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Decoding optimal ligand design for multicomponent condensates

Biomolecular condensates form via multivalent interactions among key macromolecules and are regulated through ligand binding and/or post-translational modifications. One such modification is ubiquitination, the covalent addition of ubiquitin (Ub) or polyubiquitin chains to target macromolecules for...

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Autores principales: Galagedera, Sarasi K. K., Dao, Thuy P., Enos, Suzanne E., Chaudhuri, Antara, Schmit, Jeremy D., Castañeda, Carlos A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10054939/
https://www.ncbi.nlm.nih.gov/pubmed/36993708
http://dx.doi.org/10.1101/2023.03.13.532222
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author Galagedera, Sarasi K. K.
Dao, Thuy P.
Enos, Suzanne E.
Chaudhuri, Antara
Schmit, Jeremy D.
Castañeda, Carlos A.
author_facet Galagedera, Sarasi K. K.
Dao, Thuy P.
Enos, Suzanne E.
Chaudhuri, Antara
Schmit, Jeremy D.
Castañeda, Carlos A.
author_sort Galagedera, Sarasi K. K.
collection PubMed
description Biomolecular condensates form via multivalent interactions among key macromolecules and are regulated through ligand binding and/or post-translational modifications. One such modification is ubiquitination, the covalent addition of ubiquitin (Ub) or polyubiquitin chains to target macromolecules for various cellular processes. Specific interactions between polyubiquitin chains and partner proteins, including hHR23B, NEMO, and UBQLN2, regulate condensate assembly or disassembly. Here, we used a library of designed polyubiquitin hubs and UBQLN2 as model systems for determining the driving forces of ligand-mediated phase transitions. Perturbations to the UBQLN2-binding surface of Ub or deviations from the optimal spacing between Ub units reduce the ability of hubs to modulate UBQLN2 phase behavior. By developing an analytical model that accurately described the effects of different hubs on UBQLN2 phase diagrams, we determined that introduction of Ub to UBQLN2 condensates incurs a significant inclusion energetic penalty. This penalty antagonizes the ability of polyUb hubs to scaffold multiple UBQLN2 molecules and cooperatively amplify phase separation. Importantly, the extent to which polyubiquitin hubs can promote UBQLN2 phase separation are encoded in the spacings between Ub units as found for naturally-occurring chains of different linkages and designed chains of different architectures, thus illustrating how the ubiquitin code regulates functionality via the emergent properties of the condensate. We expect our findings to extend to other condensates necessitating the consideration of ligand properties, including concentration, valency, affinity, and spacing between binding sites in studies and designs of condensates.
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spelling pubmed-100549392023-03-30 Decoding optimal ligand design for multicomponent condensates Galagedera, Sarasi K. K. Dao, Thuy P. Enos, Suzanne E. Chaudhuri, Antara Schmit, Jeremy D. Castañeda, Carlos A. bioRxiv Article Biomolecular condensates form via multivalent interactions among key macromolecules and are regulated through ligand binding and/or post-translational modifications. One such modification is ubiquitination, the covalent addition of ubiquitin (Ub) or polyubiquitin chains to target macromolecules for various cellular processes. Specific interactions between polyubiquitin chains and partner proteins, including hHR23B, NEMO, and UBQLN2, regulate condensate assembly or disassembly. Here, we used a library of designed polyubiquitin hubs and UBQLN2 as model systems for determining the driving forces of ligand-mediated phase transitions. Perturbations to the UBQLN2-binding surface of Ub or deviations from the optimal spacing between Ub units reduce the ability of hubs to modulate UBQLN2 phase behavior. By developing an analytical model that accurately described the effects of different hubs on UBQLN2 phase diagrams, we determined that introduction of Ub to UBQLN2 condensates incurs a significant inclusion energetic penalty. This penalty antagonizes the ability of polyUb hubs to scaffold multiple UBQLN2 molecules and cooperatively amplify phase separation. Importantly, the extent to which polyubiquitin hubs can promote UBQLN2 phase separation are encoded in the spacings between Ub units as found for naturally-occurring chains of different linkages and designed chains of different architectures, thus illustrating how the ubiquitin code regulates functionality via the emergent properties of the condensate. We expect our findings to extend to other condensates necessitating the consideration of ligand properties, including concentration, valency, affinity, and spacing between binding sites in studies and designs of condensates. Cold Spring Harbor Laboratory 2023-04-25 /pmc/articles/PMC10054939/ /pubmed/36993708 http://dx.doi.org/10.1101/2023.03.13.532222 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
Galagedera, Sarasi K. K.
Dao, Thuy P.
Enos, Suzanne E.
Chaudhuri, Antara
Schmit, Jeremy D.
Castañeda, Carlos A.
Decoding optimal ligand design for multicomponent condensates
title Decoding optimal ligand design for multicomponent condensates
title_full Decoding optimal ligand design for multicomponent condensates
title_fullStr Decoding optimal ligand design for multicomponent condensates
title_full_unstemmed Decoding optimal ligand design for multicomponent condensates
title_short Decoding optimal ligand design for multicomponent condensates
title_sort decoding optimal ligand design for multicomponent condensates
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10054939/
https://www.ncbi.nlm.nih.gov/pubmed/36993708
http://dx.doi.org/10.1101/2023.03.13.532222
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