all Publications

Shan, Z., Rivero-Gamez, A., Lyumkis, D., Horton, N.C. Two-Metal Ion Mechanism of DNA Cleavage by Activated, Filamentous SgrAI. (2024) Journal of Biological Chemistry.:107576 DOI: 10.1016/j.jbc.2024.107576

Dong, X., Sheng, K., Gebert, L.F.R., Aiyer, S., MacRae, I.J., Lyumkis, D., Williamson, J.R. Assembly of the bacterial ribosome with circularly permuted rRNA. (2024) Nucleic Acids Research. DOI: 10.1093/nar/gkae636

Van Veen, D., Galaz-Montoya, J.G., Shen, L., Baldwin, P., Chaudhari, A.S., Lyumkis, D., Schmid, M.F., Chiu, W., Pauly, J. Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. (2024) Int J Mol Sci. 25(10). DOI: 10.3390/ijms25105473

Sheng, K., Dong, X., Aiyer, S., Lee, J., Marquardt, S.D., Lyumkis, D., Williamson, J.R. Domain consolidation in Bacterial 50S assembly revealed by Anti-Sense Oligonucleotide Probing. (2024) bioRxiv. DOI: 10.1101/2024.05.08.593220

Biswas, A., Choudhuri, I., Arnold, E., Lyumkis, D., Haldane, A., Levy, R.M. Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure. (2024) Proceedings of the National Academy of Sciences of the United States of America. 121(15):e2316662121. DOI: 10.1073/pnas.2316662121

Dong, X., Sheng, K., Gebert, L.F.R., Aiyer, S., MacRae , I.J., Lyumkis, D. Assembly of the Bacterial Ribosome with Circularly Permuted rRNA (2024) bioRxiv. DOI: https://doi.org/10.1101/2024.04.10.588894

Van Veen, D., Galaz-Montoya, J.G., Shen, L., Baldwin, P., Chaudhari, A.S., Lyumkis, D., Schmid, M.F., Chiu, W., Pauly, J. Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. (2024) bioRxiv. DOI: 10.1101/2024.04.12.589090

Aiyer, S., Baldwin, P.R., Tan, S.M., Shan, Z., Oh, J., Mehrani, A., Bowman, M.E., Louie, G., Passos, D.O., Đorđević-Marquardt, S., Mietzsch, M., Hull, J.A., Hoshika, S., Barad, B.A., Grotjahn, D.A., McKenna, R., Agbandje-McKenna, M., Benner, S.A., Noel, J.A.P., Wang, D., Tan, Y.Z., Lyumkis, D. Overcoming resolution attenuation during tilted cryo-EM data collection. (2024) Nature Communications. 15(1):389. DOI: 10.1038/s41467-023-44555-7

Sun, Q., Biswas, A., Lyumkis, D., Levy, R., Deng, N. Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization. (2024) Viruses. 16(1). DOI: 10.3390/v16010076

Jing, T., Shan, Z., Dinh, T., Biswas, A., Jang, S., Greenwood, J., Li, M., Zhang, Z., Gray, G., Shin, H.J., Zhou, B., Passos, D., Aiyer, S., Li, Z., Craigie, R., Engelman, A.N., Kvaratskhelia, M., Lyumkis, D. Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding. (2024) bioRxiv. DOI: 10.1101/2024.01.26.577436

Haack, D.B., Rudolfs, B., Zhang, C., Lyumkis, D., Toor, N. Structural basis of branching during RNA splicing. (2023) Nature Structural & Molecular Biology. DOI: 10.1038/s41594-023-01150-0

Oh, J., Shan, Z., Hoshika, S., Xu, J., Chong, J., Benner, S.A., Lyumkis, D., Wang, D. A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase. (2023) Nature Communications. 14(1):8219. DOI: 10.1038/s41467-023-43735-9

Xie, L., Bowman, M.E., Louie, G.V., Zhang, C., Ardejani, M.S., Huang, X., Chu, Q., Donaldson, C.J., Vaughan, J.M., Shan, H., Powers, E.T., Kelly, J.W., Lyumkis, D., Noel, J.P., Saghatelian, A. Biochemistry and Protein Interactions of the CYREN Microprotein. (2023) Biochemistry. DOI: 10.1021/acs.biochem.3c00397

