Publications

@article{Mohamed_2025,
  added-at = {2025-02-26T15:21:20.000+0100},
  author = {Mohamed, Abdallah A. and Wang, Peter Y. and Bartel, David P. and Vos, Seychelle M.},
  biburl = {https://www.bibsonomy.org/bibtex/298e273ff585b765fbcd28d0b7524108b/cryoem_staff},
  doi = {10.1016/j.celrep.2024.115166},
  interhash = {98198799324ef06c69db39940954e703},
  intrahash = {98e273ff585b765fbcd28d0b7524108b},
  issn = {2211-1247},
  journal = {Cell Reports},
  keywords = {2025},
  month = jan,
  number = 1,
  pages = 115166,
  publisher = {Elsevier BV},
  timestamp = {2025-02-26T15:21:20.000+0100},
  title = {The structural basis for RNA slicing by human Argonaute2},
  url = {http://dx.doi.org/10.1016/j.celrep.2024.115166},
  volume = 44,
  year = 2025
}

@article{Zilberzwige_Tal_2025,
  added-at = {2025-02-26T15:17:54.000+0100},
  author = {Zilberzwige-Tal, Shai and Altae-Tran, Han and Kannan, Soumya and Wilkinson, Max E. and Vo, Samuel Chau-Duy-Tam and Strebinger, Daniel and Edmonds, KeHuan K. and Yao, Chun-Chen Jerry and Mears, Kepler S. and Shmakov, Sergey A. and Makarova, Kira S. and Macrae, Rhiannon K. and Koonin, Eugene V. and Zhang, Feng},
  biburl = {https://www.bibsonomy.org/bibtex/2a3212336403f367b9c47bc5a4abbacbb/cryoem_staff},
  doi = {10.1016/j.cell.2025.01.034},
  interhash = {87a989748cb2f9b344df9ac941d1a1b7},
  intrahash = {a3212336403f367b9c47bc5a4abbacbb},
  issn = {0092-8674},
  journal = {Cell},
  keywords = {2025},
  month = feb,
  publisher = {Elsevier BV},
  timestamp = {2025-02-26T15:17:54.000+0100},
  title = {Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins},
  url = {http://dx.doi.org/10.1016/j.cell.2025.01.034},
  year = 2025
}

@article{ghanbarpour2024proteolytic,
  added-at = {2025-02-26T20:31:32.000+0100},
  author = {Ghanbarpour, Alireza and Sauer, Robert T and Davis, Joseph H},
  biburl = {https://www.bibsonomy.org/bibtex/2faffd585b922b230c3924103e0d06213/cryoem_staff},
  doi = {10.1038/s41467-024-53681-9},
  interhash = {de54fad77e8a055558821ff5f0644bd7},
  intrahash = {faffd585b922b230c3924103e0d06213},
  journal = {Nature Communications},
  keywords = {2024},
  month = {November},
  number = 9681,
  timestamp = {2025-02-26T20:31:32.000+0100},
  title = {A proteolytic AAA+ machine poised to unfold protein substrates},
  volume = 15,
  year = 2024
}

@article{westmoreland2024resolution,
  added-at = {2024-11-04T22:31:04.000+0100},
  author = {Westmoreland, Dana E. and Feliciano, Patricia R. and Kang, Gyunghoon and Cui, Chang and Kim, Albert and Stubbe, JoAnne and Nocera, Daniel G. and Drennan, Catherine L.},
  biburl = {https://www.bibsonomy.org/bibtex/22aeccb9c27411da0cbd913d00030b5ef/cryoem_staff},
  doi = {10.1073/pnas.241715712},
  interhash = {817e16bcc0ea9acff727a68da5135532},
  intrahash = {2aeccb9c27411da0cbd913d00030b5ef},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  keywords = {2024},
  number = 45,
  timestamp = {2024-11-04T22:31:04.000+0100},
  title = {2.6-Å resolution cryo-EM structure of a class Ia ribonucleotide reductase trapped with mechanism-based inhibitor N3CDP},
  volume = 121,
  year = 2024
}

@article{duan2024alzheimers,
  added-at = {2024-11-04T22:15:14.000+0100},
  author = {Duan, Pu and Dregni, Aurelio J and Xu, Hong and Changolkar, Lakshmi and Lee, Virginia M-Y and Lee, Edward B and Hong, Mei},
  biburl = {https://www.bibsonomy.org/bibtex/242134189ddae47901d237a35a4185cb2/cryoem_staff},
  doi = {10.1016/j.jbc.2024.107730},
  interhash = {980bc0e09bfc05a7f8cd63d3d38de4c1},
  intrahash = {42134189ddae47901d237a35a4185cb2},
  journal = {Journal of Biological Chemistry},
  keywords = {2024},
  number = 9,
  timestamp = {2024-11-04T22:15:14.000+0100},
  title = {Alzheimer’s disease seeded tau forms paired helical filaments yet lacks seeding potential},
  volume = 300,
  year = 2024
}

@article{wilkinson2024phagetriggered,
  added-at = {2024-10-22T18:53:39.000+0200},
  author = {Wilkinson, Max E. and Li, David and Gao, Alex and Macrae, Rhiannon K. and Zhang, Feng},
  biburl = {https://www.bibsonomy.org/bibtex/2602d9887d0822313289e334c84232d2c/cryoem_staff},
  doi = {10.1126/science.adq3977},
  interhash = {8f0ffc15acc06f3d7649f94b4546bb19},
  intrahash = {602d9887d0822313289e334c84232d2c},
  journal = {Science},
  keywords = {2024},
  month = aug,
  number = 6717,
  timestamp = {2024-10-22T18:53:39.000+0200},
  title = {Phage-triggered reverse transcription assembles a toxic repetitive gene from a noncoding RNA},
  volume = 386,
  year = 2024
}

@article{biester2024capturing,
  added-at = {2024-10-22T18:51:06.000+0200},
  author = {Biester, Alison and Grahame, David A. and Drennan, Catherine L.},
  biburl = {https://www.bibsonomy.org/bibtex/24821fff8ecc45cb021de70bf0e180e1a/cryoem_staff},
  doi = {https://doi.org/10.1073/pnas.2410995121},
  interhash = {56fefe4005b67c4fb675e2b377790396},
  intrahash = {4821fff8ecc45cb021de70bf0e180e1a},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  keywords = {2024},
  month = oct,
  number = 41,
  timestamp = {2024-10-22T18:51:06.000+0200},
  title = {Capturing a methanogenic carbon monoxide dehydrogenase/acetyl-CoA synthase complex via cryogenic electron microscopy},
  volume = 121,
  year = 2024
}

@article{Wasilko2024,
  abstract = {The CC chemokine receptor 6 (CCR6) is a potential target for chronic inflammatory diseases. Previously, we reported an active CCR6 structure in complex with its cognate chemokine CCL20, revealing the molecular basis of CCR6 activation. Here, we present two inactive CCR6 structures in ternary complexes with different allosteric antagonists, CCR6/SQA1/OXM1 and CCR6/SQA1/OXM2. The oxomorpholine analogues, OXM1 and OXM2 are highly selective CCR6 antagonists which bind to an extracellular pocket and disrupt the receptor activation network. An energetically favoured U-shaped conformation in solution that resembles the bound form is observed for the active analogues. SQA1 is a squaramide derivative with close-in analogues reported as antagonists of chemokine receptors including CCR6. SQA1 binds to an intracellular pocket which overlaps with the G protein site, stabilizing a closed pocket that is a hallmark of inactive GPCRs. Minimal communication between the two allosteric pockets is observed, in contrast to the prevalent allosteric cooperativity model of GPCRs. This work highlights the versatility of GPCR antagonism by small molecules, complementing previous knowledge of CCR6 activation, and sheds light on drug discovery targeting CCR6.},
  added-at = {2024-09-23T16:26:35.000+0200},
  author = {Wasilko, David Jonathan and Gerstenberger, Brian S. and Farley, Kathleen A. and Li, Wei and Alley, Jennifer and Schnute, Mark E. and Unwalla, Ray J. and Victorino, Jorge and Crouse, Kimberly K. and Ding, Ru and Sahasrabudhe, Parag V. and Vincent, Fabien and Frisbie, Richard K. and Dermenci, Alpay and Flick, Andrew and Choi, Chulho and Chinigo, Gary and Mousseau, James J. and Trujillo, John I. and Nuhant, Philippe and Mondal, Prolay and Lombardo, Vincent and Lamb, Daniel and Hogan, Barbara J. and Minhas, Gurdeep Singh and Segala, Elena and Oswald, Christine and Windsor, Ian W. and Han, Seungil and Rappas, Mathieu and Cooke, Robert M. and Calabrese, Matthew F. and Berstein, Gabriel and Thorarensen, Atli and Wu, Huixian},
  biburl = {https://www.bibsonomy.org/bibtex/28c6bcc5568d55a117324fa95f8af4c04/cryoem_staff},
  day = 31,
  doi = {10.1038/s41467-024-52045-7},
  interhash = {7ea6f94c9bb8194e23b3933d27988879},
  intrahash = {8c6bcc5568d55a117324fa95f8af4c04},
  issn = {2041-1723},
  journal = {Nature Communications},
  keywords = {2024},
  month = aug,
  number = 1,
  pages = 7574,
  timestamp = {2024-09-23T16:26:35.000+0200},
  title = {Structural basis for CCR6 modulation by allosteric antagonists},
  url = {https://doi.org/10.1038/s41467-024-52045-7},
  volume = 15,
  year = 2024
}

The CC chemokine receptor 6 (CCR6) is a potential target for chronic inflammatory diseases. Previously, we reported an active CCR6 structure in complex with its cognate chemokine CCL20, revealing the molecular basis of CCR6 activation. Here, we present two inactive CCR6 structures in ternary complexes with different allosteric antagonists, CCR6/SQA1/OXM1 and CCR6/SQA1/OXM2. The oxomorpholine analogues, OXM1 and OXM2 are highly selective CCR6 antagonists which bind to an extracellular pocket and disrupt the receptor activation network. An energetically favoured U-shaped conformation in solution that resembles the bound form is observed for the active analogues. SQA1 is a squaramide derivative with close-in analogues reported as antagonists of chemokine receptors including CCR6. SQA1 binds to an intracellular pocket which overlaps with the G protein site, stabilizing a closed pocket that is a hallmark of inactive GPCRs. Minimal communication between the two allosteric pockets is observed, in contrast to the prevalent allosteric cooperativity model of GPCRs. This work highlights the versatility of GPCR antagonism by small molecules, complementing previous knowledge of CCR6 activation, and sheds light on drug discovery targeting CCR6.

