All Publications

  • High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs. Nature communications Ha, B., Larsen, K. P., Zhang, J., Fu, Z., Montabana, E., Jackson, L. N., Chen, D., Puglisi, E. V. 2021; 12 (1): 2500


    Reverse transcription of the HIV-1 viral RNA genome (vRNA) is an integral step in virus replication. Upon viral entry, HIV-1 reverse transcriptase (RT) initiates from a host tRNALys3 primer bound to the vRNA genome and is the target of key antivirals, such as non-nucleoside reverse transcriptase inhibitors (NNRTIs). Initiation proceeds slowly with discrete pausing events along the vRNA template. Despite prior medium-resolution structural characterization of reverse transcriptase initiation complexes (RTICs), higher-resolution structures of the RTIC are needed to understand the molecular mechanisms that underlie initiation. Here we report cryo-EM structures of the core RTIC, RTIC-nevirapine, and RTIC-efavirenz complexes at 2.8, 3.1, and 2.9A, respectively. In combination with biochemical studies, these data suggest a basis for rapid dissociation kinetics of RT from the vRNA-tRNALys3 initiation complex and reveal a specific structural mechanism of nucleic acid conformational stabilization during initiation. Finally, our results show that NNRTIs inhibit the RTIC and exacerbate discrete pausing during early reverse transcription.

    View details for DOI 10.1038/s41467-021-22628-9

    View details for PubMedID 33947853

  • Advances in understanding the initiation of HIV-1 reverse transcription. Current opinion in structural biology Krupkin, M. n., Jackson, L. N., Ha, B. n., Puglisi, E. V. 2020; 65: 175–83


    Many viruses, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Human Immunodeficiency Virus (HIV), use RNA as their genetic material. How viruses harness RNA structure and RNA-protein interactions to control their replication remains obscure. Recent advances in the characterization of HIV-1 reverse transcriptase, the enzyme that converts its single-stranded RNA genome into a double-stranded DNA copy, reveal how the reverse transcription complex evolves during initiation. Here we highlight these advances in HIV-1 structural biology and discuss how they are furthering our understanding of HIV and related ribonucleoprotein complexes implicated in viral disease.

    View details for DOI 10.1016/

    View details for PubMedID 32916568

  • Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription. Journal of molecular biology Larsen, K. P., Choi, J. n., Jackson, L. N., Kappel, K. n., Zhang, J. n., Ha, B. n., Chen, D. H., Puglisi, E. V. 2020


    A hallmark of the initiation step of HIV-1 reverse transcription, in which viral RNA genome is converted into double-stranded DNA, is that it is slow and non-processive. Biochemical studies have identified specific sites along the viral RNA genomic template in which reverse transcriptase (RT) stalls. These stalling points, which occur after the addition of 3 and 5 template dNTPs, may serve as checkpoints to regulate the precise timing of HIV-1 reverse transcription following viral entry. Structural studies of reverse transcriptase initiation complexes (RTICs) have revealed unique conformations that may explain the slow rate of incorporation, however, questions remain about the temporal evolution of the complex and features that contribute to strong pausing during initiation. Here we present cryo-electron microscopy (cryo-EM) and single-molecule characterization of an RTIC after three rounds of dNTP incorporation (+3), the first major pausing point during reverse transcription initiation. Cryo-EM structures of a + 3 extended RTIC reveal conformational heterogeneity within the RTIC core. Three distinct conformations were identified, two of which adopt unique, likely off-pathway, intermediates in the canonical polymerization cycle. Single-molecule Förster resonance energy transfer (smFRET) experiments confirm that the +3 RTIC is more structurally dynamic than earlier stage RTICs. These alternative conformations were selectively disrupted through structure-guided point mutations to shift smFRET populations back towards the on-pathway conformation. Our results support the hypothesis that conformational heterogeneity within the HIV-1 reverse transcriptase initiation complex during pausing serves as an additional means of regulating HIV-1 replication.

    View details for DOI 10.1016/j.jmb.2020.06.003

    View details for PubMedID 32512005

  • Smoothened stimulation by membrane sterols drives Hedgehog pathway activity. Nature Deshpande, I., Liang, J., Hedeen, D., Roberts, K. J., Zhang, Y., Ha, B., Latorraca, N. R., Faust, B., Dror, R. O., Beachy, P. A., Myers, B. R., Manglik, A. 2019


    Hedgehog signalling is fundamental to embryonic development and postnatal tissue regeneration1. Aberrant postnatal Hedgehog signalling leads to several malignancies, including basal cell carcinoma and paediatric medulloblastoma2. Hedgehog proteins bind to and inhibit the transmembrane cholesterol transporter Patched-1 (PTCH1), which permits activation of the seven-transmembrane transducer Smoothened (SMO) via a mechanism that is poorly understood. Here we report the crystal structure of active mouse SMO bound to both the agonist SAG21k and to an intracellular binding nanobody that stabilizes a physiologically relevant active state. Analogous to other G protein-coupled receptors, the activation of SMO is associated with subtle motions in the extracellular domain, and larger intracellular changes. In contrast to recent models3-5, a cholesterol molecule that is critical for SMO activation is bound deep within the seven-transmembrane pocket. We propose that the inactivation of PTCH1 by Hedgehog allows a transmembrane sterol to access this seven-transmembrane site (potentially through a hydrophobic tunnel), which drives the activation of SMO. These results-combined with signalling studies and molecular dynamics simulations-delineate the structural basis for PTCH1-SMO regulation, and suggest a strategy for overcoming clinical resistance to SMO inhibitors.

    View details for DOI 10.1038/s41586-019-1355-4

    View details for PubMedID 31263273

  • Self-Assembly Behaviors of a Penta-Phenylene Maltoside and Its Application for Membrane Protein Study. Chemistry, an Asian journal Ehsan, M., Kumar, A., Mortensen, J. S., Du, Y., Hariharan, P., Kumar, K. K., Ha, B., Byrne, B., Guan, L., Kobilka, B. K., Loland, C. J., Chae, P. S. 2019


    We prepared an amphiphile with a penta-phenylene lipophilic group and a branched trimaltoside head group. This new agent, designated penta-phenylene maltoside (PPM), showed a marked tendency to self-assembly into micelles via strong aromatic-aromatic interactions in aqueous media, as evidenced by 1 H NMR spectroscopy and fluorescence studies. When utilized for membrane protein studies, this new agent was superior to DDM, a gold standard conventional detergent, in stabilizing multiple proteins long term. The ability of this agent to form aromatic-aromatic interactions is likely responsible for enhanced protein stabilization when associated with a target membrane protein.

    View details for PubMedID 30969484

  • Asymmetric maltose neopentyl glycol amphiphiles for a membrane protein study: effect of detergent asymmetricity on protein stability CHEMICAL SCIENCE Bae, H., Du, Y., Hariharan, P., Mortensen, J. S., Kumar, K. K., Ha, B., Das, M., Lee, H., Loland, C. J., Guan, L., Kobilka, B. K., Chae, P. 2019; 10 (4): 1107–16

    View details for DOI 10.1039/c8sc02560f

    View details for Web of Science ID 000457342200015