Qun Liu

Research | Publications | Highlights

Research Activities

Structural biology of membrane proteins: Living organisms of animals, plants, and microbes have about 30% genes encoding membrane proteins which play essential roles in signaling, metabolism, transport across membranes, and specialized catalysis on or within the membranes. The majority of known drugs target membrane proteins. However, so far only about 1600 unique membrane proteins have been structurally characterized, which is about 1.3% of all unique structures deposited in the Protein Data Bank (PDB). Structural studies of key membrane proteins and their functional characterizations may provide insights into understanding their roles in physiology and pathology, and provide novel targets for drug development and engineering. We are equipped to study structure-function of metal transporters, lipid metabolizing enzymes, ABC transporters, protein-quality control, and transport proteins.

Structural biology of host-pathogen interactions: The COVID pandemic, caused by the viral pathogen SARS-CoV-2, has significantly harmed the human health and economy of the US and the world. Microbial pathogens of viruses, bacteria, and fungi, coexist and evolve with their hosts (humans, animals, plants, and the shared environment). With increased human activities, current and emerging pathogens pose a biothreat and could potentially lead to the next pandemic if we are not prepared for it. We are equipped to perform structure-function studies of host-pathogen interactions to understand molecular mechanisms of pathogenicity and host response. The gained knowledge will aid in the development of mitigation strategies for a secure bioeconomy and human health.

Cellular structural biology: In a living organism, genes undergo decoding via RNAs and protein assembly to form distinct structures and architectures that enable growth, reproduction, and response to environmental stimuli - the fundamental characteristics of life. As such, in a living organism including humans, cells are the smallest building blocks of life. With the world-leading synchrotron X-rays at NSLS-II and the LBMS cryo-EM facility, we are interested in capturing and studying the structure-function of cells and their response to environments, for example, pathogens, stressors, drugs, etc, using an integrative multiscale and multimodal imaging and computation approach. We hope to provide a comprehensive and systematic understanding of biological processes at biological scales of how cells interact, respond, and adapt to their environments.

Technology research and development: To facilitate the structural characterization of cells and molecules, we are developing experimental and computational technologies, including AI, in collaboration with scientists at NSLS-II, Laboratory for BioMolecular Structure (LBMS), Center for Functional Nanomaterials (CFN), and Computation and Data Sciences (CDS). The areas of current focus are 1) correlative X-ray computed tomography and X-ray fluorescence imaging; 2) correlative cryoFIB-SEM/cryoET and volume EM; 3) optical live-cell imaging; 4) AI-driven computational data analysis, integration, segmentation, aggregation, and automation.