@article{Birkholz2024,
  abstract = {In all organisms, regulation of gene expression must be adjusted to meet cellular requirements and frequently involves helix--turn--helix (HTH) domain proteins1. For instance, in the arms race between bacteria and bacteriophages, rapid expression of phage anti-CRISPR (acr) genes upon infection enables evasion from CRISPR--Cas defence; transcription is then repressed by an HTH-domain-containing anti-CRISPR-associated (Aca) protein, probably to reduce fitness costs from excessive expression2--5. However, how a single HTH regulator adjusts anti-CRISPR production to cope with increasing phage genome copies and accumulating acr mRNA is unknown. Here we show that the HTH domain of the regulator Aca2, in addition to repressing Acr synthesis transcriptionally through DNA binding, inhibits translation of mRNAs by binding conserved RNA stem-loops and blocking ribosome access. The cryo-electron microscopy structure of the approximately 40{\thinspace}kDa Aca2--RNA complex demonstrates how the versatile HTH domain specifically discriminates RNA from DNA binding sites. These combined regulatory modes are widespread in the Aca2 family and facilitate CRISPR--Cas inhibition in the face of rapid phage DNA replication without toxic acr overexpression. Given the ubiquity of HTH-domain-containing proteins, it is anticipated that many more of them elicit regulatory control by dual DNA and RNA binding.},
  added-at = {2024-08-05T20:11:48.000+0200},
  author = {Birkholz, Nils and Kamata, Kotaro and Feussner, Maximilian and Wilkinson, Max E. and Cuba Samaniego, Christian and Migur, Angela and Kimanius, Dari and Ceelen, Marijn and Went, Sam C. and Usher, Ben and Blower, Tim R. and Brown, Chris M. and Beisel, Chase L. and Weinberg, Zasha and Fagerlund, Robert D. and Jackson, Simon A. and Fineran, Peter C.},
  biburl = {https://www.bibsonomy.org/bibtex/23912d4affb12560b66d115653bfe57f1/cryoem_staff},
  day = 01,
  doi = {10.1038/s41586-024-07644-1},
  interhash = {3997f1af17a3959595c1e0872cb1f517},
  intrahash = {3912d4affb12560b66d115653bfe57f1},
  issn = {1476-4687},
  journal = {Nature},
  keywords = {2024},
  month = jul,
  number = 8021,
  pages = {670--677},
  timestamp = {2024-08-05T20:11:48.000+0200},
  title = {Phage anti-CRISPR control by an RNA- and DNA-binding helix--turn--helix protein},
  url = {https://doi.org/10.1038/s41586-024-07644-1},
  volume = 631,
  year = 2024
}

In all organisms, regulation of gene expression must be adjusted to meet cellular requirements and frequently involves helix–turn–helix (HTH) domain proteins1. For instance, in the arms race between bacteria and bacteriophages, rapid expression of phage anti-CRISPR (acr) genes upon infection enables evasion from CRISPR–Cas defence; transcription is then repressed by an HTH-domain-containing anti-CRISPR-associated (Aca) protein, probably to reduce fitness costs from excessive expression2–5. However, how a single HTH regulator adjusts anti-CRISPR production to cope with increasing phage genome copies and accumulating acr mRNA is unknown. Here we show that the HTH domain of the regulator Aca2, in addition to repressing Acr synthesis transcriptionally through DNA binding, inhibits translation of mRNAs by binding conserved RNA stem-loops and blocking ribosome access. The cryo-electron microscopy structure of the approximately 40þinspacekDa Aca2–RNA complex demonstrates how the versatile HTH domain specifically discriminates RNA from DNA binding sites. These combined regulatory modes are widespread in the Aca2 family and facilitate CRISPR–Cas inhibition in the face of rapid phage DNA replication without toxic acr overexpression. Given the ubiquity of HTH-domain-containing proteins, it is anticipated that many more of them elicit regulatory control by dual DNA and RNA binding.

@article{Kimanius2024,
  abstract = {Macromolecular structure determination by electron cryo-microscopy (cryo-EM) is limited by the alignment of noisy images of individual particles. Because smaller particles have weaker signals, alignment errors impose size limitations on its applicability. Here, we explore how image alignment is improved by the application of deep learning to exploit prior knowledge about biological macromolecular structures that would otherwise be difficult to express mathematically. We train a denoising convolutional neural network on pairs of half-set reconstructions from the electron microscopy data bank (EMDB) and use this denoiser as an alternative to a commonly used smoothness prior. We demonstrate that this approach, which we call Blush regularization, yields better reconstructions than do existing algorithms, in particular for data with low signal-to-noise ratios. The reconstruction of a protein--nucleic acid complex with a molecular weight of 40 kDa, which was previously intractable, illustrates that denoising neural networks will expand the applicability of cryo-EM structure determination for a wide range of biological macromolecules.},
  added-at = {2024-07-01T18:26:15.000+0200},
  author = {Kimanius, Dari and Jamali, Kiarash and Wilkinson, Max E. and L{\"o}vestam, Sofia and Velazhahan, Vaithish and Nakane, Takanori and Scheres, Sjors H. W.},
  biburl = {https://www.bibsonomy.org/bibtex/227a391ae33ef1ba5e57a0b551003805b/cryoem_staff},
  day = 11,
  doi = {10.1038/s41592-024-02304-8},
  interhash = {16172670b29821d327873bf859ad0930},
  intrahash = {27a391ae33ef1ba5e57a0b551003805b},
  issn = {1548-7105},
  journal = {Nature Methods},
  keywords = {2024},
  month = jun,
  timestamp = {2024-07-01T18:26:15.000+0200},
  title = {Data-driven regularization lowers the size barrier of cryo-EM structure determination},
  url = {https://doi.org/10.1038/s41592-024-02304-8},
  year = 2024
}

Macromolecular structure determination by electron cryo-microscopy (cryo-EM) is limited by the alignment of noisy images of individual particles. Because smaller particles have weaker signals, alignment errors impose size limitations on its applicability. Here, we explore how image alignment is improved by the application of deep learning to exploit prior knowledge about biological macromolecular structures that would otherwise be difficult to express mathematically. We train a denoising convolutional neural network on pairs of half-set reconstructions from the electron microscopy data bank (EMDB) and use this denoiser as an alternative to a commonly used smoothness prior. We demonstrate that this approach, which we call Blush regularization, yields better reconstructions than do existing algorithms, in particular for data with low signal-to-noise ratios. The reconstruction of a protein–nucleic acid complex with a molecular weight of 40 kDa, which was previously intractable, illustrates that denoising neural networks will expand the applicability of cryo-EM structure determination for a wide range of biological macromolecules.

@article{duan2024milligramscale,
  added-at = {2024-05-06T23:26:55.000+0200},
  author = {Duan, Pu and El Mammeri, Nadia and Hong, Mei},
  biburl = {https://www.bibsonomy.org/bibtex/2621657630c699baed8c5f23b73fa830d/cryoem_staff},
  doi = {10.1016/j.jbc.2024.107326},
  interhash = {20f7abd3bc1d6bd477e8e68e588ffd2f},
  intrahash = {621657630c699baed8c5f23b73fa830d},
  journal = {Journal of Biological Chemistry},
  keywords = {2024},
  timestamp = {2024-09-11T17:56:59.000+0200},
  title = {Milligram-Scale Assembly and NMR Fingerprint of Tau Fibrils Adopting the Alzheimer’s Disease Fold},
  url = {https://doi.org/10.1016/j.jbc.2024.107326},
  year = 2024
}

@article{madigan2024human,
  added-at = {2024-05-02T21:56:20.000+0200},
  author = {Madigan, Victoria and Zhang, Yugang and Raghavan, Rumya and Wilkinson, Max E. and Faure, Guilhem and Puccio, Elena and Segel, Michael and Lash, Blake and Macrae, Rhiannon K. and Zhang, Feng},
  biburl = {https://www.bibsonomy.org/bibtex/2200035b9a704a1edf0c4e3d3abe6f111/cryoem_staff},
  doi = {10.1073/pnas.2307812120},
  interhash = {ec59a4cddca76210591ad75ce62fc8b6},
  intrahash = {200035b9a704a1edf0c4e3d3abe6f111},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  keywords = {2024},
  month = {March},
  number = 11,
  timestamp = {2024-05-02T21:56:20.000+0200},
  title = {Human paraneoplastic antigen Ma2 (PNMA2) forms icosahedral capsids that can be engineered for mRNA delivery},
  url = {https://www.pnas.org/doi/10.1073/pnas.2307812120},
  volume = 121,
  year = 2024
}

@article{noauthororeditor2024structures,
  added-at = {2024-05-02T21:51:53.000+0200},
  author = {El Mammeri, Nadia and Dregni, Aurelio and Duan, Pu and Hong, Mei},
  biburl = {https://www.bibsonomy.org/bibtex/24af20b9366f4e6809b675ef2ca1094fd/cryoem_staff},
  doi = {10.1073/pnas.2316175121},
  interhash = {d388fc0b7f471d1725d87ed4eb46f24e},
  intrahash = {4af20b9366f4e6809b675ef2ca1094fd},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  keywords = {2024},
  month = {February},
  number = 10,
  timestamp = {2024-05-02T21:51:53.000+0200},
  title = {Structures of AT8 and PHF1 phosphomimetic tau: Insights into the posttranslational modification code of tau aggregation},
  url = {https://doi.org/10.1073/pnas.231617512},
  volume = 121,
  year = 2024
}

@article{Su_2024,
  added-at = {2024-05-02T21:46:10.000+0200},
  author = {Su, Bonnie G. and Vos, Seychelle M.},
  biburl = {https://www.bibsonomy.org/bibtex/2e91fbed2705468020f0cb494706aca60/cryoem_staff},
  doi = {10.1016/j.molcel.2024.01.023},
  interhash = {433aaf467e90bc1bd92c48996caccbf2},
  intrahash = {e91fbed2705468020f0cb494706aca60},
  issn = {1097-2765},
  journal = {Molecular Cell},
  keywords = {2024},
  month = apr,
  number = 7,
  pages = {1243-1256.e5},
  publisher = {Elsevier BV},
  timestamp = {2024-05-02T21:46:10.000+0200},
  title = {Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing},
  url = {http://dx.doi.org/10.1016/j.molcel.2024.01.023},
  volume = 84,
  year = 2024
}

@article{Fry_2024,
  added-at = {2024-02-07T20:22:17.000+0100},
  author = {Fry, Michelle Y and Navarro, Paula P and Hakim, Pusparanee and Ananda, Virly Y and Qin, Xingping and Landoni, Juan C and Rath, Sneha and Inde, Zintis and Lugo, Camila Makhlouta and Luce, Bridget E and Ge, Yifan and McDonald, Julie L and Ali, Ilzat and Ha, Leillani L and Kleinstiver, Benjamin P and Chan, David C and Sarosiek, Kristopher A and Chao, Luke H},
  biburl = {https://www.bibsonomy.org/bibtex/2dfd503916963820a35123fbf57dbcbbe/cryoem_staff},
  doi = {10.1038/s44318-024-00027-2},
  interhash = {d9b97d6c089ff4c8eda56e83c630bc59},
  intrahash = {dfd503916963820a35123fbf57dbcbbe},
  issn = {1460-2075},
  journal = {The EMBO Journal},
  keywords = {2024},
  month = jan,
  number = 3,
  pages = {391–413},
  publisher = {Springer Science and Business Media LLC},
  timestamp = {2024-02-07T20:22:17.000+0100},
  title = {In situ architecture of Opa1-dependent mitochondrial cristae remodeling},
  url = {http://dx.doi.org/10.1038/s44318-024-00027-2},
  volume = 43,
  year = 2024
}

