The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Single-domain antibody inhibitors target the coiled coil arms of the Bacillus subtilis SMC complex
Open accessPublished version of a preprint
Abstract
Synthetic nanobodies—also called sybodies—have proven valuable for stabilizing conformations of purified proteins, advancing structural and functional studies for example of transmembrane proteins. However, their utility in modulating protein function in living cells has remained less well explored. Structural Maintenance of Chromosomes (SMC) complexes facilitate chromosome organization, a fundamental process in all domains of life. In this study, we target the bacterial SMC complex, Smc-ScpAB, in Bacillus subtilis with synthetic nanobodies, aiming to identify key functional regions of the protein complex in a largely unbiased manner. We first isolate sybodies that specifically bind purified Smc-ScpAB and then express them in B. subtilis to select binders capable of disrupting Smc-ScpAB function, leading to chromosome segregation defects and cell death. Mapping and biochemical characterization show that the 14 disruptive sybodies belong to one of three library designs, target the Smc subunit near the same coiled coil arm interface and modulate its ATPase activity in two principal ways, highlighting the mid-region of the Smc coiled coil as critical feature of the SMC-DNA folding process. These findings underscore the potential of sybodies—and, by extension, designed binders—as versatile tools for probing dynamic protein function in living cells.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Bacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus
Wang, X., Brandão, H. B., Le, T. B. K., Laub, M. T., & Rudner, D. Z. (2017) · Science · doi:10.1126/science.aai8982 · Cited by 293
Flagged first, then by citations
Research works printed but not linked: 32
- Bock, 2022, A joint-ParB interface promotes Smc DNA recruitment, Cell Reports, 40, 10.1016/j.celrep.2022.111273 · DOI · Paper page
- Bürmann, 2013, An asymmetric SMC-kleisin bridge in prokaryotic condensin, Nature Structural & Molecular Biology, 20, 371, 10.1038/nsmb.2488 · DOI
- Bürmann, 2015, SMC condensin: promoting cohesion of replicon arms, Nature Structural & Molecular Biology, 22, 653, 10.1038/nsmb.3082 · DOI
- Bürmann, 2017, Tuned SMC arms drive chromosomal loading of prokaryotic condensin, Molecular Cell, 65, 861, 10.1016/j.molcel.2017.01.026 · DOI
- Cutler, 2022, Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation, Nature Methods, 19, 1438, 10.1038/s41592-022-01639-4 · DOI
- Deneka, 2021, Allosteric modulation of LRRC8 channels by targeting their cytoplasmic domains, Nature Communications, 12, 10.1038/s41467-021-25742-w · DOI
- Dénéréaz, 2024, BactEXTRACT: an R Shiny app to quickly extract, plot and analyse bacterial growth and gene expression data, Access Microbiology, 6, 10.1099/acmi.0.000742.v3 · DOI
- Diebold-Durand, 2017, Structure of full-length SMC and rearrangements required for chromosome organization, Molecular Cell, 67, 334, 10.1016/j.molcel.2017.06.010 · DOI
- Diebold-Durand, 2019, High-throughput allelic replacement screening in Bacillus subtilis, Methods in Molecular Biology, 2004, 49, 10.1007/978-1-4939-9520-2_5 · DOI
- Dominguez Mantes, 2025, Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression, Nature Methods, 22, 1495, 10.1038/s41592-025-02662-x · DOI
- Gabler, 2020, Protein sequence analysis using the MPI bioinformatics toolkit, Current Protocols in Bioinformatics, 72, 10.1002/cpbi.108 · DOI · Paper page
- Gruber, 2009, Recruitment of condensin to replication origin regions by ParB/SpoOJ promotes chromosome segregation in B. subtilis, Cell, 137, 685, 10.1016/j.cell.2009.02.035 · DOI
- Gruber, 2014, Interlinked sister chromosomes arise in the absence of condensin during fast replication in B. subtilis, Current Biology, 24, 293, 10.1016/j.cub.2013.12.049 · DOI