Selected Publications

• Liu Q, Dahmane T, Zhang Z, et al (2012) Structures from Anomalous Diffraction of Native Biological Macromolecules. Science 336:1033-1037. https://doi.org/10.1126/science.1218753
• Chang Y, Bruni R, Kloss B, et al (2014) Structural basis for a pH-sensitive calcium leak across membranes. Science 344:1131-1135. https://doi.org/10.1126/science.1252043
• Liu Q (2017) TMBIM-mediated Ca2+ homeostasis and cell death. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1864:850-857. doi: 10.1016/j.bbamcr.2016.12.023
• Guo G, Fuchs MR, Shi W, Skinner J, Berman E, Ogata CM, Hendrickson WA, McSweeney S, Liu Q (2018) Sample manipulation and data assembly for robust microcrystal synchrotron crystallography. IUCrJ 5:238-246. doi: 10.1107/s2052252518005389
• Gao Y, Xu W, Shi W, Soares A, Jakoncic J, Myers S, Martins B, Skinner J, Liu Q, Bernstein H, McSweeney S, Nazaretski E, Fuchs MR (2018) High-speed raster-scanning synchrotron serial microcrystallography with a high-precision piezo-scanner. Journal of Synchrotron Radiation 25:1362-1370. doi: 10.1107/s1600577518010354
• Guo G, Xu M, Chang Y, Luyten T, Seitaj B, Liu W, Zhu P, Bultynck G, Shi L, Quick M, Liu Q (2019) Ion and pH Sensitivity of a TMBIM Ca2+ Channel. Structure 27:1013-1021.e3. doi: 10.1016/j.str.2019.03.003
• Guo G, Zhu P, Fuchs MR, Shi W, Andi B, Gao Y, Hendrickson WA, McSweeney S, Liu Q (2019) Synchrotron microcrystal native-SAD phasing at a low energy. IUCrJ 6:532-542. doi: 10.1107/s2052252519004536
• Takemaru L, Guo G, Zhu P, Hendrickson WA, McSweeney S, Liu Q (2020) PyMDA: microcrystal data assembly using Python. Journal of Applied Crystallography 53:277-281. doi: 10.1107/s160057671901673x
• Zhu P, Yu X-H, Wang C, et al (2020) Structural basis for Ca2+-dependent activation of a plant metacaspase. Nature Communications 11:. https://doi.org/10.1038/s41467-020-15830-8
• McSweeney DM, McSweeney SM, Liu Q (2020) A self-supervised workflow for particle picking in cryo-EM. IUCrJ 7:719-727. doi: 10.1107/s2052252520007241
• Chai J, Cai Y, Pang C, et al (2021) Structural basis for SARS-CoV-2 envelope protein recognition of human cell junction protein PALS1. Nature Communications 12:. https://doi.org/10.1038/s41467-021-23533-x
• Bruni R, Laguerre A, Kaminska A, et al (2021) High-throughput cell-free screening of eukaryotic membrane protein expression in lipidic mimetics. Protein Science 31:639-651. https://doi.org/10.1002/pro.4259
• Chai L, Zhu P, Chai J, et al (2021) AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement. Crystals 11:1227. https://doi.org/10.3390/cryst11101227
• Liu W, Schoonen M, Wang T, et al (2022) Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state. Communications Biology 5:. https://doi.org/10.1038/s42003-022-03213-2
• Karasawa A, Andi B, Fuchs MR, et al (2022) Multi-crystal native-SAD phasing at 5 keV with a helium environment. IUCrJ 9:768-777. https://doi.org/10.1107/s205225252200971x
• Chai J, Guo G, McSweeney SM, et al (2023) Structural basis for enzymatic terminal C-H bond functionalization of alkanes. Nature Structural & Molecular Biology. https://doi.org/10.1038/s41594-023-00958-0
• Pang C, Chai J, Zhu P, et al (2023) Structural mechanism of intracellular autoregulation of zinc uptake in ZIP transporters. Nature Communications 14:. https://doi.org/10.1038/s41467-023-39010-6
• Dai X, Wu L, Yoo S, Liu Q (2023) Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps. Briefings in Bioinformatics 24:. https://doi.org/10.1093/bib/bbad405
• Lin Z, Zhang X, Nandi P, et al (2024) Correlative single-cell hard X-ray computed tomography and X-ray fluorescence imaging. Communications Biology 7:. https://doi.org/10.1038/s42003-024-05950-y
• Dai X, Henderson M, Yoo S, Liu Q (2025) Predicting Metal-binding Proteins and Structures Through Integration of Evolutionary-scale and Physics-based Modeling. Journal of Molecular Biology 437:168962. https://doi.org/10.1016/j.jmb.2025.168962
• Guo Y, Yang G, Liu H, et al (2025) Structure and mechanism of human vesicular polyamine transporter. Nature Communications 16:. https://doi.org/10.1038/s41467-025-59549-w
• Liu H, Henderson M, Pang Z, et al (2025) Structural determinants for pH-dependent activation of a plant metacaspase. Nature Communications 16:. https://doi.org/10.1038/s41467-025-60253-y
• Zhang X, Lin Z, Wang L, et al (2025) SwinCell: a 3D transformer and flow-based framework for improved cell segmentation. Communications Biology 8:. https://doi.org/10.1038/s42003-025-08397-x
• Pang Z, Liu H, Liu Q, Lam E (2025) Plant metacaspases orchestrate wound-induced pathways for immunity and tissue regeneration. The Plant Journal 124:. https://doi.org/10.1111/tpj.70531
• Lam E, Coll NS, Liu Q (2026) Multitasking mediators: revealing the secret jobs of plant metacaspases. Trends in Plant Science. https://doi.org/10.1016/j.tplants.2026.04.030
• Pang C, Nguyen H, Zhang Q, et al (2026) Cryo-electron microscopy structure of a zinc uptake ABC transporter. Structure. https://doi.org/10.1016/j.str.2026.04.012
• Dai X, Lin Y, Yoo S, Liu Q (2026) PEACE: Prototype-aware Effector Analysis via Contrastive Embeddings. https://doi.org/10.64898/2026.04.19.719514

Research Highlights

• Scientists Use AI to Predict Protein Structure and Function
• Scientists Find a New Way to Help Plants Fight Diseases
• Brookhaven's Top 10 Discoveries of 2024
• Pioneering the Cellular Frontier
• Department of Energy Announces $112.4 Million for Research to Support National Biopreparedness and Response
• Zinc Transporter Has Built-in Self-regulating Sensor
• Structure of 'Oil-Eating' Enzyme Opens Door to Bioengineered Catalysts
• 528th Brookhaven Lecture: Metals, Life, and a Delicate Dance
• Top-10 Areas of Amazing Science at Brookhaven Lab in 2021: Basic research battles COVID-19
• How COVID-19 Wreaks Havoc on Human Lungs
• New Approach for Solving Protein Structures from Tiny Crystals
• Brookhaven Lab to Play Major Role in Two DOE Exascale Computing Application Projects
• 2014's Top-10 Scientific Achievements at Brookhaven Lab: Scientists Reveal Details of Calcium 'Safety-Valve' in Cells.