@article{wang2023elucidating,
  abstract = {In photosynthesis, absorbed light energy transfers through a network of antenna proteins with near-unity quantum efficiency to reach the reaction center, which initiates the downstream biochemical reactions. While the energy transfer dynamics within individual antenna proteins have been extensively studied over the past decades, the dynamics between the proteins are poorly understood due to the heterogeneous organization of the network. Previously reported timescales averaged over such heterogeneity, obscuring individual interprotein energy transfer steps. Here, we isolated and interrogated interprotein energy transfer by embedding two variants of the primary antenna protein from purple bacteria, light-harvesting complex 2 (LH2), together into a near-native membrane disc, known as a nanodisc. We integrated ultrafast transient absorption spectroscopy, quantum dynamics simulations, and cryogenic electron microscopy to determine interprotein energy transfer timescales. By varying the diameter of the nanodiscs, we replicated a range of distances between the proteins. The closest distance possible between neighboring LH2, which is the most common in native membranes, is 25 Å and resulted in a timescale of 5.7 ps. Larger distances of 28 to 31 Å resulted in timescales of 10 to 14 ps. Corresponding simulations showed that the fast energy transfer steps between closely spaced LH2 increase transport distances by ∼15%. Overall, our results introduce a framework for well-controlled studies of interprotein energy transfer dynamics and suggest that protein pairs serve as the primary pathway for the efficient transport of solar energy.},
  added-at = {2024-02-07T20:30:24.000+0100},
  author = {Wang, Dihao and Fiebig, Olivia C. and Harris, Dvir and Toporik, Hila and Ji, Yi and Chuang, Chern and Nairat, Muath and Tong, Ashley L. and Ogren, John I. and Hart, Stephanie M. and Cao, Jianshu and Sturgis, James N. and Mazor, Yuval Mazor and Schlau-Cohen, Gabriela S.},
  biburl = {https://www.bibsonomy.org/bibtex/2177376f2631d61d60390abb556c1ad40/cryoem_staff},
  doi = {https://doi.org/10.1073/pnas.2220477120},
  interhash = {34d983b9ad938bf4601946f306ddf9ba},
  intrahash = {177376f2631d61d60390abb556c1ad40},
  journal = {PNAS},
  keywords = {2023},
  month = {April},
  number = 28,
  timestamp = {2024-02-07T20:30:24.000+0100},
  title = {Elucidating interprotein energy transfer dynamics within the antenna network from purple bacteria},
  url = {https://www.pnas.org/doi/10.1073/pnas.2220477120},
  volume = 120,
  year = 2023
}

In photosynthesis, absorbed light energy transfers through a network of antenna proteins with near-unity quantum efficiency to reach the reaction center, which initiates the downstream biochemical reactions. While the energy transfer dynamics within individual antenna proteins have been extensively studied over the past decades, the dynamics between the proteins are poorly understood due to the heterogeneous organization of the network. Previously reported timescales averaged over such heterogeneity, obscuring individual interprotein energy transfer steps. Here, we isolated and interrogated interprotein energy transfer by embedding two variants of the primary antenna protein from purple bacteria, light-harvesting complex 2 (LH2), together into a near-native membrane disc, known as a nanodisc. We integrated ultrafast transient absorption spectroscopy, quantum dynamics simulations, and cryogenic electron microscopy to determine interprotein energy transfer timescales. By varying the diameter of the nanodiscs, we replicated a range of distances between the proteins. The closest distance possible between neighboring LH2, which is the most common in native membranes, is 25 Å and resulted in a timescale of 5.7 ps. Larger distances of 28 to 31 Å resulted in timescales of 10 to 14 ps. Corresponding simulations showed that the fast energy transfer steps between closely spaced LH2 increase transport distances by ∼15%. Overall, our results introduce a framework for well-controlled studies of interprotein energy transfer dynamics and suggest that protein pairs serve as the primary pathway for the efficient transport of solar energy.

@article{wilkinson2023structure,
  abstract = {Non–long terminal repeat (non-LTR) retrotransposons, or long interspersed nuclear elements (LINEs), are an abundant class of eukaryotic transposons that insert into genomes by target-primed reverse transcription (TPRT). During TPRT, a target DNA sequence is nicked and primes reverse transcription of the retrotransposon RNA. Here, we report the cryo–electron microscopy structure of the Bombyx mori R2 non-LTR retrotransposon initiating TPRT at its ribosomal DNA target. The target DNA sequence is unwound at the insertion site and recognized by an upstream motif. An extension of the reverse transcriptase (RT) domain recognizes the retrotransposon RNA and guides the 3′ end into the RT active site to template reverse transcription. We used Cas9 to retarget R2 in vitro to non-native sequences, suggesting future use as a reprogrammable RNA-based gene-insertion tool.},
  added-at = {2024-02-07T20:25:31.000+0100},
  author = {Wilkinson, Max E. and Frangieh, Chris. and Macrae, Rhiannon K. and Zhang, Feng},
  biburl = {https://www.bibsonomy.org/bibtex/2dffa68319eef99e06fd837b254899c21/cryoem_staff},
  doi = {DOI: 10.1126/science.adg7883},
  interhash = {42230ccb2823b6c5062eadb621808a8b},
  intrahash = {dffa68319eef99e06fd837b254899c21},
  journal = {Science},
  keywords = {2023},
  month = {April},
  number = 6642,
  pages = {301-308},
  timestamp = {2024-02-07T20:25:31.000+0100},
  title = {Structure of the R2 non-LTR retrotransposon initiating target-primed reverse transcription},
  url = {https://www.science.org/doi/full/10.1126/science.adg7883},
  volume = 380,
  year = 2023
}

Non–long terminal repeat (non-LTR) retrotransposons, or long interspersed nuclear elements (LINEs), are an abundant class of eukaryotic transposons that insert into genomes by target-primed reverse transcription (TPRT). During TPRT, a target DNA sequence is nicked and primes reverse transcription of the retrotransposon RNA. Here, we report the cryo–electron microscopy structure of the Bombyx mori R2 non-LTR retrotransposon initiating TPRT at its ribosomal DNA target. The target DNA sequence is unwound at the insertion site and recognized by an upstream motif. An extension of the reverse transcriptase (RT) domain recognizes the retrotransposon RNA and guides the 3′ end into the RT active site to template reverse transcription. We used Cas9 to retarget R2 in vitro to non-native sequences, suggesting future use as a reprogrammable RNA-based gene-insertion tool.

@article{Vasquez2023,
  abstract = {Iron-sulfur clusters are essential for life and defects in their biosynthesis lead to human diseases. The mechanism of cluster assembly and delivery to cytosolic and nuclear client proteins via the cytosolic iron-sulfur cluster assembly (CIA) pathway is not well understood. Here we report cryo-EM structures of the HEAT-repeat protein Met18 from Saccharomyces cerevisiae, a key component of the CIA targeting complex (CTC) that identifies cytosolic and nuclear client proteins and delivers a mature iron-sulfur cluster. We find that in the absence of other CTC proteins, Met18 adopts tetrameric and hexameric states. Using mass photometry and negative stain EM, we show that upon the addition of Cia2, these higher order oligomeric states of Met18 disassemble. We also use pulldown assays to identify residues of critical importance for Cia2 binding and recognition of the Leu1 client, many of which are buried when Met18 oligomerizes. Our structures show conformations of Met18 that have not been previously observed in any Met18 homolog, lending support to the idea that a highly flexible Met18 may be key to how the CTC is able to deliver iron-sulfur clusters to client proteins of various sizes and shapes, i.e. Met18 conforms to the dimensions needed.},
  added-at = {2024-02-07T20:21:48.000+0100},
  author = {Vasquez, Sheena and Marquez, Melissa D. and Brignole, Edward J. and Vo, Amanda and Kong, Sunnie and Park, Christopher and Perlstein, Deborah L. and Drennan, Catherine L.},
  biburl = {https://www.bibsonomy.org/bibtex/2c5a1021db5dd590277a3a46a96a4bac5/cryoem_staff},
  day = 18,
  doi = {10.1038/s42003-023-05579-3},
  interhash = {86745262a79013fa25ddde3af3c6eb2b},
  intrahash = {c5a1021db5dd590277a3a46a96a4bac5},
  issn = {2399-3642},
  journal = {Communications Biology},
  keywords = {2023},
  month = dec,
  number = 1,
  pages = 1276,
  timestamp = {2024-02-07T20:21:48.000+0100},
  title = {Structural and biochemical investigations of a HEAT-repeat protein involved in the cytosolic iron-sulfur cluster assembly pathway},
  url = {https://doi.org/10.1038/s42003-023-05579-3},
  volume = 6,
  year = 2023
}

Iron-sulfur clusters are essential for life and defects in their biosynthesis lead to human diseases. The mechanism of cluster assembly and delivery to cytosolic and nuclear client proteins via the cytosolic iron-sulfur cluster assembly (CIA) pathway is not well understood. Here we report cryo-EM structures of the HEAT-repeat protein Met18 from Saccharomyces cerevisiae, a key component of the CIA targeting complex (CTC) that identifies cytosolic and nuclear client proteins and delivers a mature iron-sulfur cluster. We find that in the absence of other CTC proteins, Met18 adopts tetrameric and hexameric states. Using mass photometry and negative stain EM, we show that upon the addition of Cia2, these higher order oligomeric states of Met18 disassemble. We also use pulldown assays to identify residues of critical importance for Cia2 binding and recognition of the Leu1 client, many of which are buried when Met18 oligomerizes. Our structures show conformations of Met18 that have not been previously observed in any Met18 homolog, lending support to the idea that a highly flexible Met18 may be key to how the CTC is able to deliver iron-sulfur clusters to client proteins of various sizes and shapes, i.e. Met18 conforms to the dimensions needed.

@article{Markert2023,
  abstract = {Acetylation of histones is a key post-translational modification that guides gene expression regulation. In yeast, the class I histone deacetylase containing Rpd3S complex plays a critical role in the suppression of spurious transcription by removing histone acetylation from actively transcribed genes. The S. cerevisiae Rpd3S complex has five subunits (Rpd3, Sin3, Rco1, Eaf3, and Ume1) but its subunit stoichiometry and how the complex engages nucleosomes to achieve substrate specificity remains elusive. Here we report the cryo-EM structure of the complete Rpd3S complex bound to a nucleosome. Sin3 and two copies of subunits Rco1 and Eaf3 encircle the deacetylase subunit Rpd3 and coordinate the positioning of Ume1. The Rpd3S complex binds both trimethylated H3 tails at position lysine 36 and makes multiple additional contacts with the nucleosomal DNA and the H2A--H2B acidic patch. Direct regulation via the Sin3 subunit coordinates binding of the acetylated histone substrate to achieve substrate specificity.},
  added-at = {2024-02-07T20:21:20.000+0100},
  author = {Markert, Jonathan W. and Vos, Seychelle M. and Farnung, Lucas},
  biburl = {https://www.bibsonomy.org/bibtex/22027c34146e25a909cb049522e49bbdb/cryoem_staff},
  day = 08,
  doi = {10.1038/s41467-023-43968-8},
  interhash = {3cf5dbbe50e2753a2b09b25c9b7789dc},
  intrahash = {2027c34146e25a909cb049522e49bbdb},
  issn = {2041-1723},
  journal = {Nature Communications},
  keywords = {2023},
  month = dec,
  number = 1,
  pages = 8128,
  timestamp = {2024-02-07T20:21:20.000+0100},
  title = {Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex},
  url = {https://doi.org/10.1038/s41467-023-43968-8},
  volume = 14,
  year = 2023
}

Acetylation of histones is a key post-translational modification that guides gene expression regulation. In yeast, the class I histone deacetylase containing Rpd3S complex plays a critical role in the suppression of spurious transcription by removing histone acetylation from actively transcribed genes. The S. cerevisiae Rpd3S complex has five subunits (Rpd3, Sin3, Rco1, Eaf3, and Ume1) but its subunit stoichiometry and how the complex engages nucleosomes to achieve substrate specificity remains elusive. Here we report the cryo-EM structure of the complete Rpd3S complex bound to a nucleosome. Sin3 and two copies of subunits Rco1 and Eaf3 encircle the deacetylase subunit Rpd3 and coordinate the positioning of Ume1. The Rpd3S complex binds both trimethylated H3 tails at position lysine 36 and makes multiple additional contacts with the nucleosomal DNA and the H2A–H2B acidic patch. Direct regulation via the Sin3 subunit coordinates binding of the acetylated histone substrate to achieve substrate specificity.