Sheng, K., Li, N., Rabuck-Gibbons, J.N., Dong, X., Lyumkis, D., Williamson, J.R. Assembly landscape for the bacterial large ribosomal subunit. (2023) Nature Communications. 14(1):5220. DOI: 10.1038/s41467-023-40859-w

Li, M., Oliveira Passos, D., Shan, Z., Smith, S.J., Sun, Q., Biswas, A., Choudhuri, I., Strutzenberg, T.S., Haldane, A., Deng, N., Li, Z., Zhao, X.Z., Briganti, L., Kvaratskhelia, M., Burke, T.R., Levy, R.M., Hughes, S.H., Craigie, R., Lyumkis, D. Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants. (2023) Science Advances. 9(29):eadg5953. DOI: 10.1126/sciadv.adg5953

Dong, X., Doerfel, L.K., Sheng, K., Rabuck-Gibbons, J.N., Popova, A.M., Lyumkis, D., Williamson, J.R. Near-physiological in vitro assembly of 50S ribosomes involves parallel pathways. (2023) Nucleic Acids Research. DOI: 10.1093/nar/gkad082

Lyumkis, D., Horton, N.C. The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI. (2022) Biochemical Society Transactions. DOI: 10.1042/BST20220547

Sheng, K., Li, N., Rabuck-Gibbons, J.N., Ding, X., Lyumkis, D., Williamson, J.R. Unsupervised Voxel-based Segmentation reveals a Landscape of Bacterial Ribosome Large Subunit Early Assembly (2022) bioRiv. DOI: https://doi.org/10.1101/2022.11.09.515851

Jóźwik, I.K., Li, W., Zhang, D.W., Wong, D., Grawenhoff, J., Ballandras-Colas, A., Aiyer, S., Cherepanov, P., Engelman, A.N., Lyumkis, D. B-to-A transition in target DNA during retroviral integration. (2022) Nucleic Acids Research. DOI: 10.1093/nar/gkac644

Harrison, J.J.E.K., Oliveira Passos, D., Bruhn, J.F., Bauman, J.D., Tuberty, L., DeStefano, J.J., Xavier Ruiz, F., Lyumkis, D., Arnold, E. Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation (2022) Science Advances. DOI: https://doi.org/10.1126/sciadv.abn9874

Aiyer, S., Strutzenberg, T.S., Bowman, M.E., Noel, J.P., Lyumkis, D. Single-Particle Cryo-EM Data Collection with Stage Tilt using Leginon. (2022) JoVE.(185) DOI: 10.3791/64136

Ballandras-Colas, A., Chivukula, V., Gruszka, D.T., Shan, Z., Singh, P.K., Pye, V.E., McLean, R.K., Bedwell, G.J., Li, W., Nans, A., Cook, N.J., Fadel, H.J., Poeschla, E.M., Griffiths, D.J., Vargas, J., Taylor, I.A., Lyumkis, D., Yardimci, H., Engelman, A.N., Cherepanov, P. Multivalent interactions essential for lentiviral integrase function. (2022) Nature Communications. 13(1):2416. DOI: 10.1038/s41467-022-29928-8

Horton, N., Ghadirian, N., Shan, Z., Lyumkis, D. Mechanism of Activation of SgrAI via Enzyme Filamentation and Mechanism of DNA Sequence Specificity Expansion. (2022) FASEB Journal. 36 Suppl 1:THIS IS ONLY AN ABSTRACT. DOI: 10.1096/fasebj.2022.36.S1.0R839

Rabuck-Gibbons, J.N., Lyumkis, D., Williamson, J.R. Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates. (2022) Structure. DOI: 10.1016/j.str.2021.12.005

Shan, Z., Ghadirian, N., Lyumkis, D., Horton, N.C. Pre-Transition State and Apo Structures of the Filament-Forming Enzyme SgrAI Elucidate Mechanisms of Activation and Substrate Specificity. (2022) Journal of Biological Chemistry.:101760 DOI: 10.1016/j.jbc.2022.101760

Passos, D.O., Li, M., Craigie, R., Lyumkis, D. Book chapter – Retroviral integrase: Structure, mechanism, and inhibition (2021) The Enzymes. 50:249-300. DOI: https://doi.org/10.1016/bs.enz.2021.06.007

