Publications

Acknowledgements


Acknowledging QCB Support in Publications
All papers supported in full or in part by the QCB should acknowledge QCB funding in the Acknowledgements section as follows: “This work was supported by NSF grant 2243257, the National Science Foundation Science and Technology Center for Quantitative Cell Biology.”

Center Publications

2024

Qinyu Hao, Minxue Liu, Swapna Vidhur Daulatabad, Saba Gaffari, You Jin Song, Rajneesh Srivastava, Shivang Bhaskar, Anurupa Moitra, Hazel Mangan, Elizabeth Tseng, Rachel B Gilmore, Susan M Frier, Xin Chen, Chengliang Wang, Sui Huang, Stormy Chamberlain, Hong Jin, Jonas Korlach, Brian McStay, Saurabh Sinha, Sarath Chandra Janga, Supriya G Prasanth, Kannanganattu V Prasanth (2024) Monoallelically expressed noncoding RNAs form nucleolar territories on NOR-containing chromosomes and regulate rRNA expression eLife 13:e80684 https://doi.org/10.7554/eLife.80684

 

2023

Ghaemi, Z., Nafiu, O., Tajkhorshid, E. Gruebele, M. and Hu, Jianming. A computational spatial whole-Cell model for hepatitis B viral infection and drug interactions. Sci Rep 13, 21392 (2023). https://doi.org/10.1038/s41598-023-45998-0

Pre-Center Publications


Director Zaida Luthey-Schulten

  • Benjamin R. Gilbert , Zane R. Thornburg, Troy A. Brier, Jan A. Stevens, Fabian Grünewald, John E. Stone, Siewert J. Marrink. and Zaida Luthey-Schulten, (2023) “Dynamics of Chromosome Organization in a Minimal Bacterial Cell”, Frontiers in Cell and Developmental Biology, https://doi.org/10.3389/fcell.2023.1214962
  • JA Stevens, F Grünewald, PA van Tilburg, M König, BR Gilbert, TA Brier, Z. R. Thornburg, Z. Luthey-Schulten, S.J. Marrink “Molecular Dynamics Simulations of an Entire Cell”, Frontiers in Chemistry, Doi: 10.3389/fchem.2023.1106495.
  • Luthey-Schulten, Z. Thornburg, Z., Gilbert, B. (2022) “Integrating cellular and molecular structures and dynamics into whole cell models” Current Opinion Structural Biology, https://doi.org/10.1016/j.sbi.2022.102392
  • Thornburg, Z., Bianchi, D., Brier, T. Gilbert, B., Earnest, T., Melo, M, Safronova, N., Saenz, J., Cook, A. Wise, K. Hutchinson, C., Smith, H., Glass, J. Luthey-Schulten, Z. (2022), “Fundamental Behaviors Emerge from Simulations of a Living Minimal Cell”. Cell, doi:10.1016/j.cell.2021.12.025.
  • Luthey-Schulten, Zaida (2021). Integrating experiments, theory, and simulations into whole cell models. Nature Methods, https://doi.org/10.1038/s41592-021-01150-2.
  • Gilbert, B,. Thornburg, Z., Lam, V., Rashid, F., Glass J., Villa, E., Dame, R., Luthey-Schulten, Z. (2021). Generating chromosome geometries in a minimal cell from cryo-electron tomograms and chromosome conformation capture maps. Frontiers in Molecular Biosciences doi: 10.3389/fmolb.2021.644133.
  • Singharoy, A., Maffeo, C., Delgado-Magnero, K. H., Swainsbury, D. J. K., Sener, M., Kleinekathofer, U., Vant, J.W., Nguyen, J., Hitchcock, A., Isralewitz, B., Teo, I., Chandler, D.E., Stone, J.E., Phillips, J.C., Pogorelov, T.V., Mallus, M., Chipot, C., Luthey-Schulten, Z., Tieleman, D.P., Hunter, C. N., Tajkhorshid, E., Aksimentiev, A., Schulten, K. (2019). Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism. Cell, 179(5), 1098–1111. https://doi.org/10.1016/j.cell.2019.10.021
  • Breuer, M., Earnest, T. M., Merryman, C., Wise, K. S., Sun, L., Lynott, M. R., Hutchison, C.A., Smith, H.O., Lapek, J.D., Gonzalez, D.J., Crecy-Lagard, V., Haas, D., Hanson, A.D., Labhsetwar, P., Glass, J.I., Luthey-Schulten, Z. (2019). Essential Metabolism for a Minimal Cell. ELife. https://doi.org/10.7554/eLife.36842.001
  • Earnest, T. M., Watanabe, R., Stone, J. E., Mahamid, J., Baumeister, W., Villa, E., & Luthey-Schulten, Z. (2017). Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations. J. Phys. Chem. B, 121(15), 3871-3881. https://doi.org/10.1021/acs.jpcb.7b00672
  • Hallock, M. J., Stone, J. E., Roberts, E., Fry, C., & Luthey-Schulten, Z. (2014). Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations. ParallelComputing, 40(5-6), 86-99. https://doi.org/10.1016/j.parco.2014.03.009