@article{Grassetti_2023,
  added-at = {2024-02-07T20:20:57.000+0100},
  author = {Grassetti, Andrew V. and May, Mira B. and Davis, Joseph H.},
  biburl = {https://www.bibsonomy.org/bibtex/26c9f9c32ca72be5b59fbac2d603c8291/cryoem_staff},
  doi = {10.3791/66023},
  interhash = {1e70574b4cdb4c3b45ae25ce6a57f707},
  intrahash = {6c9f9c32ca72be5b59fbac2d603c8291},
  issn = {1940-087X},
  journal = {Journal of Visualized Experiments},
  keywords = {2023},
  month = nov,
  number = 201,
  publisher = {MyJove Corporation},
  timestamp = {2024-02-07T20:20:57.000+0100},
  title = {Application of Monolayer Graphene to Cryo-Electron Microscopy Grids for High-resolution Structure Determination},
  url = {http://dx.doi.org/10.3791/66023},
  year = 2023
}

@article{Ghanbarpour2023,
  abstract = {AAA+ proteases degrade intracellular proteins in a highly specific manner. E. coli ClpXP, for example, relies on a C-terminal ssrA tag or other terminal degron sequences to recognize proteins, which are then unfolded by ClpX and subsequently translocated through its axial channel and into the degradation chamber of ClpP for proteolysis. Prior cryo-EM structures reveal that the ssrA tag initially binds to a ClpX conformation in which the axial channel is closed by a pore-2 loop. Here, we show that substrate-free ClpXP has a nearly identical closed-channel conformation. We destabilize this closed-channel conformation by deleting residues from the ClpX pore-2 loop. Strikingly, open-channel ClpXP variants degrade non-native proteins lacking degrons faster than the parental enzymes in vitro but degraded GFP-ssrA more slowly. When expressed in E. coli, these open channel variants behave similarly to the wild-type enzyme in assays of filamentation and phage-Mu plating but resulted in reduced growth phenotypes at elevated temperatures or when cells were exposed to sub-lethal antibiotic concentrations. Thus, channel closure is an important determinant of ClpXP degradation specificity.},
  added-at = {2024-02-07T20:20:28.000+0100},
  author = {Ghanbarpour, Alireza and Cohen, Steven E. and Fei, Xue and Kinman, Laurel F. and Bell, Tristan A. and Zhang, Jia Jia and Baker, Tania A. and Davis, Joseph H. and Sauer, Robert T.},
  biburl = {https://www.bibsonomy.org/bibtex/24f40e1244c1a38efef32cc856ae1ee77/cryoem_staff},
  day = 10,
  doi = {10.1038/s41467-023-43145-x},
  interhash = {c0af36a768b5e925cae2a5882ee1b482},
  intrahash = {4f40e1244c1a38efef32cc856ae1ee77},
  issn = {2041-1723},
  journal = {Nature Communications},
  keywords = {2023},
  month = nov,
  number = 1,
  pages = 7281,
  timestamp = {2024-02-07T20:20:28.000+0100},
  title = {A closed translocation channel in the substrate-free AAA+ ClpXP protease diminishes rogue degradation},
  url = {https://doi.org/10.1038/s41467-023-43145-x},
  volume = 14,
  year = 2023
}

AAA+ proteases degrade intracellular proteins in a highly specific manner. E. coli ClpXP, for example, relies on a C-terminal ssrA tag or other terminal degron sequences to recognize proteins, which are then unfolded by ClpX and subsequently translocated through its axial channel and into the degradation chamber of ClpP for proteolysis. Prior cryo-EM structures reveal that the ssrA tag initially binds to a ClpX conformation in which the axial channel is closed by a pore-2 loop. Here, we show that substrate-free ClpXP has a nearly identical closed-channel conformation. We destabilize this closed-channel conformation by deleting residues from the ClpX pore-2 loop. Strikingly, open-channel ClpXP variants degrade non-native proteins lacking degrons faster than the parental enzymes in vitro but degraded GFP-ssrA more slowly. When expressed in E. coli, these open channel variants behave similarly to the wild-type enzyme in assays of filamentation and phage-Mu plating but resulted in reduced growth phenotypes at elevated temperatures or when cells were exposed to sub-lethal antibiotic concentrations. Thus, channel closure is an important determinant of ClpXP degradation specificity.

@article{Vaccaro_2023,
  added-at = {2024-02-07T20:20:06.000+0100},
  author = {Vaccaro, Francesca A. and Faber, Daphne A. and Andree, Gisele A. and Born, David A. and Kang, Gyunghoon and Fonseca, Dallas R. and Jost, Marco and Drennan, Catherine L.},
  biburl = {https://www.bibsonomy.org/bibtex/2b5936d56f42a114af2c9408ca911ced6/cryoem_staff},
  doi = {10.1016/j.jbc.2023.105109},
  interhash = {1e05dad265a1ebcb424bc66787570a59},
  intrahash = {b5936d56f42a114af2c9408ca911ced6},
  issn = {0021-9258},
  journal = {Journal of Biological Chemistry},
  keywords = {2023},
  month = sep,
  number = 9,
  pages = 105109,
  publisher = {Elsevier BV},
  timestamp = {2024-02-07T20:20:06.000+0100},
  title = {Structural insight into G-protein chaperone-mediated maturation of a bacterial adenosylcobalamin-dependent mutase},
  url = {http://dx.doi.org/10.1016/j.jbc.2023.105109},
  volume = 299,
  year = 2023
}

@article{Dodge_2023,
  added-at = {2024-02-07T20:19:43.000+0100},
  author = {Dodge, Greg J. and Bernstein, Hannah M. and Imperiali, Barbara},
  biburl = {https://www.bibsonomy.org/bibtex/2480ff4825ac77d20207205abbb3ee165/cryoem_staff},
  doi = {10.1016/j.pep.2023.106273},
  interhash = {9d373b2b16e5bad72602ad98aa6545f1},
  intrahash = {480ff4825ac77d20207205abbb3ee165},
  issn = {1046-5928},
  journal = {Protein Expression and Purification},
  keywords = {2023},
  month = jul,
  pages = 106273,
  publisher = {Elsevier BV},
  timestamp = {2024-02-07T20:19:43.000+0100},
  title = {A generalizable protocol for expression and purification of membrane-bound bacterial phosphoglycosyl transferases in liponanoparticles},
  url = {http://dx.doi.org/10.1016/j.pep.2023.106273},
  volume = 207,
  year = 2023
}

@article{Saito2023,
  abstract = {RNA-guided systems, which use complementarity between a guide RNA and target nucleic acid sequences for recognition of genetic elements, have a central role in biological processes in both prokaryotes and eukaryotes. For example, the prokaryotic CRISPR--Cas systems provide adaptive immunity for bacteria and archaea against foreign genetic elements. Cas effectors such as Cas9 and Cas12 perform guide-RNA-dependent DNA cleavage1. Although a few eukaryotic RNA-guided systems have been studied, including RNA interference2 and ribosomal RNA modification3, it remains unclear whether eukaryotes have RNA-guided endonucleases. Recently, a new class of prokaryotic RNA-guided systems (termed OMEGA) was reported4,5. The OMEGA effector TnpB is the putative ancestor of Cas12 and has RNA-guided endonuclease activity4,6. TnpB may also be the ancestor of the eukaryotic transposon-encoded Fanzor (Fz) proteins4,7, raising the possibility that eukaryotes are also equipped with CRISPR--Cas or OMEGA-like programmable RNA-guided endonucleases. Here we report the biochemical characterization of Fz, showing that it is an RNA-guided DNA endonuclease. We also show that Fz can be reprogrammed for human genome engineering applications. Finally, we resolve the structure of Spizellomyces punctatus Fz at 2.7{\thinspace}{\AA} using cryogenic electron microscopy, showing the conservation of core regions among Fz, TnpB and Cas12, despite diverse cognate RNA structures. Our results show that Fz is a eukaryotic OMEGA system, demonstrating that RNA-guided endonucleases are present in all three domains of life.},
  added-at = {2024-02-07T20:18:22.000+0100},
  author = {Saito, Makoto and Xu, Peiyu and Faure, Guilhem and Maguire, Samantha and Kannan, Soumya and Altae-Tran, Han and Vo, Sam and Desimone, AnAn and Macrae, Rhiannon K. and Zhang, Feng},
  biburl = {https://www.bibsonomy.org/bibtex/221ee86a0d4a5ea9fc05f695fbf378753/cryoem_staff},
  day = 01,
  doi = {10.1038/s41586-023-06356-2},
  interhash = {5c5b74c183aa38f98f3fc434f204cdd7},
  intrahash = {21ee86a0d4a5ea9fc05f695fbf378753},
  issn = {1476-4687},
  journal = {Nature},
  keywords = {2023},
  month = aug,
  number = 7974,
  pages = {660--668},
  timestamp = {2024-02-07T20:18:22.000+0100},
  title = {Fanzor is a eukaryotic programmable RNA-guided endonuclease},
  url = {https://doi.org/10.1038/s41586-023-06356-2},
  volume = 620,
  year = 2023
}

RNA-guided systems, which use complementarity between a guide RNA and target nucleic acid sequences for recognition of genetic elements, have a central role in biological processes in both prokaryotes and eukaryotes. For example, the prokaryotic CRISPR–Cas systems provide adaptive immunity for bacteria and archaea against foreign genetic elements. Cas effectors such as Cas9 and Cas12 perform guide-RNA-dependent DNA cleavage1. Although a few eukaryotic RNA-guided systems have been studied, including RNA interference2 and ribosomal RNA modification3, it remains unclear whether eukaryotes have RNA-guided endonucleases. Recently, a new class of prokaryotic RNA-guided systems (termed OMEGA) was reported4,5. The OMEGA effector TnpB is the putative ancestor of Cas12 and has RNA-guided endonuclease activity4,6. TnpB may also be the ancestor of the eukaryotic transposon-encoded Fanzor (Fz) proteins4,7, raising the possibility that eukaryotes are also equipped with CRISPR–Cas or OMEGA-like programmable RNA-guided endonucleases. Here we report the biochemical characterization of Fz, showing that it is an RNA-guided DNA endonuclease. We also show that Fz can be reprogrammed for human genome engineering applications. Finally, we resolve the structure of Spizellomyces punctatus Fz at 2.7þinspaceÅ using cryogenic electron microscopy, showing the conservation of core regions among Fz, TnpB and Cas12, despite diverse cognate RNA structures. Our results show that Fz is a eukaryotic OMEGA system, demonstrating that RNA-guided endonucleases are present in all three domains of life.