Lyumkis, D. Book Chapter: Preferred Orientation. How to recognize and deal with adverse effects. (2021) Single-particle Cryo-EM of Biological Macromolecules. DOI: 10.1088/978-0-7503-3039-8

Smith, S.J., Zhao, X.Z., Passos, D.O., Pye, V.E., Cherepanov, P., Lyumkis, D., Burke, T.R., Hughes, S.H. HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants. (2021) ACS Infect Dis. DOI: 10.1021/acsinfecdis.0c00819

Smith, S.J., Zhao, X.Z., Passos, D.O., Lyumkis, D., Burke, T.R., Hughes, S.H. Integrase Strand Transfer Inhibitors Are Effective Anti-HIV Drugs. (2021) Viruses. 13(2). DOI: 10.3390/v13020205

Aiyer, S., Zhang, C., Baldwin, P.R., Lyumkis, D. Evaluating Local and Directional Resolution of Cryo-EM Density Maps. (2020) Methods in Molecular Biology. 2215:161-187. DOI: 10.1007/978-1-0716-0966-8_8

Jóźwik, I.K., Passos, D.O., Lyumkis, D. Structural Biology of HIV Integrase Strand Transfer Inhibitors. (2020) Trends in Pharmacological Sciences. DOI: 10.1016/j.tips.2020.06.003

Baldwin, P.R., Lyumkis, D. Tools for visualizing and analyzing Fourier space sampling in Cryo-EM. (2020) Progress in Biophysics and Molecular Biology. DOI: 10.1016/j.pbiomolbio.2020.06.003

Brugger, C., Zhang, C., Suhanovsky, M.M., Kim, D.D., Sinclair, A.N., Lyumkis, D., Deaconescu, A.M. Molecular determinants for dsDNA translocation by the transcription-repair coupling and evolvability factor Mfd. (2020) Nature Communications. 11(1):3740. DOI: 10.1038/s41467-020-17457-1

Smith, S.J., Zhao, X.Z., Passos, D.O., Lyumkis, D., Burke, T.R., Hughes, S.H. HIV-1 Integrase Inhibitors that are active against Drug-Resistant Integrase Mutants. (2020) Antimicrobial Agents and Chemotherapy. DOI: 10.1128/AAC.00611-20

Passos, D.O., Li, M., Jóźwik, I.K., Zhao, X.Z., Santos-Martins, D., Yang, R., Smith, S.J., Jeon, Y., Forli, S., Hughes, S.H., Burke, T.R., Craigie, R., Lyumkis, D. Structural basis for strand transfer inhibitor binding to HIV intasomes. (2020) Science. DOI: 10.1126/science.aay8015

Rabuck-Gibbons, J.N., Popova, A.M., Greene, E.M., Cervantes, C.F., Lyumkis, D., Williamson, J.R. SrmB Rescues Trapped Ribosome Assembly Intermediates. (2019) Journal of Molecular Biology. DOI: 10.1016/j.jmb.2019.12.013

Baldwin, P.R., Lyumkis, D. Non-Uniformity of Projection Distributions Attenuates Resolution in Cryo-EM. (2019) Prog. Biophys. Mol. Biol. DOI: 10.1016/j.pbiomolbio.2019.09.002

Polley, S., Lyumkis, D., Horton, N.C. Mechanism of Filamentation-Induced Allosteric Activation of the SgrAI Endonuclease. (2019) Structure. 27(10):1497-1507. DOI: 10.1016/j.str.2019.08.001

Haack, D.B., Yan, X., Zhang, C., Hingey, J., Lyumkis, D., Baker, T.S., Toor, N. Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA. (2019) Cell. 178(3):612-623.e12. DOI: 10.1016/j.cell.2019.06.035

Koneru, P.C., Francis, A.C., Deng, N., Rebensburg, S.V., Hoyte, A.C., Lindenberger, J., Adu-Ampratwum, D., Larue, R.C., Wempe, M.F., Engelman, A.N., Lyumkis, D., Fuchs, J.R., Levy, R.M., Melikyan, G.B., Kvaratskhelia, M. HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. (2019) Elife. 8. DOI: 10.7554/eLife.46344