Associate Director Martin Gruebele

  • Z. Ghaemi, M.Gruebele, E.Tajkhorshid, “Molecular Mechanism of Capsid Disassembly in Hepatitis B Virus,” Proc. Nat. Acad Sci. USA 118, e2102530118 (2021).
  • Z. Ghaemi, J. R. Peterson, M.Gruebele, and Z. Luthey-Schulten, "An In-Silico Human Cell Platform For Spatio-Temporal Modeling," PLoS Comput. Biol. 16, e1007717 (2020).
  • P. Tripathi, B. Mehrafrooz, A.Aksimentiev, S. E. Jackson, M.Gruebele, and M. Wanunu, “An inverted region in the translocation kinetics of a knotted protein,” J. Phys. Chem. Lett., submitted (2023).
  • M. Boob, M. Gruebele, and T. Pogorelov “TMAO: protecting proteins from feeling the heat,” Biophys. J. 122, 1414-1422 (2023).
  • I. Srivastava,. B. Lew, Y. Wang,. J. Ludwig, S. Bangru, S. Pandit, Z. Wang, S. Blair, M. Gruebele, S. Nie, V. Gruev, “Cell-Membrane Coated Nanoparticles for Tumor Delineation and Qualitative Estimation of Cancer Biomarkers at Single Wavelength Excitation in Murine and Phantom Models,” ACS Nano 8465-8482 (2023).
  • P. Tripathi, A. Firouzbakht, M. Gruebele, and M. Wanunu, “Direct observation of single-protein transition state passage during translocation through a nanopore,” J. Phys. Chem. Lett. 13, 5918-5924 (2022).
  • G. Gopan, Z. Ghaemi, C. Davis and M. Gruebele, “Spliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM,” Nucl. Acids Res. 50, 8193–8206 (2022).
  • P. Tripathi, A. Firouzbakht, M. Gruebele, and M. Wanunu, “Threading Proteins at the Speed Limit of Folding,” Proc. Nat. Acad Sci. USA 119, e2202779119 (2022).
  • M. Rickard, H. Luo, A. De Lio, M. Gruebele and T. Pogorelov, “Impact of the cellular environment on ATP conformations,” J. Phys. Chem. Lett.13, 9809-9814 (2022).

