IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-35370-7.html
   My bibliography  Save this article

Condensates formed by prion-like low-complexity domains have small-world network structures and interfaces defined by expanded conformations

Author

Listed:
  • Mina Farag

    (Washington University in St. Louis)

  • Samuel R. Cohen

    (Washington University in St. Louis)

  • Wade M. Borcherds

    (St. Jude Children’s Research Hospital)

  • Anne Bremer

    (St. Jude Children’s Research Hospital)

  • Tanja Mittag

    (St. Jude Children’s Research Hospital)

  • Rohit V. Pappu

    (Washington University in St. Louis)

Abstract

Biomolecular condensates form via coupled associative and segregative phase transitions of multivalent associative macromolecules. Phase separation coupled to percolation is one example of such transitions. Here, we characterize molecular and mesoscale structural descriptions of condensates formed by intrinsically disordered prion-like low complexity domains (PLCDs). These systems conform to sticker-and-spacers architectures. Stickers are cohesive motifs that drive associative interactions through reversible crosslinking and spacers affect the cooperativity of crosslinking and overall macromolecular solubility. Our computations reproduce experimentally measured sequence-specific phase behaviors of PLCDs. Within simulated condensates, networks of reversible inter-sticker crosslinks organize PLCDs into small-world topologies. The overall dimensions of PLCDs vary with spatial location, being most expanded at and preferring to be oriented perpendicular to the interface. Our results demonstrate that even simple condensates with one type of macromolecule feature inhomogeneous spatial organizations of molecules and interfacial features that likely prime them for biochemical activity.

