EJ Fine

All Publications

• Structural basis of opioid receptor activation by PCP and ketamine. Nature structural & molecular biology Jiang, Q., Han, J., Fine, E. J., Ramos-Gonzalez, N., Rangari, V. A., Ruiz, M. V., Critz, M. L., Suomivuori, C. M., Wang, J., Albert, T. L., Whiddon, K., Li, K., Robertson, M. J., Huang, X. P., Land, B. B., Majumdar, S., Fay, J. F., Dror, R. O., Che, T. 2026

  Abstract

  Ketamine offers rapid relief for treatment-resistant depression and severe pain in the clinic, providing immediate benefits that traditional medications often fail to deliver. While its antagonistic action at the N-methyl-D-aspartate receptor (NMDAR) is a key mechanism, ketamine's dual nature as both a promising treatment and a drug with abuse potential suggests its therapeutic effects extend beyond NMDAR inhibition. Here we provide structural evidence of human opioid receptors bound to ketamine and its parent analog phencyclidine (PCP), supporting that both ligands can directly bind and activate opioid receptors. The structures, together with site-directed mutagenesis and structure-activity relationship studies, identify key motifs involved in ketamine and PCP recognition and efficacy modulation. Furthermore, we determine the structure of the ligand-free state of human κ opioid receptor, revealing molecular details before ligand engagement. Compared to PCP, ketamine displays more notable binding dynamics in the orthosteric site that may contribute to its unique pharmacology at opioid receptors. Our findings highlight the importance of including opioid receptors to fully understand ketamine's versatility in clinical settings.

  View details for DOI 10.1038/s41594-026-01839-y

  View details for PubMedID 42332075

  View details for PubMedCentralID 4556466

• Structural dynamics of kappa opioid receptor interactions with β-arrestin 1. Nature communications Han, J., Fine, E. J., Jiang, Q., Zhuang, Y., Suomivuori, C. M., Chen, Z. W., Denn, E., Whiddon, K., Li, K., Evers, A. S., Fuller, J., Carter, J., Fay, J. F., Chen, M., Dror, R. O., Che, T. 2026

  Abstract

  Opioid receptors signal through Gi/o protein and β-arrestin pathways that mediate distinct effects of opiate drugs. While opioid binding and G protein activation are well studied, β-arrestin recruitment remains poorly understood. Here, we determine the complex structure of the kappa opioid receptor (KOR) with β-arrestin1 (βarr1) at 2.60 Å resolution using cryogenic electron microscopy. Structural and mass spectrometry analyses reveal multiple phosphorylation sites and a phospholipid-binding site that specifically enhances arrestin recruitment. The KOR-βarr1 complex adopts a core interaction and exhibits notable differences from other GPCR-βarr1 complexes. Comparisons with the structures of KOR-Nb39 and KOR-Gi1 complexes also reveal distinct structural features in the orthosteric binding site and the KOR-transducer interface that affect signaling bias. Using extensive 3D variation analysis and molecular dynamics simulations, we identify a range of conformational dynamics in both the receptor and βarr1, suggesting an allosteric pathway for arrestin's entry and exit.

  View details for DOI 10.1038/s41467-026-73968-3

  View details for PubMedID 42243110

• Structure of mitochondrial pyruvate carrier and its inhibition mechanism NATURE He, Z., Zhang, J., Xu, Y., Fine, E. J., Suomivuori, C., Dror, R. O., Feng, L. 2025

  Abstract

  The mitochondrial pyruvate carrier (MPC) governs the entry of pyruvate-a central metabolite that bridges cytosolic glycolysis with mitochondrial oxidative phosphorylation-into the mitochondrial matrix1-5. It thus serves as a pivotal metabolic gatekeeper and has fundamental roles in cellular metabolism. Moreover, MPC is a key target for drugs aimed at managing diabetes, non-alcoholic steatohepatitis and neurodegenerative diseases4-6. However, despite MPC's critical roles in both physiology and medicine, the molecular mechanisms underlying its transport function and how it is inhibited by drugs have remained largely unclear. Here our structural findings on human MPC define the architecture of this vital transporter, delineate its substrate-binding site and translocation pathway, and reveal its major conformational states. Furthermore, we explain the binding and inhibition mechanisms of MPC inhibitors. Our findings provide the molecular basis for understanding MPC's function and pave the way for the development of more-effective therapeutic reagents that target MPC.