Team Leader Rohit Bhargava

    • Hsieh, P.-H., Phal, Y., Prasanth, K.V., Bhargava, R. Cell Phase Identification in a Three-Dimensional Engineered Tumor Model by Infrared Spectroscopic Imaging (2023) Analytical Chemistry, 95 (6), pp. 3349-3357. DOI: 10.1021/acs.analchem.2c04554
    • Kenkel, S., Gryka, M., Chen, L., Confer, M.P., Rao, A., Robinson, S., Prasanth, K.V., Bhargava, R. Chemical imaging of cellular ultrastructure by null-deflection infrared spectroscopic measurements (2022) Proceedings of the National Academy of Sciences of the United States of America, 119 (47), art. no. e2210516119, . DOI: 10.1073/pnas.2210516119
    • Falahkheirkhah, K., Yeh, K., Mittal, S., Pfister, L., Bhargava, R. Deep learning-based protocols to enhance infrared imaging systems (2021) Chemometrics and Intelligent Laboratory Systems, 217, art. no. 104390, . DOI: 10.1016/j.chemolab.2021.104390
    • Phal, Y., Yeh, K., Bhargava, R. Concurrent vibrational circular dichroism measurements with infrared spectroscopic imaging (2021) Analytical Chemistry, 93 (3), pp. 1294-1303. https://www.scopus.com/inward/record.uri?eid=2-s2.0- DOI: 10.1021/acs.analchem.0c00323
    • Kenkel, S., Mittal, S., Bhargava, R. Closed-loop atomic force microscopy-infrared spectroscopic imaging for nanoscale molecular characterization (2020) Nature Communications, 11 (1), art. no. 3225, . DOI: 10.1038/s41467-020-17043-5

    Team Leader Angad Mehta

    • Cournoyer JE, Altman SD, Gao YL, Wallace CL, Zhang D, Lo GH, Haskin NT, Mehta AP. Engineering artificial photosynthetic life-forms through endosymbiosis. Nat Commun. 2022 Apr 26;13(1):2254. doi: 10.1038/s41467-022-29961-7. PMID: 35474066; PMCID: PMC9042829.
    • Ornelas MY, Thomas AY, Johnson Rosas LI, Scoville RO, Mehta AP. Synthetic Platforms for Characterizing and Targeting of SARS-CoV-2 Genome Capping Enzymes. ACS Synth Biol. 2022 Nov 18;11(11):3759-3771. doi: 10.1021/acssynbio.2c00359. Epub 2022 Nov 4. PMID: 36331143; PMCID: PMC9662071.
    • Ornelas MY, Thomas AY, Johnson Rosas LI, Medina GN, Mehta AP. Characterization, Directed Evolution, and Targeting of DNA Virus-Encoded RNA Capping Enzymes Using Phenotypic Yeast Platforms. ACS Chem Biol. 2023 Aug 18;18(8):1808-1820. doi: 10.1021/acschembio.3c00243. Epub 2023 Jul 27. PMID: 37498174.

    Team Leader Emad Tajkhorshid

    • S. Dehghani-Ghahnaviyeh, Z. Zhao, E. Tajkhorshid (2022) Lipid-mediated organization of prestin in the outer hair cell membrane and its implications in sound amplification. Nature Communications, 13:6877.
    • K. Kapoor*, T. Chen*, and E. Tajkhorshid (2022) Post-Translational Modifications Optimize the Ability of SARS-CoV-2 Spike for Effective Interaction with Host Cell Receptors. PNAS, 119: e2119761119.
    • J. Vermaas, C. Mayne, E. Shinn, and E. Tajkhorshid (2022) Assembly and Analysis of Cell-Scale Membrane Envelopes. J. Chem. Inf. Modeling, 62, 602–617. (cover article)
    • I. Singaram, A. Sharma, S. Pant, M. Lihan, M.-J. Park, P. Buwaneka, Y. Hu, N. Mahmud, Y.-M. Kim, V. Gevorgyan, I. Khan, E. Tajkhorshid, and W. Cho (2023) Targeting lipid-protein interaction for drug development: Development of a novel resistance-proof Syk inhibitor for acute myeloid leukemia. Nat. Chem. Biol., 19: 239–250.
    • D. Yang, Z. Zhao, E. Tajkhorshid, and E. Gouaux (2023) Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants. PNAS, 120 (29), e2304602120.
    • H. Jeong, S. Clark, A. Goehring, S. Dehghani-Ghahnaviyeh, A. Rasouli, E. Tajkhorshid, and E. Gouaux (2022) Structure of C. elegans TMC-1 complex illuminates auditory mechanosensory transduction. Nature, 610: 796–803.
    • A. K. Vasan*, N. Haloi*, R. J. Ulrich, M. E. Metcalf, P. C. Wen, W. W. Metcalf, P. J. Hergenrother, D. Shukla, and E. Tajkhorshid (2022) Role of internal loop dynamics in antibiotic permeability of outer membrane porins. PNAS, 119 (8), e2117009119.
    • R. Dastvan, A. Rasouli*, S. Dehghani-Ghahnaviyeh*, S. Gies, and E. Tajkhorshid (2022) Proton-driven alternating access in a spinster transporter, an emerging family of broad-specificity efflux pumps. Nature Communications, 13: 5161.

