIM assembly integrates enzymatic activity into biological function. Therefore, an important aspect of our work is to understand, by applying structural biology approaches, how these domains are arranged at the level of quaternary structure.

Recommended Reading

Review of TRIMs in innate immunity:

McNab et al. (2011) Curr Opin Immunol 23, 46-56

Our work on TRIM proteins:

Sanchez et al. (2014) Proc Natl Acad Sci USA111, 2494-2499