Ion binding with charge inversion combined with screening modulates DEAD box helicase phase transitions

Michael D. Crabtree; Jack Holland; Arvind S. Pillai; Purnima S. Kompella; Leon Babl; Noah N. Turner; James T. Eaton; Georg K. A. Hochberg; Dirk G. A. L. Aarts; Christina Redfield; Andrew J. Baldwin; Timothy J. Nott

doi:10.1016/j.celrep.2023.113375

Ion binding with charge inversion combined with screening modulates DEAD box helicase phase transitions

Michael D. Crabtree, Jack Holland, Arvind S. Pillai, Purnima S. Kompella, Leon Babl, Noah N. Turner, James T. Eaton, Georg K. A. Hochberg, Dirk G. A. L. Aarts, Christina Redfield, Andrew J. Baldwin^*, Timothy J. Nott^*

^*Corresponding author for this work

Chemistry

Research output: Contribution to journal › Article › peer-review

5 Citations (Scopus)

Abstract

Membraneless organelles, or biomolecular condensates, enable cells to compartmentalize material and processes into unique biochemical environments. While specific, attractive molecular interactions are known to stabilize biomolecular condensates, repulsive interactions, and the balance between these opposing forces, are largely unexplored. Here, we demonstrate that repulsive and attractive electrostatic interactions regulate condensate stability, internal mobility, interfaces, and selective partitioning of molecules both in vitro and in cells. We find that signaling ions, such as calcium, alter repulsions between model Ddx3 and Ddx4 condensate proteins by directly binding to negatively charged amino acid sidechains and effectively inverting their charge, in a manner fundamentally dissimilar to electrostatic screening. Using a polymerization model combined with generalized stickers and spacers, we accurately quantify and predict condensate stability over a wide range of pH, salt concentrations, and amino acid sequences. Our model provides a general quantitative treatment for understanding how charge and ions reversibly control condensate stability.

Original language	English
Article number	113375
Journal	Cell Reports
Volume	42
Issue number	11
Early online date	18 Nov 2023
DOIs	https://doi.org/10.1016/j.celrep.2023.113375
Publication status	Published - 28 Nov 2023

Keywords

intrinsically disordered protein
phase transition
multivalent ions
ion binding
transition temperature
net charge
membraneless organelles
biomolecular condensates
RNA helicase
Ca2+

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Crabtree, M. D., Holland, J., Pillai, A. S., Kompella, P. S., Babl, L., Turner, N. N., Eaton, J. T., Hochberg, G. K. A., Aarts, D. G. A. L., Redfield, C., Baldwin, A. J., & Nott, T. J. (2023). Ion binding with charge inversion combined with screening modulates DEAD box helicase phase transitions. Cell Reports, 42(11), Article 113375. https://doi.org/10.1016/j.celrep.2023.113375

@article{faacea58ce204df7823f28e413e0b758,

title = "Ion binding with charge inversion combined with screening modulates DEAD box helicase phase transitions",

abstract = "Membraneless organelles, or biomolecular condensates, enable cells to compartmentalize material and processes into unique biochemical environments. While specific, attractive molecular interactions are known to stabilize biomolecular condensates, repulsive interactions, and the balance between these opposing forces, are largely unexplored. Here, we demonstrate that repulsive and attractive electrostatic interactions regulate condensate stability, internal mobility, interfaces, and selective partitioning of molecules both in vitro and in cells. We find that signaling ions, such as calcium, alter repulsions between model Ddx3 and Ddx4 condensate proteins by directly binding to negatively charged amino acid sidechains and effectively inverting their charge, in a manner fundamentally dissimilar to electrostatic screening. Using a polymerization model combined with generalized stickers and spacers, we accurately quantify and predict condensate stability over a wide range of pH, salt concentrations, and amino acid sequences. Our model provides a general quantitative treatment for understanding how charge and ions reversibly control condensate stability.",

keywords = "intrinsically disordered protein, phase transition, multivalent ions, ion binding, transition temperature, net charge, membraneless organelles, biomolecular condensates, RNA helicase, Ca2+",

author = "Crabtree, {Michael D.} and Jack Holland and Pillai, {Arvind S.} and Kompella, {Purnima S.} and Leon Babl and Turner, {Noah N.} and Eaton, {James T.} and Hochberg, {Georg K. A.} and Aarts, {Dirk G. A. L.} and Christina Redfield and Baldwin, {Andrew J.} and Nott, {Timothy J.}",