Aleksei Aksimentiev

  • Xin Shi, Anna-Katharina Pumm, Christopher Maffeo, Fabian Kohler, Wenxuan Zhao, Daniel Verschueren, Aleksei Aksimentiev, Hendrik Dietz, Cees Dekker. ­A nanopore-powered DNA turbine. Nature Nanotechnology, Accepted (2023).
  • Luning Yu, Xinqi Kang, Fanjun Li, Behzad Mehrafrooz, Amr Makhamreh, Ali Fallahi, Aleksei Aksimentiev, Min Chen, Meni Wanunu. Unidirectional Single-File Transport of Full-Length Proteins Through a Nanopore. Nature Biotechnology 41: 1130–1139 (2023). Cover.
  • Kaikai Chen, Adnan Choudhary, Sarah Sandler, Christopher Maffeo, Caterina Ducati, Aleksei Aksimentiev, Ulrich F. Keyser Super-resolution detection of DNA nanostructures using a nanopore. Advanced Materials 35: 2207434 (2023).
  • Christopher Maffeo, Lauren Quednau, James Wilson, Aleksei Aksimentiev. DNA double helix, a tiny electromotor. Nature Nanotechnology 18: 238–242 (2023).
  • David Winogradoff, Han-YiChou, Christopher Maffeo, Aleksei Aksimentiev. Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex. Nature Communications 13:5138 (2022).
  • Henry Brinkerhoff, Albert S. W. Kang, Jingqian Liu, Aleksei Aksimentiev, Cees Dekker. Multiple re-reads of single proteins at single-amino-acid resolution using nanopores. Science 374, 1509-1513 (2021).
  • Jejoong Yoo, Sangwoo Park, Christopher Maffeo, Taekjip Ha, and Aleksei Aksimentiev. DNA Sequence and Methylation Prescribe the Inside-Out Conformational Dynamics and Bending Energetics of DNA Minicircles. Nucleic Acids Research 49, 11459–11475 (2021).

Mark Anastasio

  • C. Xi, M. E. Kandel, S. He, C. Hu, Y. J. Lee, K. Sullivan, G. Tracey, H.J. Chung, H.J. Kong,M. A. Anastasio, and G. Popescu.Artificial confocal microscopy for deep label-free imaging. Nature Photonics, 2023: 1-9.
  • R. Deshpande, A. Avachat, F. J. Brooks, and M.A. Anastasio. Investigating the robustness of a deep learning-based method for quantitative phase retrieval from propagation-based x-ray phase contrast measurements under laboratory conditions. Physics in Medicine & Biology, 2023, 68, no. 8: 085005.
  • Kelkar VA, Gotsis DS, Brooks FJ, KC P, Myers KJ, Zeng R, Anastasio M.A. Assessing the ability of generative adversarial networks to learn canonical medical image statistics. IEEE Transactions on Medical Imaging, In Press, 2023.
  • C. Hu, S. He, Y.J. Lee, Y. He, E.M. Kong, H. Li, M.A. Anastasio, G. Popescu G: Live-dead assay on unlabeled cells using phase imaging with computational specificity.Nature Communications. 2022 Feb 7;13(1):1-8.