@article{Chen_2023,
  added-at = {2024-02-07T20:17:59.000+0100},
  author = {Chen, Tianyang and Banda, Harish and Yang, Luming and Li, Jian and Zhang, Yugang and Parenti, Riccardo and Dincă, Mircea},
  biburl = {https://www.bibsonomy.org/bibtex/268fd282d4246918e6dc0e9f4ff2e5536/cryoem_staff},
  doi = {10.1016/j.joule.2023.03.011},
  interhash = {45da9f5c187bcc011fcc839722894082},
  intrahash = {68fd282d4246918e6dc0e9f4ff2e5536},
  issn = {2542-4351},
  journal = {Joule},
  keywords = {2023},
  month = may,
  number = 5,
  pages = {986–1002},
  publisher = {Elsevier BV},
  timestamp = {2024-02-07T20:17:59.000+0100},
  title = {High-rate, high-capacity electrochemical energy storage in hydrogen-bonded fused aromatics},
  url = {http://dx.doi.org/10.1016/j.joule.2023.03.011},
  volume = 7,
  year = 2023
}

@article{ghanbarpour2023adaptor,
  abstract = {Energy-dependent protein degradation by the AAA+ ClpXP protease helps maintain protein homeostasis in bacteria and eukaryotic organelles of bacterial origin. In Escherichia coli and many other proteobacteria, the SspB adaptor assists ClpXP in degrading ssrA-tagged polypeptides produced as a consequence of tmRNA-mediated ribosome rescue. By tethering these incomplete ssrA-tagged proteins to ClpXP, SspB facilitates their efficient degradation at low substrate concentrations. How this process occurs structurally is unknown. Here, we present a cryo-EM structure of the SspB adaptor bound to a GFP-ssrA substrate and to ClpXP. This structure provides evidence for simultaneous contacts of SspB and ClpX with the ssrA tag within the tethering complex, allowing direct substrate handoff concomitant with the initiation of substrate translocation. Furthermore, our structure reveals that binding of the substrate·adaptor complex induces unexpected conformational changes within the spiral structure of the AAA+ ClpX hexamer and its interaction with the ClpP tetradecamer.},
  added-at = {2024-02-07T20:17:10.000+0100},
  author = {Ghanbarpour, Alireza and Fei, Xue and Baker, Tania A. and Davis, Joseph H. and Sauer, Robert T.},
  biburl = {https://www.bibsonomy.org/bibtex/2de11904ee208dc1d2e8ccc08b73f6f2a/cryoem_staff},
  doi = {https://doi.org/10.1073/pnas.2219044120},
  interhash = {c1cdac151b58e404626a4b797fdc971d},
  intrahash = {de11904ee208dc1d2e8ccc08b73f6f2a},
  journal = {PNAS},
  keywords = {2023},
  month = {January},
  number = 6,
  timestamp = {2024-02-07T20:17:10.000+0100},
  title = {The SspB adaptor drives structural changes in the AAA+ ClpXP protease during ssrA-tagged substrate delivery},
  url = {https://www.pnas.org/doi/10.1073/pnas.2219044120},
  volume = 120,
  year = 2023
}

Energy-dependent protein degradation by the AAA+ ClpXP protease helps maintain protein homeostasis in bacteria and eukaryotic organelles of bacterial origin. In Escherichia coli and many other proteobacteria, the SspB adaptor assists ClpXP in degrading ssrA-tagged polypeptides produced as a consequence of tmRNA-mediated ribosome rescue. By tethering these incomplete ssrA-tagged proteins to ClpXP, SspB facilitates their efficient degradation at low substrate concentrations. How this process occurs structurally is unknown. Here, we present a cryo-EM structure of the SspB adaptor bound to a GFP-ssrA substrate and to ClpXP. This structure provides evidence for simultaneous contacts of SspB and ClpX with the ssrA tag within the tethering complex, allowing direct substrate handoff concomitant with the initiation of substrate translocation. Furthermore, our structure reveals that binding of the substrate·adaptor complex induces unexpected conformational changes within the spiral structure of the AAA+ ClpX hexamer and its interaction with the ClpP tetradecamer.

@article{Parsons2023,
  abstract = {Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.},
  added-at = {2024-02-07T20:12:45.000+0100},
  author = {Parsons, Molly F. and Allan, Matthew F. and Li, Shanshan and Shepherd, Tyson R. and Ratanalert, Sakul and Zhang, Kaiming and Pullen, Krista M. and Chiu, Wah and Rouskin, Silvi and Bathe, Mark},
  biburl = {https://www.bibsonomy.org/bibtex/24e680761fb9efb214bd284a93a9c5525/cryoem_staff},
  day = 24,
  doi = {10.1038/s41467-023-36156-1},
  interhash = {8a5f8534ba7d91ce1cde7d3e58d4ccdb},
  intrahash = {4e680761fb9efb214bd284a93a9c5525},
  issn = {2041-1723},
  journal = {Nature Communications},
  keywords = {2023},
  month = jan,
  number = 1,
  pages = 382,
  timestamp = {2024-02-07T20:12:45.000+0100},
  title = {3D RNA-scaffolded wireframe origami},
  url = {https://doi.org/10.1038/s41467-023-36156-1},
  volume = 14,
  year = 2023
}

Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.

@article{Barotov_2022,
  added-at = {2024-02-07T20:12:13.000+0100},
  author = {Barotov, Ulugbek and Thanippuli Arachchi, Dimuthu H. and Klein, Megan D. and Zhang, Juanye and Šverko, Tara and Bawendi, Moungi G.},
  biburl = {https://www.bibsonomy.org/bibtex/27ee3bc5b311423a028f7911d89c21425/cryoem_staff},
  doi = {10.1002/adom.202201471},
  interhash = {51919b9c9aec0cc0b329da037cb3c2a6},
  intrahash = {7ee3bc5b311423a028f7911d89c21425},
  issn = {2195-1071},
  journal = {Advanced Optical Materials},
  keywords = {2022},
  month = nov,
  number = 2,
  publisher = {Wiley},
  timestamp = {2024-02-07T20:12:13.000+0100},
  title = {Near‐Unity Superradiant Emission from Delocalized Frenkel Excitons in a Two‐Dimensional Supramolecular Assembly},
  url = {http://dx.doi.org/10.1002/adom.202201471},
  volume = 11,
  year = 2022
}

@article{Strecker_2022,
  added-at = {2024-02-07T20:11:52.000+0100},
  author = {Strecker, Jonathan and Demircioglu, F. Esra and Li, David and Faure, Guilhem and Wilkinson, Max E. and Gootenberg, Jonathan S. and Abudayyeh, Omar O. and Nishimasu, Hiroshi and Macrae, Rhiannon K. and Zhang, Feng},
  biburl = {https://www.bibsonomy.org/bibtex/2eead8968b8a8f0cfaeeee7f016e44a8b/cryoem_staff},
  doi = {10.1126/science.add7450},
  interhash = {e2f64df4d578b5740aa042a852bef6b5},
  intrahash = {eead8968b8a8f0cfaeeee7f016e44a8b},
  issn = {1095-9203},
  journal = {Science},
  keywords = {2022},
  month = nov,
  number = 6622,
  pages = {874–881},
  publisher = {American Association for the Advancement of Science (AAAS)},
  timestamp = {2024-02-07T20:11:52.000+0100},
  title = {RNA-activated protein cleavage with a CRISPR-associated endopeptidase},
  url = {http://dx.doi.org/10.1126/science.add7450},
  volume = 378,
  year = 2022
}

@article{Kim2022,
  abstract = {ClpAP, a two-ring AAA+ protease, degrades N-end-rule proteins bound by the ClpS adaptor. Here we present high-resolution cryo-EM structures of Escherichia coli ClpAPS complexes, showing how ClpA pore loops interact with the ClpS N-terminal extension (NTE), which is normally intrinsically disordered. In two classes, the NTE is bound by a spiral of pore-1 and pore-2 loops in a manner similar to substrate-polypeptide binding by many AAA+ unfoldases. Kinetic studies reveal that pore-2 loops of the ClpA D1 ring catalyze the protein remodeling required for substrate delivery by ClpS. In a third class, D2 pore-1 loops are rotated, tucked away from the channel and do not bind the NTE, demonstrating asymmetry in engagement by the D1 and D2 rings. These studies show additional structures and functions for key AAA+ elements. Pore-loop tucking may be used broadly by AAA+ unfoldases, for example, during enzyme pausing/unloading.},
  added-at = {2024-02-07T20:11:31.000+0100},
  author = {Kim, Sora and Fei, Xue and Sauer, Robert T. and Baker, Tania A.},
  biburl = {https://www.bibsonomy.org/bibtex/214c10f42eef9066f3c895195d790a486/cryoem_staff},
  day = 01,
  doi = {10.1038/s41594-022-00850-3},
  interhash = {815116e94f27fabcaf1394a175431f70},
  intrahash = {14c10f42eef9066f3c895195d790a486},
  issn = {1545-9985},
  journal = {Nature Structural {\&} Molecular Biology},
  keywords = {2022},
  month = nov,
  number = 11,
  pages = {1068--1079},
  timestamp = {2024-02-07T20:11:31.000+0100},
  title = {AAA+ protease-adaptor structures reveal altered conformations and ring specialization},
  url = {https://doi.org/10.1038/s41594-022-00850-3},
  volume = 29,
  year = 2022
}

ClpAP, a two-ring AAA+ protease, degrades N-end-rule proteins bound by the ClpS adaptor. Here we present high-resolution cryo-EM structures of Escherichia coli ClpAPS complexes, showing how ClpA pore loops interact with the ClpS N-terminal extension (NTE), which is normally intrinsically disordered. In two classes, the NTE is bound by a spiral of pore-1 and pore-2 loops in a manner similar to substrate-polypeptide binding by many AAA+ unfoldases. Kinetic studies reveal that pore-2 loops of the ClpA D1 ring catalyze the protein remodeling required for substrate delivery by ClpS. In a third class, D2 pore-1 loops are rotated, tucked away from the channel and do not bind the NTE, demonstrating asymmetry in engagement by the D1 and D2 rings. These studies show additional structures and functions for key AAA+ elements. Pore-loop tucking may be used broadly by AAA+ unfoldases, for example, during enzyme pausing/unloading.