Lyumkis, D. Challenges and Opportunities in Cryo-EM Single-Particle Analysis. (2019) Journal of Biological Chemistry. DOI: 10.1074/jbc.REV118.005602

Zhang, C., Cantara, W., Jeon, Y., Musier-Forsyth, K., Grigorieff, N., Lyumkis, D. Analysis of discrete local variability and structural covariance in macromolecular assemblies using Cryo-EM and focused classification. (2018) Ultramicroscopy. DOI: 10.1016/j.ultramic.2018.11.016

Tan, Y.Z., Aiyer, S., Mietzsch, M., Hull, J.A., McKenna, R., Grieger, J., Samulski, R.J., Baker, T.S., Agbandje-McKenna, M., Lyumkis, D. Sub-2 Å Ewald curvature corrected structure of an AAV2 capsid variant. (2018) Nature Communications. 9(1):3628. DOI: 10.1038/s41467-018-06076-6

Zhang, C., Konermann, S., Brideau, N.J., Lotfy, P., Wu, X., Novick, S.J., Strutzenberg, T., Griffin, P.R., Hsu, P.D., Lyumkis, D. Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d. (2018) Cell. 175(1):212-223.e17. DOI: 10.1016/j.cell.2018.09.001

Tan, Y.Z., Baldwin, P.R., Davis, J.H., Williamson, J.R., Potter, C.S., Carragher, B., Lyumkis, D. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. (2017) Nature Methods. 14(8):793-796. DOI: 10.1038/nmeth.4347

Ozorowski, G., Pallesen, J., de Val, N., Lyumkis, D., Cottrell, C.A., Torres, J.L., Copps, J., Stanfield, R.L., Cupo, A., Pugach, P., Moore, J.P., Wilson, I.A., Ward, A.B. Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike. (2017) Nature. 547(7663):360-363. DOI: 10.1038/nature23010

Passos, D.O., Li, M., Yang, R., Rebensburg, S.V., Ghirlando, R., Jeon, Y., Shkriabai, N., Kvaratskhelia, M., Craigie, R., Lyumkis, D. Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome. (2017) Science. 355(6320):89-92. DOI: 10.1126/science.aah5163

Davis, J.H., Tan, Y.Z., Carragher, B., Potter, C.S., Lyumkis, D., Williamson, J.R. Modular Assembly of the Bacterial Large Ribosomal Subunit. (2016) Cell. 167(6):1610-1622.e15. DOI: 10.1016/j.cell.2016.11.020

Polley, S., Passos, D.O., Huang, D.B., Mulero, M.C., Mazumder, A., Biswas, T., Verma, I.M., Lyumkis, D., Ghosh, G. Structural Basis for the Activation of IKK1/α. (2016) Cell Reports. 17(8):1907-1914. DOI: 10.1016/j.celrep.2016.10.067

Ballandras-Colas, A., Brown, M., Cook, N.J., Dewdney, T.G., Demeler, B., Cherepanov, P., Lyumkis, D., Engelman, A.N. Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function. (2016) Nature. 530(7590):358-61. DOI: 10.1038/nature16955

Passos, D.O., Lyumkis, D. Single-particle cryoEM analysis at near-atomic resolution from several thousand asymmetric subunits. (2015) Journal of Structural Biology. 192(2):235-44. DOI: 10.1016/j.jsb.2015.10.002

Lee, J.H., de Val, N., Lyumkis, D., Ward, A.B. Model Building and Refinement of a Natively Glycosylated HIV-1 Env Protein by High-Resolution Cryoelectron Microscopy. (2015) Structure. 23(10):1943-51. DOI: 10.1016/j.str.2015.07.020

Lyumkis, D., Oliveira dos Passos, D., Tahara, E.B., Webb, K., Bennett, E.J., Vinterbo, S., Potter, C.S., Carragher, B., Joazeiro, C.A. Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex. (2014) Proceedings of the National Academy of Sciences of the United States of America. 111(45):15981-6. DOI: 10.1073/pnas.1413882111

Sashital, D.G., Greeman, C.A., Lyumkis, D., Potter, C.S., Carragher, B., Williamson, J.R. A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli. (2014) Elife. 3. DOI: 10.7554/eLife.04491

