Current Funded Projects

Crystal structures of human importins

Nucleocytoplasmic Transport – Nucleocytoplasmic transport is central to the functioning of eukaryotic cells and is an integral part of the processes that lead to most human diseases. The nuclear availability of essential molecules such as transcription factors, DNA replication factors, and oncogenes is emerging as a powerful way to control gene expression, cellular differentiation, and transformation and a novel and promising target for pharmacological intervention. In the first part of my career, I elucidated the molecular basis for the recognition of classical (Cingolani et al., Nature, 1999) and non-classical (Cingolani et al., Mol Cell, 2002) import substrates by human importin beta. In the last two decades, my lab became interested in deciphering how signaling molecules linked to diseases (e.g., NF-kB, STAT1, Hepatitis B Virus, etc.) are translocated into the cell nucleus by human importins and the cellular cues regulating these complex pathways. The long-term goal of our work is to devise new therapeutics that reduce the aberrant nuclear translocation of signaling factors linked to cancer.

Similarity between NPC passage and TDP-43 disaggregation

Mechanisms of TDP-43 aggregation – We are pursuing basic and translational studies on the ALS-related RNA-binding protein TDP-43 in collaboration with the lab of Dr. Lin Guo at Thomas Jefferson University. We found that TDP-43 is imported into the nucleus by a heterodimer of importin alpha1/beta1, which recognizes an N-terminal NLS and disrupts dimerization of TDP-43 N-terminal Domain (NTD) upstream of the NLS (Doll et al., Cell Reports, 2022). Our working hypothesis is that disruption of NTD dimerization reduces TDP-43 C-terminal prion-like domain (CTD) aggregation, possibly explaining the reported chaperone-like activity of importins (Guo et al., Cell, 2018). Our research seeks to decipher the mechanisms governing TDP-43 aggregation and the role of importins as cytoplasmic chaperones. We strive to devise new therapeutics that prevent or reduce the aberrant aggregation of TDP-43 in neurons.

Cryo-EM reconstruction of the Pseudomonas-phage E217

Bacteriophage Structure and Assembly – Our work aims to understand how double-stranded DNA viruses such as herpesviruses and tailed bacteriophages package their large genomes (~40-250 kb) inside empty precursor capsids (‘procapsids’), as well as eject the genomes inside infected cells. Both processes occur through the portal protein that changes conformation during genome packaging (Lokareddy et al., Nature Commun, 2017). Our recent work focuses on the Podoviridae DNA-ejectosomes (Swanson et al., Mol Cell, 2021) and Pseudomonas-phages of potential application to phage therapy (Li et al., Nat Commun, 2023). In collaboration with Dr. Federica Briani at the University of Milan, IT, we employ biochemical, bioinformatic, and cryo-EM single-particle analysis to decipher the machines and mechanisms used by Pseudomonas phages to attach the bacterium cell envelope, eject their genome into the host, and package newly replicated genomes into precursor capsids.

Crystal structure of Mtb DppA protein

Bacterial Virulence Factors – In collaboration with Dr. Michael Niederwies at UAB, we have studied Mycobacterium tuberculosis (MtB) virulence factors. We determined the first atomic structure of the Mtb Necrotizing Toxin (TNT) in complex with the Immunity factor IFT (Sun et al. Nature Struc Mol Biol, 2011). TNT hydrolyzes the essential co-enzyme nicotinamide adenine dinucleotide (NAD+) in the cytosol of Mtb-infected macrophages. Our current work focuses on the machinery required for iron uptake in Mtb. We have determined the atomic structure of the dipeptide permease Dpp that is essential for heme uptake across the inner membrane of Mtb (Mitra et al., Nat Commun, 2019). We are now focusing on the membrane-anchored PPE36 and PPE62 proteins required for both heme and hemoglobin utilization.