Yann Chemla

  • Carney S.P., Ma W., Whitley K.D., Jia H., Lohman T.M., Luthey-Schulten Z., Chemla Y.R. (2021) "Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase." Nat Commun. 12(1):7015. doi: 10.1038/s41467-021-27304-6.
  • Rhine K., Makurath M.A., Liu J., Skanchy S., Lopez C., Catalan K.F., Ma Y., Fare C.M., Shorter J., Ha T., Chemla Y.R., Myong S. (2020) "ALS/FTLD-Linked Mutations in FUS Glycine Residues Cause Accelerated Gelation and Reduced Interactions with Wild-Type FUS." Mol Cell. 80(4):666-681.e8.
  • Ma W., Whitley K.D., Chemla Y.R., Luthey-Schulten Z., Schulten K. (2018) "Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase." Elife. pii: e34186.
  • Comstock M.J., Whitley K.D., Jia H., Sokoloski J., Lohman T.M., Ha T., Chemla Y.R. (2015) "Direct observation of structure-function relationship in a nucleic acid-processing enzyme" Science 348(6232):352-354.
  • Arslan S., Khafizov R., Thomas C.D., Chemla Y.R., Ha T. (2015) "Engineering of a superhelicase through conformational control" Science 348(6232):344-347.

Taekjip Ha

  • Y. Liu, R. S. Zou, S. He, Y. Nihongaki, X. Li, S. Razavi, B. Wu and T. Ha, “Very fast CRISPR on demand”, Science 368, 1265–1269 (2020).
  • Y. Wang, W.T. Cottle, H. Wang, X.A. Feng, J. Mallon, M. Gavrilov, S. Bailey and T. Ha, “Genome Oligopaint via Local Denaturing Fluorescence In situ Hybridization”, Molecular Cell 81:1566-1577 (2021).
  • A. Basu, D. Bobrovnikov, B. Cieza, J. P. Arcon, Z. Qureshi, M. Orozco and T. Ha, “Deciphering the mechanical code of the genome and epigenome” Nature Struct. Mol. Bio. 29, 1178-1187 (2022).
  • R. S. Zou, A. Marin-Gonzalez, Y. Liu, H. B. Liu, L. Shen, R. Dveirin, J.X.J. Luo, R. Kalhor and T. Ha, “Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites” Nature Cell Biology 24, 1433-1444 (2022).
  • A. Basu, D.G. Bobrovnikov, Z. Qureshi, T. Kayikcioglu, T.T.M. Ngo, A. Ranjan, S. Eustermann, B. Cieza, M.T. Morgan, M. Hejna, H.T. Rube, K.P. Hopfner, C. Wolberger, J.S. Song and T. Ha, “Measuring DNA mechanics on the genome scale” Nature 589, 462-467 (2021).

Erik Lindahl

  • Lundborg M, Narangifard A, Wennberg CL, Lindahl E, Daneholt B, Norlén L. (2018) Human skin barrier structure and function analysed by cryo-EM and molecular dynamics simulation. J. Struct. Biol. 203(2), 149-161
  • Zhuang Y, Noviello CM, Hibbs RE, Howard RJ, Lindahl E (2022) Differential interactions of resting, activated, and desensitized states of α7 nicotinic acetylcholine receptor with lipidic modulators. Proc. Natl. Acad. Sci. USA. 119(43), e2208081119
  • Lycksell M, Rovšnik U, Bergh C, Johansen NT, Martel A, Porcar L, Arleth L, Howard RJ, Lindahl E (2021). Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering. Proc. Natl. Acad. Sci. USA 118 (37), e2108006118
  • Cowgill J, Fan C, Haloi N, Tobiasson V, Zhuang Y, Howard RJ, Lindahl E (2023). Structure and dynamics of differential ligand binding in the human ρ-type GABA(A) receptor. Neuron 111, 1-15. https://doi.org/10.1016/j.neuron.2023.08.006
  • Bergh C, Rovsnik U, Howard RJ. Lindahl E. (2023) Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM. eLife, in press.