@article{Hirano2022,
  abstract = {RNA-guided systems, such as CRISPR--Cas, combine programmable substrate recognition with enzymatic function, a combination that has been used advantageously to develop powerful molecular technologies1,2. Structural studies of these systems have illuminated how the RNA and protein jointly recognize and cleave their substrates, guiding rational engineering for further technology development3. Recent work identified a new class of RNA-guided systems, termed OMEGA, which include IscB, the likely ancestor of Cas9, and the nickase IsrB, a homologue of IscB lacking the HNH nuclease domain4. IsrB consists of only around 350 amino acids, but its small size is counterbalanced by a relatively large RNA guide (roughly 300-nt $\omega$RNA). Here, we report the cryogenic-electron microscopy structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in complex with its cognate $\omega$RNA and a target DNA. We find the overall structure of the IsrB protein shares a common scaffold with Cas9. In contrast to Cas9, however, which uses a recognition (REC) lobe to facilitate target selection, IsrB relies on its $\omega$RNA, part of which forms an intricate ternary structure positioned analogously to REC. Structural analyses of IsrB and its $\omega$RNA as well as comparisons to other RNA-guided systems highlight the functional interplay between protein and RNA, advancing our understanding of the biology and evolution of these diverse systems.},
  added-at = {2024-02-07T20:11:11.000+0100},
  author = {Hirano, Seiichi and Kappel, Kalli and Altae-Tran, Han and Faure, Guilhem and Wilkinson, Max E. and Kannan, Soumya and Demircioglu, F. Esra and Yan, Rui and Shiozaki, Momoko and Yu, Zhiheng and Makarova, Kira S. and Koonin, Eugene V. and Macrae, Rhiannon K. and Zhang, Feng},
  biburl = {https://www.bibsonomy.org/bibtex/2500fc0230ccbb1f52235732c290ce70b/cryoem_staff},
  day = 01,
  doi = {10.1038/s41586-022-05324-6},
  interhash = {97b1eb51728309fdbab12bdcd89c499c},
  intrahash = {500fc0230ccbb1f52235732c290ce70b},
  issn = {1476-4687},
  journal = {Nature},
  keywords = {2022},
  month = oct,
  number = 7932,
  pages = {575--581},
  timestamp = {2024-02-07T20:11:11.000+0100},
  title = {Structure of the OMEGA nickase IsrB in complex with $\omega$RNA and target DNA},
  url = {https://doi.org/10.1038/s41586-022-05324-6},
  volume = 610,
  year = 2022
}

RNA-guided systems, such as CRISPR–Cas, combine programmable substrate recognition with enzymatic function, a combination that has been used advantageously to develop powerful molecular technologies1,2. Structural studies of these systems have illuminated how the RNA and protein jointly recognize and cleave their substrates, guiding rational engineering for further technology development3. Recent work identified a new class of RNA-guided systems, termed OMEGA, which include IscB, the likely ancestor of Cas9, and the nickase IsrB, a homologue of IscB lacking the HNH nuclease domain4. IsrB consists of only around 350 amino acids, but its small size is counterbalanced by a relatively large RNA guide (roughly 300-nt $ω$RNA). Here, we report the cryogenic-electron microscopy structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in complex with its cognate $ω$RNA and a target DNA. We find the overall structure of the IsrB protein shares a common scaffold with Cas9. In contrast to Cas9, however, which uses a recognition (REC) lobe to facilitate target selection, IsrB relies on its $ω$RNA, part of which forms an intricate ternary structure positioned analogously to REC. Structural analyses of IsrB and its $ω$RNA as well as comparisons to other RNA-guided systems highlight the functional interplay between protein and RNA, advancing our understanding of the biology and evolution of these diverse systems.

@article{Weaver2022,
  abstract = {Genomic DNA is continually exposed to endogenous and exogenous factors that promote DNA damage. Eukaryotic genomic DNA is packaged into nucleosomes, which present a barrier to accessing and effectively repairing DNA damage. The mechanisms by which DNA repair proteins overcome this barrier to repair DNA damage in the nucleosome and protect genomic stability is unknown. Here, we determine how the base excision repair (BER) endonuclease AP-endonuclease 1 (APE1) recognizes and cleaves DNA damage in the nucleosome. Kinetic assays determine that APE1 cleaves solvent-exposed AP sites in the nucleosome with 3 − 6 orders of magnitude higher efficiency than occluded AP sites. A cryo-electron microscopy structure of APE1 bound to a nucleosome containing a solvent-exposed AP site reveal that APE1 uses a DNA sculpting mechanism for AP site recognition, where APE1 bends the nucleosomal DNA to access the AP site. Notably, additional biochemical and structural characterization of occluded AP sites identify contacts between the nucleosomal DNA and histone octamer that prevent efficient processing of the AP site by APE1. These findings provide a rationale for the position-dependent activity of BER proteins in the nucleosome and suggests the ability of BER proteins to sculpt nucleosomal DNA drives efficient BER in chromatin.},
  added-at = {2024-02-07T20:10:42.000+0100},
  author = {Weaver, Tyler M. and Hoitsma, Nicole M. and Spencer, Jonah J. and Gakhar, Lokesh and Schnicker, Nicholas J. and Freudenthal, Bret D.},
  biburl = {https://www.bibsonomy.org/bibtex/2f867abb19d8ada7aa069460aa975ddab/cryoem_staff},
  day = 14,
  doi = {10.1038/s41467-022-33057-7},
  interhash = {5965f916425f02452858e5c9dba92d14},
  intrahash = {f867abb19d8ada7aa069460aa975ddab},
  issn = {2041-1723},
  journal = {Nature Communications},
  keywords = {2022},
  month = sep,
  number = 1,
  pages = 5390,
  timestamp = {2024-02-07T20:10:42.000+0100},
  title = {Structural basis for APE1 processing DNA damage in the nucleosome},
  url = {https://doi.org/10.1038/s41467-022-33057-7},
  volume = 13,
  year = 2022
}

Genomic DNA is continually exposed to endogenous and exogenous factors that promote DNA damage. Eukaryotic genomic DNA is packaged into nucleosomes, which present a barrier to accessing and effectively repairing DNA damage. The mechanisms by which DNA repair proteins overcome this barrier to repair DNA damage in the nucleosome and protect genomic stability is unknown. Here, we determine how the base excision repair (BER) endonuclease AP-endonuclease 1 (APE1) recognizes and cleaves DNA damage in the nucleosome. Kinetic assays determine that APE1 cleaves solvent-exposed AP sites in the nucleosome with 3 − 6 orders of magnitude higher efficiency than occluded AP sites. A cryo-electron microscopy structure of APE1 bound to a nucleosome containing a solvent-exposed AP site reveal that APE1 uses a DNA sculpting mechanism for AP site recognition, where APE1 bends the nucleosomal DNA to access the AP site. Notably, additional biochemical and structural characterization of occluded AP sites identify contacts between the nucleosomal DNA and histone octamer that prevent efficient processing of the AP site by APE1. These findings provide a rationale for the position-dependent activity of BER proteins in the nucleosome and suggests the ability of BER proteins to sculpt nucleosomal DNA drives efficient BER in chromatin.

@article{Navarro2022,
  abstract = {The bacterial division apparatus catalyses the synthesis and remodelling of septal peptidoglycan (sPG) to build the cell wall layer that fortifies the daughter cell poles. Understanding of this essential process has been limited by the lack of native three-dimensional views of developing septa. Here, we apply state-of-the-art cryogenic electron tomography (cryo-ET) and fluorescence microscopy to visualize the division site architecture and sPG biogenesis dynamics of the Gram-negative bacterium Escherichia coli. We identify a wedge-like sPG structure that fortifies the ingrowing septum. Experiments with strains defective in sPG biogenesis revealed that the septal architecture and mode of division can be modified to more closely resemble that of other Gram-negative (Caulobacter crescentus) or Gram-positive (Staphylococcus aureus) bacteria, suggesting that a conserved mechanism underlies the formation of different septal morphologies. Finally, analysis of mutants impaired in amidase activation ($\Delta$envC $\Delta$nlpD) showed that cell wall remodelling affects the placement and stability of the cytokinetic ring. Taken together, our results support a model in which competition between the cell elongation and division machineries determines the shape of cell constrictions and the poles they form. They also highlight how the activity of the division system can be modulated to help generate the diverse array of shapes observed in the bacterial domain.},
  added-at = {2024-02-07T20:10:09.000+0100},
  author = {Navarro, Paula P. and Vettiger, Andrea and Ananda, Virly Y. and Llopis, Paula Montero and Allolio, Christoph and Bernhardt, Thomas G. and Chao, Luke H.},
  biburl = {https://www.bibsonomy.org/bibtex/20b2032048abbe7d9da754fc8f1c9adc3/cryoem_staff},
  day = 01,
  doi = {10.1038/s41564-022-01210-z},
  interhash = {ae5240a82bb51046e13198ce6c6bb4c1},
  intrahash = {0b2032048abbe7d9da754fc8f1c9adc3},
  issn = {2058-5276},
  journal = {Nature Microbiology},
  keywords = {2022},
  month = oct,
  number = 10,
  pages = {1621--1634},
  timestamp = {2024-02-07T20:10:09.000+0100},
  title = {Cell wall synthesis and remodelling dynamics determine division site architecture and cell shape in Escherichia coli},
  url = {https://doi.org/10.1038/s41564-022-01210-z},
  volume = 7,
  year = 2022
}

The bacterial division apparatus catalyses the synthesis and remodelling of septal peptidoglycan (sPG) to build the cell wall layer that fortifies the daughter cell poles. Understanding of this essential process has been limited by the lack of native three-dimensional views of developing septa. Here, we apply state-of-the-art cryogenic electron tomography (cryo-ET) and fluorescence microscopy to visualize the division site architecture and sPG biogenesis dynamics of the Gram-negative bacterium Escherichia coli. We identify a wedge-like sPG structure that fortifies the ingrowing septum. Experiments with strains defective in sPG biogenesis revealed that the septal architecture and mode of division can be modified to more closely resemble that of other Gram-negative (Caulobacter crescentus) or Gram-positive (Staphylococcus aureus) bacteria, suggesting that a conserved mechanism underlies the formation of different septal morphologies. Finally, analysis of mutants impaired in amidase activation ($Δ$envC $Δ$nlpD) showed that cell wall remodelling affects the placement and stability of the cytokinetic ring. Taken together, our results support a model in which competition between the cell elongation and division machineries determines the shape of cell constrictions and the poles they form. They also highlight how the activity of the division system can be modulated to help generate the diverse array of shapes observed in the bacterial domain.

@article{Gao_2022,
  added-at = {2024-02-07T20:08:34.000+0100},
  author = {Gao, Linyi Alex and Wilkinson, Max E. and Strecker, Jonathan and Makarova, Kira S. and Macrae, Rhiannon K. and Koonin, Eugene V. and Zhang, Feng},
  biburl = {https://www.bibsonomy.org/bibtex/268688dc4e80cd8fe18852cd92f0cc872/cryoem_staff},
  doi = {10.1126/science.abm4096},
  interhash = {34f91bbacbce68d13653c081972d99d0},
  intrahash = {68688dc4e80cd8fe18852cd92f0cc872},
  issn = {1095-9203},
  journal = {Science},
  keywords = {2022},
  month = aug,
  number = 6607,
  publisher = {American Association for the Advancement of Science (AAAS)},
  timestamp = {2024-02-07T20:08:34.000+0100},
  title = {Prokaryotic innate immunity through pattern recognition of conserved viral proteins},
  url = {http://dx.doi.org/10.1126/science.abm4096},
  volume = 377,
  year = 2022
}

@article{Valenstein2022,
  abstract = {Mechanistic target of rapamycin complex 1 (mTORC1) controls growth by regulating anabolic and catabolic processes in response to environmental cues, including nutrients1,2. Amino acids signal to mTORC1 through the Rag GTPases, which are regulated by several protein complexes, including GATOR1 and GATOR2. GATOR2, which has five components (WDR24, MIOS, WDR59, SEH1L and SEC13), is required for amino acids to activate mTORC1 and interacts with the leucine and arginine sensors SESN2 and CASTOR1, respectively3--5. Despite this central role in nutrient sensing, GATOR2 remains mysterious as its subunit stoichiometry, biochemical function and structure are unknown. Here we used cryo-electron microscopy to determine the three-dimensional structure of the human GATOR2 complex. We found that GATOR2 adopts a large (1.1{\thinspace}MDa), two-fold symmetric, cage-like architecture, supported by an octagonal scaffold and decorated with eight pairs of WD40 $\beta$-propellers. The scaffold contains two WDR24, four MIOS and two WDR59 subunits circularized via two distinct types of junction involving non-catalytic RING domains and $\alpha$-solenoids. Integration of SEH1L and SEC13 into the scaffold through $\beta$-propeller blade donation stabilizes the GATOR2 complex and reveals an evolutionary relationship to the nuclear pore and membrane-coating complexes6. The scaffold orients the WD40 $\beta$-propeller dimers, which mediate interactions with SESN2, CASTOR1 and GATOR1. Our work reveals the structure of an essential component of the nutrient-sensing machinery and provides a foundation for understanding the function of GATOR2 within the mTORC1 pathway.},
  added-at = {2024-02-07T20:08:06.000+0100},
  author = {Valenstein, Max L. and Rogala, Kacper B. and Lalgudi, Pranav V. and Brignole, Edward J. and Gu, Xin and Saxton, Robert A. and Chantranupong, Lynne and Kolibius, Jonas and Quast, Jan-Philipp and Sabatini, David M.},
  biburl = {https://www.bibsonomy.org/bibtex/254bcc5b691df3b9095cabdf352e777b6/cryoem_staff},
  day = 01,
  doi = {10.1038/s41586-022-04939-z},
  interhash = {dd7d744b0802726d635c773e66159938},
  intrahash = {54bcc5b691df3b9095cabdf352e777b6},
  issn = {1476-4687},
  journal = {Nature},
  keywords = {2022},
  month = jul,
  number = 7919,
  pages = {610--616},
  timestamp = {2024-02-07T20:08:06.000+0100},
  title = {Structure of the nutrient-sensing hub GATOR2},
  url = {https://doi.org/10.1038/s41586-022-04939-z},
  volume = 607,
  year = 2022
}

