In our lab we are interested in the assembly of higher-order macromolecular structures such as viral shells or multi-subunit cellular machines. We are trying to understand how the physical interactions at protein interfaces drive the assembly process and contribute to the function of the assembled structure. One of the goals of our studies is to identify critical protein-protein contacts that could potentially be blocked for therapeutic purposes. Inhibition of protein-protein interactions remains one of the major challenges and opportunities of modern molecular pharmacology, and we seek to develop novel drug-discovery strategies that combine NMR spectroscopy, computational methods and chemical biology tools.

At this time there are three active projects in the lab: (1) Function of the major homology region (MHR) in HIV assembly. (2) Structural Basis of Retroviral Restriction by TRIM5alpha. (3) Assembly of the DNA-repair machinery.

Function of the MHR in HIV assembly. Disruption of viral assembly within the infected cell is a potential therapeutic strategy, and we are specifically interested in HIV assembly which is driven by self-association of multiple copies of the gag polyprotein at the plasma membrane.


Our recent results have shed light on the elusive function of the most conserved element within the gag: the major homology region (MHR). Currently we are trying to elucidate the molecular mechanisms of the MHR function and to explore it as a therapeutic target.

References:
    Ivanov D, Tsodikov OV, Kasanov J, Ellenberger T, Wagner G, Collins T (2007). Domain-swapped dimerization of the HIV-1 capsid C-terminal domain. Proc. Natl. Acad. Sci. U S A 104:4353-8.
    Ivanov D, Stone JR, Maki JL, Collins T, Wagner G (2005). Mammalian SCAN domain dimer is a domain-swapped homolog of the HIV capsid C-terminal domain. Mol. Cell 17: 137-43.
    Gronenborn AM (2009). Protein acrobatics in pairs--dimerization via domain swapping. Curr. Opin. Struct. Biol. 19:39-49.
    Kingston RL, Vogt VM (2005). Domain swapping and retroviral assembly. Mol. Cell 17:166-7.

Retroviral restriction by TRIM5alpha. TRIM5alpha proteins bind retroviral capsids after cell entry and restrict retroviral infection by blocking reverse transcription and/or integration of the viral genetic material. This novel mechanism of cellular immunity against retroviruses appears to determine the species tropism of the primate immunodeficiency viruses active today.

Species-specific differences in TRIM5alpha activity arise from differences in TRIM5alpha affinity for the capsid. For example, human TRIM5alpha binds HIV capsid weakly and does not restrict HIV. Remarkably, deletion of a single amino acid in huTRIM5alpha restores its affinity for the HIV capsid and HIV restriction. Capsid recognition is mediated by the B30.2 domain of TRIM5alpha, but the structural basis of TRIM5alpha-CA interactions is unknown. We are trying to understand how structural differences at the B30.2-capsid interface explain species-specific differences in TRIM5alpha activity and explore whether the inability of the human protein to restrict HIV could be restored by pharmacological means. This project has recently been funded by the NIH.

References:
    Brandariz-Nuņez A, Roa A, Valle-Casuso JC, Biris N, Ivanov D, Diaz-Griffero F (2012) Contribution of SUMO-interacting motifs and SUMOylation to the antiretroviral properties of TRIM5alpha. Virology [Epub ahead of print] PubMed PMID: 23084420
    Biris N, Yang Y, Taylor AB, Tomashevski A, Guo M, Hart PJ, Diaz-Griffero F, Ivanov DN (2012) Structure of the rhesus monkey TRIM5alpha PRYSPRY domain, the HIV capsid recognition module. Proc. Natl. Acad. Sci. U S A 109(33): 13278-83.

Assembly of the DNA-repair machinery. Recently we elucidated the structural basis for the recruitment of XPF-ERCC1 heteronuclease to sites of DNA damage in Nucleotide Excision Repair (NER). XPF-ERCC1 recruitment is enabled by the binding of the independently folded central domain of ERCC1 to the short unstructured segment in the N-terminal region of the damage verification protein XPA. The central domain of ERCC1 has evolved from an endonuclease domain, but its active site is missing catalytic residues and has instead been adapted for XPA binding. We hypothesize that many other protein recruitment events in DNA repair are performed by interaction domains with enzyme-like structural features. These protein-protein interactions may have localized geometries favorable for small-molecule inhibition. We currently focus our efforts on the FancM-FAAP24 heterodimer, a homolog of XPF-ERCC1 that functions in the Fanconi Anemia Pathway of DNA repair.


DNA repair is intimately linked to cancer. On the one hand DNA-repair defects lead to genomic instability and higher risk of cancer development, while on the other, cancerous cells may become dependent on particular DNA-repair pathways for efficient proliferation and for resistance to chemo- and/or radiation therapy. Inhibition of DNA repair may, therefore, expand the therapeutic window of the widely used drugs such as cisplatin and others, the utility of which is still limited by their toxicity and by acquired resistance. Furthermore, several key proteins in DNA repair have recently been shown to be synthetically lethal with oncogenic mutations, suggesting that DNA repair inhibitors could be used to selectively target cancer cells.

References:
    Tsodikov OV, Ivanov D, Orelli B, Staresincic L, Shoshani I, Oberman R, Schärer OD, Wagner G, Ellenberger T (2007). Structural Basis for the Recruitment of ERCC1-XPF to Nucleotide Excision Repair Complexes by XPA. EMBO J. 26:4768-76.
    Croteau DL, Peng Y, Van Houten B (2008). DNA repair gets physical: mapping an XPA-binding site on ERCC1. DNA Repair 7:819-26.
    Ljungman M (2009). Targeting the DNA damage response in cancer. Chem. Rev. 109:2929-50.
    Reinhardt HC, Jiang H, Hemann MT, Yaffe MB (2009). Exploiting synthetic lethal interactions for targeted cancer therapy. Cell Cycle 8:3112-9.