Julia Mahamid

  • de Teresa-Trueba I, Goetz SK, Mattausch A, Stojanovska F, Zimmerli C, Toro-Nahuelpan M, Cheng DWC, Tollervey F, Pape C, Beck B, Kreshuk A, Mahamid J, Zaugg J (2023). Convolutional networks for supervised mining of molecular patterns within cellular context. Nature Methods 20, 284–294.
  • Zhang X, Sridharan S, Zagoriy I, Eugster Oegema C, Ching C, Pflaesterer T, Fung KHH, Poser I, Müller C, Hyman AA, Savitski M, Mahamid J (2022). Molecular mechanisms of stress-induced reactivation in mumps virus condensates. Cell 186, 1877-1894.
  • D’Imprima E, Garcia Montero M, Gawrzak S, Ronchi P, Zagoriy I, Schwab Y, Jechlinger M, Mahamid J (2023). Light and electron microscopy continuum resolution imaging of 3D cell cultures.Developmental Cell 58, 616-632.
  • Xue L, Lenz S, Zimmermann-Kogadeeva M, Tegunov D, Cramer P, Bork P, Rappsilber J, Mahamid J (2022). Visualizing translation dynamics at atomic detail in a bacterial cell. Nature 610: 05–211.
  • Bose M, Mahamid J, Ephrussi A (2022). Liquid-to-solid phase transition of oskar RNP granules is essential for their function in the Drosophila germline. Cell 185(8):1308-1324.
  • Klumpe S, Fung HKH, Goetz SK, Zagoriy I, Hampoelz B, Zhang X, Erdmann PS, Baumbach J, Müller CW, Beck M, Plitzko JM, Mahamid J (2021). A Modular Platform for Automated Cryo-FIB Workflows.eLife 2021;10:e70506.

Siewert-Jan Marrink

  • B.R. Gilbert, Z.R. Thornburg, T.A. Brier, J.A. Stevens, F. Grunewald, J.E. Stone, S.J. Marrink, Z.A. Luthey-Schulten. Dynamics of Chromosome Organization in a Minimal Bacterial Cell. Front. Cell Dev. Biol., 2023, online. doi:10.3389/fcell.2023.1214962
  • J.A. Stevens, F. Grünewald, P.A.M. van Tilburg, M. König, B.R. Gilbert, T.A. Brier, Z.R. Thornburg, Z. Luthey-Schulten, S.J. Marrink. Molecular dynamics simulation of an entire cell. Frontiers in Chemistry 11, 2023. doi:10.3389/fchem.2023.1106495
  • W. Pezeshkian, F. Grünewald, O. Narykov, S. Lu, T.A. Wassenaar, S.J. Marrink, D. Korkin. Molecular architecture of SARS-CoV-2 envelope by integrative modeling. Structure 31 (4), 492-503, 2023. doi:10.1016/j.str.2023.02.006

Paola Mera

  • Erlandson, A., Gade, P., Menikpurage, I.P., Kim, C.Y. and Mera, P.E.(2022) The UvrA-like protein Ecm16 requires ATPase activity to render resistance against echinomycin.Mol Microbiol, 117, 1434-1446. https://www.ncbi.nlm.nih.gov/pubmed/35534931
  • Gade, P., Erlandson, A., Ullah, A., Chen, X., Mathews, II, Mera, P.E. and Kim, C.Y. (2023) Structural and functional analyses of the echinomycin resistance conferring protein Ecm16 fromStreptomyces lasalocidi.Sci Rep, 13, 7980.https://www.ncbi.nlm.nih.gov/pubmed/37198233
  • Menikpurage, I.P., Puentes-Rodriguez, S.G., Elaksher, R.A. and Mera, P.E.(2023) ParA's Impact beyond Chromosome Segregation in Caulobacter crescentus. J Bacteriol, 205, e0029622.https://www.ncbi.nlm.nih.gov/pubmed/36692299
  • Puentes-Rodriguez, S.G., Norcross, J.D. and Mera, P.E.(2023) To let go or not to let go: how ParA can impact the release of the chromosomal anchoring in Caulobacter crescentus. bioRxiv. https://www.ncbi.nlm.nih.gov/pubmed/37090538 (under revision)

Paul Selvin

  • Shukla, S., Troitskaia, A., Swarna, N., Maity, B.K., Tjioe, M., Bookwalter, C.S., Trybus, K.M., Chemla, Y.R., and Selvin, P.R. (2022). High-throughput force measurement of individual kinesin-1 motors during multi-motor transport. Nanoscale14, 12463–12475. 10.1039/d2nr01701f.