Mechanistic target of rapamycin complex 1 (mTORC1) controls growth by regulating anabolic and catabolic processes in response to environmental cues, including nutrients1,2. Amino acids signal to mTORC1 through the Rag GTPases, which are regulated by several protein complexes, including GATOR1 and GATOR2. GATOR2, which has five components (WDR24, MIOS, WDR59, SEH1L and SEC13), is required for amino acids to activate mTORC1 and interacts with the leucine and arginine sensors SESN2 and CASTOR1, respectively3–5. Despite this central role in nutrient sensing, GATOR2 remains mysterious as its subunit stoichiometry, biochemical function and structure are unknown. Here we used cryo-electron microscopy to determine the three-dimensional structure of the human GATOR2 complex. We found that GATOR2 adopts a large (1.1þinspaceMDa), two-fold symmetric, cage-like architecture, supported by an octagonal scaffold and decorated with eight pairs of WD40 $β$-propellers. The scaffold contains two WDR24, four MIOS and two WDR59 subunits circularized via two distinct types of junction involving non-catalytic RING domains and $α$-solenoids. Integration of SEH1L and SEC13 into the scaffold through $β$-propeller blade donation stabilizes the GATOR2 complex and reveals an evolutionary relationship to the nuclear pore and membrane-coating complexes6. The scaffold orients the WD40 $β$-propeller dimers, which mediate interactions with SESN2, CASTOR1 and GATOR1. Our work reveals the structure of an essential component of the nutrient-sensing machinery and provides a foundation for understanding the function of GATOR2 within the mTORC1 pathway.

@article{noauthororeditor2022httpsdoiorg103389fmolb2022903148,
  added-at = {2024-02-07T20:07:36.000+0100},
  author = {Levitz, Talya S. and Weckener, Miriam and Fong, Ivan and Naismith, James H. and Drennan, Catherine L. and Brignole, Edward J. and Clare, Daniel K. and Darrow, Michele C.},
  biburl = {https://www.bibsonomy.org/bibtex/2e34b83ab0573e489d86953b624aa0439/cryoem_staff},
  interhash = {51371f982b2d439beeab9363ec6f32da},
  intrahash = {e34b83ab0573e489d86953b624aa0439},
  journal = {Frontiers in Molecular Biosciences},
  keywords = {2022},
  month = {June},
  timestamp = {2024-02-07T20:07:36.000+0100},
  title = {https://doi.org/10.3389/fmolb.2022.903148},
  url = {https://www.frontiersin.org/articles/10.3389/fmolb.2022.903148/full},
  volume = {Volume 9},
  year = 2022
}

@article{Wang_2022,
  added-at = {2024-02-07T20:03:11.000+0100},
  author = {Wang, Xiao and Li, Shanshan and Jun, Hyungmin and John, Torsten and Zhang, Kaiming and Fowler, Hannah and Doye, Jonathan P.K. and Chiu, Wah and Bathe, Mark},
  biburl = {https://www.bibsonomy.org/bibtex/23246ec0a800fb3231178d13782fd1ab1/cryoem_staff},
  doi = {10.1126/sciadv.abn0039},
  interhash = {cd997e7c4fe6d17e975535b0c381b7c6},
  intrahash = {3246ec0a800fb3231178d13782fd1ab1},
  issn = {2375-2548},
  journal = {Science Advances},
  keywords = {2022},
  month = may,
  number = 20,
  publisher = {American Association for the Advancement of Science (AAAS)},
  timestamp = {2024-02-07T20:03:11.000+0100},
  title = {Planar 2D wireframe DNA origami},
  url = {http://dx.doi.org/10.1126/sciadv.abn0039},
  volume = 8,
  year = 2022
}

@article{Chen_2022,
  added-at = {2024-02-07T20:02:45.000+0100},
  author = {Chen, Tianyang and Dou, Jin-Hu and Yang, Luming and Sun, Chenyue and Oppenheim, Julius J. and Li, Jian and Dincă, Mircea},
  biburl = {https://www.bibsonomy.org/bibtex/286bbaaaa4410b6c9369b48f5e63aa899/cryoem_staff},
  doi = {10.1021/jacs.2c00614},
  interhash = {64311df0438dcd3bb4b29159e5f00c77},
  intrahash = {86bbaaaa4410b6c9369b48f5e63aa899},
  issn = {1520-5126},
  journal = {Journal of the American Chemical Society},
  keywords = {2022},
  month = mar,
  number = 12,
  pages = {5583–5593},
  publisher = {American Chemical Society (ACS)},
  timestamp = {2024-02-07T20:02:45.000+0100},
  title = {Dimensionality Modulates Electrical Conductivity in Compositionally Constant One-, Two-, and Three-Dimensional Frameworks},
  url = {http://dx.doi.org/10.1021/jacs.2c00614},
  volume = 144,
  year = 2022
}

@article{Levitz_2022,
  added-at = {2024-02-07T20:02:12.000+0100},
  author = {Levitz, Talya S. and Brignole, Edward J. and Fong, Ivan and Darrow, Michele C. and Drennan, Catherine L.},
  biburl = {https://www.bibsonomy.org/bibtex/245943752a0b1a103c38b76c5039a3fdf/cryoem_staff},
  doi = {10.1016/j.jsb.2021.107825},
  interhash = {c118961e0aafd48394d796bfce79d1ab},
  intrahash = {45943752a0b1a103c38b76c5039a3fdf},
  issn = {1047-8477},
  journal = {Journal of Structural Biology},
  keywords = {2022},
  month = mar,
  number = 1,
  pages = 107825,
  publisher = {Elsevier BV},
  timestamp = {2024-02-07T20:02:12.000+0100},
  title = {Effects of chameleon dispense-to-plunge speed on particle concentration, complex formation, and final resolution: A case study using the Neisseria gonorrhoeae ribonucleotide reductase inactive complex},
  url = {http://dx.doi.org/10.1016/j.jsb.2021.107825},
  volume = 214,
  year = 2022
}

@article{Vasquez_2022,
  added-at = {2024-02-07T20:01:46.000+0100},
  author = {Vasquez, Sheena and Brignole, Edward J. and Marquez, Melissa D. and Perlstein, Deborah L. and Drennan, Catherine L.},
  biburl = {https://www.bibsonomy.org/bibtex/25195af4a1d48804055666f916489886d/cryoem_staff},
  doi = {10.1016/j.bpj.2021.11.518},
  interhash = {26a7632dbd93ad00a870d55ffd30e3cf},
  intrahash = {5195af4a1d48804055666f916489886d},
  issn = {0006-3495},
  journal = {Biophysical Journal},
  keywords = {2022},
  month = feb,
  number = 3,
  pages = {452a},
  publisher = {Elsevier BV},
  timestamp = {2024-02-07T20:01:46.000+0100},
  title = {Cryo-EM structural determination of Met18, a scaffold protein for iron-sulfur protein maturation},
  url = {http://dx.doi.org/10.1016/j.bpj.2021.11.518},
  volume = 121,
  year = 2022
}

@article{Zeng2022,
  abstract = {Polymers that extend covalently in two dimensions have attracted recent attention1,2 as a means of combining the mechanical strength and in-plane energy conduction of conventional two-dimensional (2D) materials3,4 with the low densities, synthetic processability and organic composition of their one-dimensional counterparts. Efforts so far have proven successful in forms that do not allow full realization of these properties, such as polymerization at flat interfaces5,6 or fixation of monomers in immobilized lattices7--9. Another frequently employed synthetic approach is to introduce microscopic reversibility, at the cost of bond stability, to achieve 2D crystals after extensive error correction10,11. Here we demonstrate a homogenous 2D irreversible polycondensation that results in a covalently bonded 2D polymeric material that is chemically stable and highly processable. Further processing yields highly oriented, free-standing films that have a 2D elastic modulus and yield strength of 12.7{\thinspace}{\textpm} 3.8{\thinspace}gigapascals and 488{\thinspace}{\textpm} 57{\thinspace}megapascals, respectively. This synthetic route provides opportunities for 2D materials in applications ranging from composite structures to barrier coating materials.},
  added-at = {2024-02-07T20:01:19.000+0100},
  author = {Zeng, Yuwen and Gordiichuk, Pavlo and Ichihara, Takeo and Zhang, Ge and Sandoz-Rosado, Emil and Wetzel, Eric D. and Tresback, Jason and Yang, Jing and Kozawa, Daichi and Yang, Zhongyue and Kuehne, Matthias and Quien, Michelle and Yuan, Zhe and Gong, Xun and He, Guangwei and Lundberg, Daniel James and Liu, Pingwei and Liu, Albert Tianxiang and Yang, Jing Fan and Kulik, Heather J. and Strano, Michael S.},
  biburl = {https://www.bibsonomy.org/bibtex/2cd33ce3202192f8346aeef776b48f547/cryoem_staff},
  day = 01,
  doi = {10.1038/s41586-021-04296-3},
  interhash = {9d603e7e7020a389a973a0a99feef500},
  intrahash = {cd33ce3202192f8346aeef776b48f547},
  issn = {1476-4687},
  journal = {Nature},
  keywords = {2022},
  month = feb,
  number = 7895,
  pages = {91--95},
  timestamp = {2024-02-07T20:01:19.000+0100},
  title = {Irreversible synthesis of an ultrastrong two-dimensional polymeric material},
  url = {https://doi.org/10.1038/s41586-021-04296-3},
  volume = 602,
  year = 2022
}

Polymers that extend covalently in two dimensions have attracted recent attention1,2 as a means of combining the mechanical strength and in-plane energy conduction of conventional two-dimensional (2D) materials3,4 with the low densities, synthetic processability and organic composition of their one-dimensional counterparts. Efforts so far have proven successful in forms that do not allow full realization of these properties, such as polymerization at flat interfaces5,6 or fixation of monomers in immobilized lattices7–9. Another frequently employed synthetic approach is to introduce microscopic reversibility, at the cost of bond stability, to achieve 2D crystals after extensive error correction10,11. Here we demonstrate a homogenous 2D irreversible polycondensation that results in a covalently bonded 2D polymeric material that is chemically stable and highly processable. Further processing yields highly oriented, free-standing films that have a 2D elastic modulus and yield strength of 12.7þinspace\textpm 3.8þinspacegigapascals and 488þinspace\textpm 57þinspacemegapascals, respectively. This synthetic route provides opportunities for 2D materials in applications ranging from composite structures to barrier coating materials.