  View details for DOI 10.1038/s41586-025-08667-y

  View details for Web of Science ID 001437462200001

  View details for PubMedID 40044865

  View details for PubMedCentralID 1166210

• Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids PROTEIN ENGINEERING DESIGN & SELECTION Haloi, N., Huang, S., Nichols, A. L., Fine, E. J., Friesenhahn, N. J., Marotta, C. B., Dougherty, D. A., Lindahl, E., Howard, R. J., Mayo, S. L., Lester, H. A. 2024; 37

  Abstract

  We developed fluorescent protein sensors for nicotine with improved sensitivity. For iNicSnFR12 at pH 7.4, the proportionality constant for ∆F/F0vs [nicotine] (δ-slope, 2.7 μM-1) is 6.1-fold higher than the previously reported iNicSnFR3a. The activated state of iNicSnFR12 has a fluorescence quantum yield of at least 0.6. We measured similar dose-response relations for the nicotine-induced absorbance increase and fluorescence increase, suggesting that the absorbance increase leads to the fluorescence increase via the previously described nicotine-induced conformational change, the 'candle snuffer' mechanism. Molecular dynamics (MD) simulations identified a binding pose for nicotine, previously indeterminate from experimental data. MD simulations also showed that Helix 4 of the periplasmic binding protein (PBP) domain appears tilted in iNicSnFR12 relative to iNicSnFR3a, likely altering allosteric network(s) that link the ligand binding site to the fluorophore. In thermal melt experiments, nicotine stabilized the PBP of the tested iNicSnFR variants. iNicSnFR12 resolved nicotine in diluted mouse and human serum at 100 nM, the peak [nicotine] that occurs during smoking or vaping, and possibly at the decreasing levels during intervals between sessions. NicSnFR12 was also partially activated by unidentified endogenous ligand(s) in biofluids. Improved iNicSnFR12 variants could become the molecular sensors in continuous nicotine monitors for animal and human biofluids.

  View details for DOI 10.1093/protein/gzae003

  View details for Web of Science ID 001173155400001

  View details for PubMedID 38302088

  View details for PubMedCentralID PMC10896302

• Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids. bioRxiv : the preprint server for biology Haloi, N., Huang, S., Nichols, A. L., Fine, E. J., Friesenhahn, N. J., Marotta, C. B., Dougherty, D. A., Lindahl, E., Howard, R. J., Mayo, S. L., Lester, H. A. 2024

  Abstract

  We developed fluorescent protein sensors for nicotine with improved sensitivity. For iNicSnFR12 at pH 7.4, the proportionality constant for DeltaF/F0 vs [nicotine] (delta-slope, 2.7 muM-1) is 6.1-fold higher than the previously reported iNicSnFR3a. The activated state of iNicSnFR12 has a fluorescence quantum yield of at least 0.6. We measured similar dose-response relations for the nicotine-induced absorbance increase and fluorescence increase, suggesting that the absorbance increase leads to the fluorescence increase via the previously described nicotine-induced conformational change, the "candle snuffer" mechanism. Molecular dynamics (MD) simulations identified a binding pose for nicotine, previously indeterminate from experimental data. MD simulations also showed that Helix 4 of the periplasmic binding protein (PBP) domain appears tilted in iNicSnFR12 relative to iNicSnFR3a, likely altering allosteric network(s) that link the ligand binding site to the fluorophore. In thermal melt experiments, nicotine stabilized the PBP of the tested iNicSnFR variants. iNicSnFR12 resolved nicotine in diluted mouse and human serum at 100 nM, the peak [nicotine] that occurs during smoking or vaping, and possibly at the decreasing levels during intervals between sessions. NicSnFR12 was also partially activated by unidentified endogenous ligand(s) in biofluids. Improved iNicSnFR12 variants could become the molecular sensors in continuous nicotine monitors for animal and human biofluids.

  View details for DOI 10.1101/2023.01.16.524298

  View details for PubMedID 36712031

• Structural insights into binding of therapeutic channel blockers in NMDA receptors NATURE STRUCTURAL & MOLECULAR BIOLOGY Chou, T., Epstein, M., Michalski, K., Fine, E., Biggin, P. C., Furukawa, H. 2022; 29 (6): 507-+

  Abstract

  Excitatory signaling mediated by N-methyl-D-aspartate receptor (NMDAR) is critical for brain development and function, as well as for neurological diseases and disorders. Channel blockers of NMDARs are of medical interest owing to their potential for treating depression, Alzheimer's disease, and epilepsy. However, precise mechanisms underlying binding and channel blockade have remained limited owing to challenges in obtaining high-resolution structures at the binding site within the transmembrane domains. Here, we monitor the binding of three clinically important channel blockers: phencyclidine, ketamine, and memantine in GluN1-2B NMDARs at local resolutions of 2.5-3.5 Å around the binding site using single-particle electron cryo-microscopy, molecular dynamics simulations, and electrophysiology. The channel blockers form different extents of interactions with the pore-lining residues, which control mostly off-speeds but not on-speeds. Our comparative analyses of the three unique NMDAR channel blockers provide a blueprint for developing therapeutic compounds with minimal side effects.

  View details for DOI 10.1038/s41594-022-00772-0

  View details for Web of Science ID 000802860000002

  View details for PubMedID 35637422

  View details for PubMedCentralID PMC10075384