- Hirano, 2004, Positive and negative regulation of SMC-DNA interactions by ATP and accessory proteins, The EMBO Journal, 23, 2664, 10.1038/sj.emboj.7600264 · DOI
- Hutter, 2019, The extracellular gate shapes the energy profile of an ABC exporter, Nature Communications, 10, 10.1038/s41467-019-09892-6 · DOI
- Kruse, 2013, Activation and allosteric modulation of a muscarinic acetylcholine receptor, Nature, 504, 101, 10.1038/nature12735 · DOI
- Liu, 2025, The SMC hinge is a selective gate for obstacle bypass, Nature Communications, 16, 10.1038/s41467-025-65408-5 · DOI
- Marko, 2019, DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes, Nucleic Acids Research, 47, 6956, 10.1093/nar/gkz497 · DOI
- Minnen, 2016, Control of Smc coiled coil architecture by the ATPase heads facilitates targeting to chromosomal ParB/parS and release onto flanking DNA, Cell Reports, 14, 2003, 10.1016/j.celrep.2016.01.066 · DOI
- Pacesa, 2025, One-shot design of functional protein binders with BindCraft, Nature, 646, 483, 10.1038/s41586-025-09429-6 · DOI
- Rasmussen, 2011, Structure of a nanobody-stabilized active state of the β(2) adrenoceptor, Nature, 469, 175, 10.1038/nature09648 · DOI
- Seeger, 2012, Tuning the drug efflux activity of an ABC transporter in vivo by in vitro selected DARPin binders, PLOS ONE, 7, 10.1371/journal.pone.0037845 · DOI
- Soh, 2015, Molecular basis for SMC rod formation and its dissolution upon DNA binding, Molecular Cell, 57, 290, 10.1016/j.molcel.2014.11.023 · DOI
- Stringer, 2021, Cellpose: a generalist algorithm for cellular segmentation, Nature Methods, 18, 100, 10.1038/s41592-020-01018-x · DOI · Paper page
- Sullivan, 2009, Recruitment of SMC by ParB-parS organizes the origin region and promotes efficient chromosome segregation, Cell, 137, 697, 10.1016/j.cell.2009.04.044 · DOI
- Vazquez Nunez, 2019, Transient DNA occupancy of the SMC interarm space in prokaryotic condensin, Molecular Cell, 75, 209, 10.1016/j.molcel.2019.05.001 · DOI
- Vazquez Nunez, 2021, Gradual opening of Smc arms in prokaryotic condensin, Cell Reports, 35, 10.1016/j.celrep.2021.109051 · DOI
- Wang, 2014, The SMC condensin complex is required for origin segregation in Bacillus subtilis, Current Biology, 24, 287, 10.1016/j.cub.2013.11.050 · DOI
- Wilhelm, 2025, SMC condensin entraps chromosomal DNA by an ATP hydrolysis dependent loading mechanism in Bacillus subtilis, eLife, 13, 10.7554/eLife.06659 · DOI
- Yatskevich, 2019, Organization of chromosomal DNA by SMC complexes, Annual Review of Genetics, 53, 445, 10.1146/annurev-genet-112618-043633 · DOI
- Zimmermann, 2018, Synthetic single domain antibodies for the conformational trapping of membrane proteins, eLife, 7, 10.7554/eLife.34317 · DOI
- Zimmermann, 2020, Generation of synthetic nanobodies against delicate proteins, Nature Protocols, 15, 1707, 10.1038/s41596-020-0304-x · DOI
Metadata
- Authors
- Gosselin, O. J., Taschner, M., Huber-Hürlimann, L. M., Seeger, M. A., & Gruber, S.
- Affiliations
- University of Lausanne (CH)
- Institute of Medical Microbiology, University of Zurich
- University of Zurich (CH)
- Corresponding author
- Gruber, Stephan
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2026-05-19
- Volume
- 15
- ISSN
- 2050-084X (ISSN-L)
- OpenAlex
- W4415349225
- Cited by
- 0
- References
- 2
- FWCI
- 0.00
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- eLife (acceptedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- IRIS (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich)
- Funders
- HORIZON EUROPE European Research Council (724482)
- Swiss National Science Foundation (310030_215138)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- SMC complex, Bacillus subtilis, coiled coil, DNA loop extrusion, chromosome segregation, ATPase activity, protein function modulation, nanobodies, DNA folding
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