Lyumkis, D., Julien, J.P., de Val, N., Cupo, A., Potter, C.S., Klasse, P.J., Burton, D.R., Sanders, R.W., Moore, J.P., Carragher, B., Wilson, I.A., Ward, A.B. Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. (2013) Science. 342(6165):1484-90. DOI: 10.1126/science.1245627

Julien, J.P., Cupo, A., Sok, D., Stanfield, R.L., Lyumkis, D., Deller, M.C., Klasse, P.J., Burton, D.R., Sanders, R.W., Moore, J.P., Ward, A.B., Wilson, I.A. Crystal structure of a soluble cleaved HIV-1 envelope trimer. (2013) Science. 342(6165):1477-83. DOI: 10.1126/science.1245625

Lyumkis, D., Vinterbo, S., Potter, C.S., Carragher, B. Optimod–an automated approach for constructing and optimizing initial models for single-particle electron microscopy. (2013) Journal of Structural Biology. 184(3):417-26. DOI: 10.1016/j.jsb.2013.10.009

Lyumkis, D., Talley, H., Stewart, A., Shah, S., Park, C.K., Tama, F., Potter, C.S., Carragher, B., Horton, N.C. Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization. (2013) Structure. 21(10):1848-58. DOI: 10.1016/j.str.2013.08.012

Lyumkis, D., Brilot, A.F., Theobald, D.L., Grigorieff, N. Likelihood-based classification of cryo-EM images using FREALIGN. (2013) Journal of Structural Biology. 183(3):377-388. DOI: 10.1016/j.jsb.2013.07.005

Yoshioka, C., Lyumkis, D., Carragher, B., Potter, C.S. Maskiton: Interactive, web-based classification of single-particle electron microscopy images. (2013) Journal of Structural Biology. 182(2):155-63. DOI: 10.1016/j.jsb.2013.02.007

Lyumkis, D., Doamekpor, S.K., Bengtson, M.H., Lee, J.W., Toro, T.B., Petroski, M.D., Lima, C.D., Potter, C.S., Carragher, B., Joazeiro, C.A. Single-particle EM reveals extensive conformational variability of the Ltn1 E3 ligase. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(5):1702-7. DOI: 10.1073/pnas.1210041110

Campbell, M.G., Cheng, A., Brilot, A.F., Moeller, A., Lyumkis, D., Veesler, D., Pan, J., Harrison, S.C., Potter, C.S., Carragher, B., Grigorieff, N. Movies of ice-embedded particles enhance resolution in electron cryo-microscopy. (2012) Structure. 20(11):1823-8. DOI: 10.1016/j.str.2012.08.026

Milazzo, A.C., Cheng, A., Moeller, A., Lyumkis, D., Jacovetty, E., Polukas, J., Ellisman, M.H., Xuong, N.H., Carragher, B., Potter, C.S. Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy. (2011) Journal of Structural Biology. 176(3):404-8. DOI: 10.1016/j.jsb.2011.09.002

Voss, N.R., Lyumkis, D., Cheng, A., Lau, P.W., Mulder, A., Lander, G.C., Brignole, E.J., Fellmann, D., Irving, C., Jacovetty, E.L., Leung, A., Pulokas, J., Quispe, J.D., Winkler, H., Yoshioka, C., Carragher, B., Potter, C.S. A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy. (2010) Journal of Structural Biology. 169(3):389-98. DOI: 10.1016/j.jsb.2009.12.005

Lyumkis, D., Moeller, A., Cheng, A., Herold, A., Hou, E., Irving, C., Jacovetty, E.L., Lau, P.W., Mulder, A.M., Pulokas, J., Quispe, J.D., Voss, N.R., Potter, C.S., Carragher, B. Automation in single-particle electron microscopy connecting the pieces. (2010) Meth. Enzymol. 483:291-338. DOI: 10.1016/S0076-6879(10)83015-0

Lander, G.C., Stagg, S.M., Voss, N.R., Cheng, A., Fellmann, D., Pulokas, J., Yoshioka, C., Irving, C., Mulder, A., Lau, P.W., Lyumkis, D., Potter, C.S., Carragher, B. Appion: an integrated, database-driven pipeline to facilitate EM image processing. (2009) Journal of Structural Biology. 166(1):95-102. DOI: 10.1016/j.jsb.2009.01.002