@article{Barotov_2021,
  added-at = {2024-02-07T20:00:40.000+0100},
  author = {Barotov, Ulugbek and Klein, Megan D. and Wang, Lili and Bawendi, Moungi G.},
  biburl = {https://www.bibsonomy.org/bibtex/2554b10b625bff4a2bbb641c9cf30697a/cryoem_staff},
  doi = {10.1021/acs.jpcc.1c09033},
  interhash = {bd7230cde34795caf8bc29adfc17cac8},
  intrahash = {554b10b625bff4a2bbb641c9cf30697a},
  issn = {1932-7455},
  journal = {The Journal of Physical Chemistry C},
  keywords = {2021},
  month = dec,
  number = 1,
  pages = {754–763},
  publisher = {American Chemical Society (ACS)},
  timestamp = {2024-02-07T20:00:40.000+0100},
  title = {Designing Highly Luminescent Molecular Aggregates via Bottom-Up Nanoscale Engineering},
  url = {http://dx.doi.org/10.1021/acs.jpcc.1c09033},
  volume = 126,
  year = 2021
}

@article{Banda_2021,
  added-at = {2024-02-07T19:59:59.000+0100},
  author = {Banda, Harish and Dou, Jin‐Hu and Chen, Tianyang and Zhang, Yugang and Dincă, Mircea},
  biburl = {https://www.bibsonomy.org/bibtex/2508b5c0dfc2346c0ee11b66c5a874ba0/cryoem_staff},
  doi = {10.1002/anie.202112811},
  interhash = {9c281e38124be6e504d7ba908d444702},
  intrahash = {508b5c0dfc2346c0ee11b66c5a874ba0},
  issn = {1521-3773},
  journal = {Angewandte Chemie International Edition},
  keywords = {2021},
  month = nov,
  number = 52,
  pages = {27119–27125},
  publisher = {Wiley},
  timestamp = {2024-02-07T19:59:59.000+0100},
  title = {Dual‐Ion Intercalation and High Volumetric Capacitance in a Two‐Dimensional Non‐Porous Coordination Polymer},
  url = {http://dx.doi.org/10.1002/anie.202112811},
  volume = 60,
  year = 2021
}

@article{Schuller2021,
  abstract = {Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE)1--3. These multi-megadalton structures are composed of about thirty different nucleoporins that are distributed in three main substructures (the inner, cytoplasmic and nucleoplasmic rings) around the central transport channel4--6. Here we use cryo-electron tomography on DLD-1 cells that were prepared using cryo-focused-ion-beam milling to generate a structural model for the human NPC in its native environment. We show that---compared with previous human NPC models obtained from purified NEs---the inner ring in our model is substantially wider; the volume of the central channel is increased by 75{\%} and the nucleoplasmic and cytoplasmic rings are reorganized. Moreover, the NPC membrane exhibits asymmetry around the inner-ring complex. Using targeted degradation of Nup96, a scaffold nucleoporin of the cytoplasmic and nucleoplasmic rings, we observe the interdependence of each ring in modulating the central channel and maintaining membrane asymmetry. Our findings highlight the inherent flexibility of the NPC and suggest that the cellular environment has a considerable influence on NPC dimensions and architecture.},
  added-at = {2024-02-07T19:59:25.000+0100},
  author = {Schuller, Anthony P. and Wojtynek, Matthias and Mankus, David and Tatli, Meltem and Kronenberg-Tenga, Rafael and Regmi, Saroj G. and Dip, Phat V. and Lytton-Jean, Abigail K. R. and Brignole, Edward J. and Dasso, Mary and Weis, Karsten and Medalia, Ohad and Schwartz, Thomas U.},
  biburl = {https://www.bibsonomy.org/bibtex/2ad77071b0e3de43ce4dfe45af734162f/cryoem_staff},
  day = 01,
  doi = {10.1038/s41586-021-03985-3},
  interhash = {c2ea612e346e9829273f92ecf6199ab1},
  intrahash = {ad77071b0e3de43ce4dfe45af734162f},
  issn = {1476-4687},
  journal = {Nature},
  keywords = {2021},
  month = oct,
  number = 7882,
  pages = {667--671},
  timestamp = {2024-02-07T19:59:25.000+0100},
  title = {The cellular environment shapes the nuclear pore complex architecture},
  url = {https://doi.org/10.1038/s41586-021-03985-3},
  volume = 598,
  year = 2021
}

Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE)1–3. These multi-megadalton structures are composed of about thirty different nucleoporins that are distributed in three main substructures (the inner, cytoplasmic and nucleoplasmic rings) around the central transport channel4–6. Here we use cryo-electron tomography on DLD-1 cells that were prepared using cryo-focused-ion-beam milling to generate a structural model for the human NPC in its native environment. We show that—compared with previous human NPC models obtained from purified NEs—the inner ring in our model is substantially wider; the volume of the central channel is increased by 75% and the nucleoplasmic and cytoplasmic rings are reorganized. Moreover, the NPC membrane exhibits asymmetry around the inner-ring complex. Using targeted degradation of Nup96, a scaffold nucleoporin of the cytoplasmic and nucleoplasmic rings, we observe the interdependence of each ring in modulating the central channel and maintaining membrane asymmetry. Our findings highlight the inherent flexibility of the NPC and suggest that the cellular environment has a considerable influence on NPC dimensions and architecture.

@article{D1EN00002K,
  abstract = {Self-assembled nanoribbons from small molecule amphiphiles with a structural domain to impart mechanical stability and chelating head groups are reported for the remediation of lead from contaminated water. The nanoribbons{'} remediation capacity is affected by pH and the presence of competing cations{,} and can be modulated by head group choice.},
  added-at = {2024-02-07T19:58:32.000+0100},
  author = {Christoff-Tempesta, Ty and Ortony, Julia H.},
  biburl = {https://www.bibsonomy.org/bibtex/262c077405709647a5065a8a15af56558/cryoem_staff},
  doi = {10.1039/D1EN00002K},
  interhash = {0239f0def0b98555a75a40118263fffd},
  intrahash = {62c077405709647a5065a8a15af56558},
  journal = {Environ. Sci.: Nano},
  keywords = {2021},
  number = 6,
  pages = {1536-1542},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2024-02-07T19:58:32.000+0100},
  title = {Emerging investigator series: aramid amphiphile nanoribbons for the remediation of lead from contaminated water},
  url = {http://dx.doi.org/10.1039/D1EN00002K},
  volume = 8,
  year = 2021
}

Self-assembled nanoribbons from small molecule amphiphiles with a structural domain to impart mechanical stability and chelating head groups are reported for the remediation of lead from contaminated water. The nanoribbons' remediation capacity is affected by pH and the presence of competing cations, and can be modulated by head group choice.

@article{Dou2021,
  abstract = {Electrically conducting 2D metal--organic frameworks (MOFs) have attracted considerable interest, as their hexagonal 2D lattices mimic graphite and other 2D van der Waals stacked materials. However, understanding their intrinsic properties remains a challenge because their crystals are too small or of too poor quality for crystal structure determination. Here, we report atomically precise structures of a family of 2D $\pi$-conjugated MOFs derived from large single crystals of sizes up to 200{\thinspace}$\mu$m, allowing atomic-resolution analysis by a battery of high-resolution diffraction techniques. A designed ligand core rebalances the in-plane and out-of-plane interactions that define anisotropic crystal growth. We report two crystal structure types exhibiting analogous 2D honeycomb-like sheets but distinct packing modes and pore contents. Single-crystal electrical transport measurements distinctively demonstrate anisotropic transport normal and parallel to the $\pi$-conjugated sheets, revealing a clear correlation between absolute conductivity and the nature of the metal cation and 2D sheet packing motif.},
  added-at = {2024-02-07T19:57:26.000+0100},
  author = {Dou, Jin-Hu and Arguilla, Maxx Q. and Luo, Yi and Li, Jian and Zhang, Weizhe and Sun, Lei and Mancuso, Jenna L. and Yang, Luming and Chen, Tianyang and Parent, Lucas R. and Skorupskii, Grigorii and Libretto, Nicole J. and Sun, Chenyue and Yang, Min Chieh and Dip, Phat Vinh and Brignole, Edward J. and Miller, Jeffrey T. and Kong, Jing and Hendon, Christopher H. and Sun, Junliang and Dinc{\u{a}}, Mircea},
  biburl = {https://www.bibsonomy.org/bibtex/2697b81a2bfd6b0cc10c0995bce19b825/cryoem_staff},
  day = 01,
  doi = {10.1038/s41563-020-00847-7},
  interhash = {09834de4bd039d6570d477f02247a74f},
  intrahash = {697b81a2bfd6b0cc10c0995bce19b825},
  issn = {1476-4660},
  journal = {Nature Materials},
  keywords = {2021},
  month = feb,
  number = 2,
  pages = {222--228},
  timestamp = {2024-02-07T19:58:45.000+0100},
  title = {Atomically precise single-crystal structures of electrically conducting 2D metal--organic frameworks},
  url = {https://doi.org/10.1038/s41563-020-00847-7},
  volume = 20,
  year = 2021
}

Electrically conducting 2D metal–organic frameworks (MOFs) have attracted considerable interest, as their hexagonal 2D lattices mimic graphite and other 2D van der Waals stacked materials. However, understanding their intrinsic properties remains a challenge because their crystals are too small or of too poor quality for crystal structure determination. Here, we report atomically precise structures of a family of 2D $π$-conjugated MOFs derived from large single crystals of sizes up to 200þinspace$μ$m, allowing atomic-resolution analysis by a battery of high-resolution diffraction techniques. A designed ligand core rebalances the in-plane and out-of-plane interactions that define anisotropic crystal growth. We report two crystal structure types exhibiting analogous 2D honeycomb-like sheets but distinct packing modes and pore contents. Single-crystal electrical transport measurements distinctively demonstrate anisotropic transport normal and parallel to the $π$-conjugated sheets, revealing a clear correlation between absolute conductivity and the nature of the metal cation and 2D sheet packing motif.

@article{Rogala_2019,
  added-at = {2024-02-07T19:53:13.000+0100},
  author = {Rogala, Kacper B. and Gu, Xin and Kedir, Jibril F. and Abu-Remaileh, Monther and Bianchi, Laura F. and Bottino, Alexia M. S. and Dueholm, Rikke and Niehaus, Anna and Overwijn, Daan and Fils, Ange-Célia Priso and Zhou, Sherry X. and Leary, Daniel and Laqtom, Nouf N. and Brignole, Edward J. and Sabatini, David M.},
  biburl = {https://www.bibsonomy.org/bibtex/2e517e4f140810812440b7545864b2aae/cryoem_staff},
  doi = {10.1126/science.aay0166},
  interhash = {ec5f6787345ce82f303f41da141daa1c},
  intrahash = {e517e4f140810812440b7545864b2aae},
  issn = {1095-9203},
  journal = {Science},
  keywords = {2019},
  month = oct,
  number = 6464,
  pages = {468–475},
  publisher = {American Association for the Advancement of Science (AAAS)},
  timestamp = {2024-02-07T19:53:13.000+0100},
  title = {Structural basis for the docking of mTORC1 on the lysosomal surface},
  url = {http://dx.doi.org/10.1126/science.aay0166},
  volume = 366,
  year = 2019
}