Suggested Citation

  • Mina Farag & Samuel R. Cohen & Wade M. Borcherds & Anne Bremer & Tanja Mittag & Rohit V. Pappu, 2022. "Condensates formed by prion-like low-complexity domains have small-world network structures and interfaces defined by expanded conformations," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-35370-7
    DOI: 10.1038/s41467-022-35370-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-35370-7
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-35370-7?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Jiang, R. & Murthy, D.N.P., 2011. "A study of Weibull shape parameter: Properties and significance," Reliability Engineering and System Safety, Elsevier, vol. 96(12), pages 1619-1626.
    2. Duncan J. Watts & Steven H. Strogatz, 1998. "Collective dynamics of ‘small-world’ networks," Nature, Nature, vol. 393(6684), pages 440-442, June.
    3. Ibraheem Alshareedah & Mahdi Muhammad Moosa & Matthew Pham & Davit A. Potoyan & Priya R. Banerjee, 2021. "Programmable viscoelasticity in protein-RNA condensates with disordered sticker-spacer polypeptides," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    4. Pilong Li & Sudeep Banjade & Hui-Chun Cheng & Soyeon Kim & Baoyu Chen & Liang Guo & Marc Llaguno & Javoris V. Hollingsworth & David S. King & Salman F. Banani & Paul S. Russo & Qiu-Xing Jiang & B. Tra, 2012. "Phase transitions in the assembly of multivalent signalling proteins," Nature, Nature, vol. 483(7389), pages 336-340, March.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Furqan Dar & Samuel R. Cohen & Diana M. Mitrea & Aaron H. Phillips & Gergely Nagy & Wellington C. Leite & Christopher B. Stanley & Jeong-Mo Choi & Richard W. Kriwacki & Rohit V. Pappu, 2024. "Biomolecular condensates form spatially inhomogeneous network fluids," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Min Lee & Hyungseok C. Moon & Hyeonjeong Jeong & Dong Wook Kim & Hye Yoon Park & Yongdae Shin, 2024. "Optogenetic control of mRNA condensation reveals an intimate link between condensate material properties and functions," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    3. Andres R. Tejedor & Ignacio Sanchez-Burgos & Maria Estevez-Espinosa & Adiran Garaizar & Rosana Collepardo-Guevara & Jorge Ramirez & Jorge R. Espinosa, 2022. "Protein structural transitions critically transform the network connectivity and viscoelasticity of RNA-binding protein condensates but RNA can prevent it," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    4. Mrityunjoy Kar & Laura T. Vogel & Gaurav Chauhan & Suren Felekyan & Hannes Ausserwöger & Timothy J. Welsh & Furqan Dar & Anjana R. Kamath & Tuomas P. J. Knowles & Anthony A. Hyman & Claus A. M. Seidel, 2024. "Solutes unmask differences in clustering versus phase separation of FET proteins," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    5. Miriam Linsenmeier & Maria Hondele & Fulvio Grigolato & Eleonora Secchi & Karsten Weis & Paolo Arosio, 2022. "Dynamic arrest and aging of biomolecular condensates are modulated by low-complexity domains, RNA and biochemical activity," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    6. Huan Wang & Chuang Ma & Han-Shuang Chen & Ying-Cheng Lai & Hai-Feng Zhang, 2022. "Full reconstruction of simplicial complexes from binary contagion and Ising data," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    7. Vinayak, & Raghuvanshi, Adarsh & kshitij, Avinash, 2023. "Signatures of capacity development through research collaborations in artificial intelligence and machine learning," Journal of Informetrics, Elsevier, vol. 17(1).
    8. Supriya Tiwari & Pallavi Basu, 2024. "Quasi-randomization tests for network interference," Papers 2403.16673, arXiv.org, revised Oct 2024.
    9. Anzhi Sheng & Qi Su & Aming Li & Long Wang & Joshua B. Plotkin, 2023. "Constructing temporal networks with bursty activity patterns," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    10. Shuangcheng Alivia Wu & Chenchen Shen & Xiaoqiong Wei & Xiawei Zhang & Siwen Wang & Xinxin Chen & Mauricio Torres & You Lu & Liangguang Leo Lin & Huilun Helen Wang & Allen H. Hunter & Deyu Fang & Shen, 2023. "The mechanisms to dispose of misfolded proteins in the endoplasmic reticulum of adipocytes," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    11. Samrachana Adhikari & Beau Dabbs, 2018. "Social Network Analysis in R: A Software Review," Journal of Educational and Behavioral Statistics, , vol. 43(2), pages 225-253, April.
    12. Wang, Xiaojie & Slamu, Wushour & Guo, Wenqiang & Wang, Sixiu & Ren, Yan, 2022. "A novel semi local measure of identifying influential nodes in complex networks," Chaos, Solitons & Fractals, Elsevier, vol. 158(C).
    13. Lin, Dan & Wu, Jiajing & Xuan, Qi & Tse, Chi K., 2022. "Ethereum transaction tracking: Inferring evolution of transaction networks via link prediction," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 600(C).
    14. Zheng Shen & Daxiao Sun & Adriana Savastano & Sára Joana Varga & Maria-Sol Cima-Omori & Stefan Becker & Alf Honigmann & Markus Zweckstetter, 2023. "Multivalent Tau/PSD-95 interactions arrest in vitro condensates and clusters mimicking the postsynaptic density," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    15. Ferreira, D.S.R. & Ribeiro, J. & Oliveira, P.S.L. & Pimenta, A.R. & Freitas, R.P. & Dutra, R.S. & Papa, A.R.R. & Mendes, J.F.F., 2022. "Spatiotemporal analysis of earthquake occurrence in synthetic and worldwide data," Chaos, Solitons & Fractals, Elsevier, vol. 165(P2).
    16. Mario V. Tomasello & Mauro Napoletano & Antonios Garas & Frank Schweitzer, 2017. "The rise and fall of R&D networks," Industrial and Corporate Change, Oxford University Press and the Associazione ICC, vol. 26(4), pages 617-646.
    17. Beatrice Ramm & Dominik Schumacher & Andrea Harms & Tamara Heermann & Philipp Klos & Franziska Müller & Petra Schwille & Lotte Søgaard-Andersen, 2023. "Biomolecular condensate drives polymerization and bundling of the bacterial tubulin FtsZ to regulate cell division," Nature Communications, Nature, vol. 14(1), pages 1-24, December.
    18. Qinghu Liao & Wenwen Dong & Boxin Zhao, 2023. "A New Strategy to Solve “the Tragedy of the Commons” in Sustainable Grassland Ecological Compensation: Experience from Inner Mongolia, China," Sustainability, MDPI, vol. 15(12), pages 1-24, June.
    19. Dewan, Isha & Dijoux, Yann, 2015. "Modelling repairable systems with an early life under competing risks and asymmetric virtual age," Reliability Engineering and System Safety, Elsevier, vol. 144(C), pages 215-224.
    20. Xinyu Huang & Dongming Chen & Dongqi Wang & Tao Ren, 2020. "MINE: Identifying Top- k Vital Nodes in Complex Networks via Maximum Influential Neighbors Expansion," Mathematics, MDPI, vol. 8(9), pages 1-25, August.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-35370-7. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.