note = "Funding Information: M.D.C. and T.J.N. thank Micron Oxford for microscopy support and M. Maj for support with flow cytometry experiments. T.J.N. thanks F. Barr and members of the Barr group for the gift of HeLa cells and support with tissue culture. We thank M. Krishnan for discussions on charge-inversion and seeing the significance of this mechanism in our data. We thank the Engineering and Physical Sciences Research Council (EPSRC) (EP/R029849/1) and the Wellcome Institutional Strategic Support Fund, John Fell Fund, and Edward Penley Abraham Cephalosporin Fund at the University of Oxford for funding the 950 MHz NMR facility. A.J.B. is supported by ERC grant 101002859 . For the purpose of open access, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission. Funding for this work came from a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant 202320/Z/16/Z ) awarded to T.J.N. T.J.N. and M.D.C. thank New College, Oxford, for support. L.B. thanks Studienstiftung des deutschen Volkes, and J.H. acknowledges the Synthetic Biology Centre for Doctoral Training (EPSRC grant EP/L016494/1) for support. G.K.A.H. is support by the Max Planck Society. Funding Information: M.D.C. and T.J.N. thank Micron Oxford for microscopy support and M. Maj for support with flow cytometry experiments. T.J.N. thanks F. Barr and members of the Barr group for the gift of HeLa cells and support with tissue culture. We thank M. Krishnan for discussions on charge-inversion and seeing the significance of this mechanism in our data. We thank the Engineering and Physical Sciences Research Council (EPSRC) (EP/R029849/1) and the Wellcome Institutional Strategic Support Fund, John Fell Fund, and Edward Penley Abraham Cephalosporin Fund at the University of Oxford for funding the 950 MHz NMR facility. A.J.B. is supported by ERC grant 101002859. For the purpose of open access, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission. Funding for this work came from a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant 202320/Z/16/Z) awarded to T.J.N. T.J.N. and M.D.C. thank New College, Oxford, for support. L.B. thanks Studienstiftung des deutschen Volkes, and J.H. acknowledges the Synthetic Biology Centre for Doctoral Training (EPSRC grant EP/L016494/1) for support. G.K.A.H. is support by the Max Planck Society. Conceptualization, M.D.C. and T.J.N.; methodology, M.D.C. and A.J.B.; resources, J.T.E. D.G.A.L.A. and C.R.; data curation, C.R.; investigation, M.D.C. J.H. A.S.P. P.S.K. L.B. N.N.T. and T.J.N.; formal analysis, M.D.C. J.H. A.S.P. A.J.B. and T.J.N.; visualization, M.D.C. A.J.B. and T.J.N.; writing – original draft, M.D.C.; writing – review & editing, J.H. G.K.A.H. D.G.A.L.A. A.J.B. and T.J.N.; funding acquisition, T.J.N.; supervision, T.J.N. The authors declare no competing interests. Publisher Copyright: {\textcopyright} 2023 The Authors",

year = "2023",

month = nov,

day = "28",

doi = "10.1016/j.celrep.2023.113375",

language = "English",

volume = "42",

journal = "Cell Reports",

issn = "2211-1247",

publisher = "Elsevier BV",

number = "11",

}

TY - JOUR

T1 - Ion binding with charge inversion combined with screening modulates DEAD box helicase phase transitions

AU - Crabtree, Michael D.

AU - Holland, Jack

AU - Pillai, Arvind S.

AU - Kompella, Purnima S.

AU - Babl, Leon

AU - Turner, Noah N.

AU - Eaton, James T.

AU - Hochberg, Georg K. A.

AU - Aarts, Dirk G. A. L.

AU - Redfield, Christina

AU - Baldwin, Andrew J.

AU - Nott, Timothy J.

N1 - Funding Information: M.D.C. and T.J.N. thank Micron Oxford for microscopy support and M. Maj for support with flow cytometry experiments. T.J.N. thanks F. Barr and members of the Barr group for the gift of HeLa cells and support with tissue culture. We thank M. Krishnan for discussions on charge-inversion and seeing the significance of this mechanism in our data. We thank the Engineering and Physical Sciences Research Council (EPSRC) (EP/R029849/1) and the Wellcome Institutional Strategic Support Fund, John Fell Fund, and Edward Penley Abraham Cephalosporin Fund at the University of Oxford for funding the 950 MHz NMR facility. A.J.B. is supported by ERC grant 101002859 . For the purpose of open access, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission. Funding for this work came from a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant 202320/Z/16/Z ) awarded to T.J.N. T.J.N. and M.D.C. thank New College, Oxford, for support. L.B. thanks Studienstiftung des deutschen Volkes, and J.H. acknowledges the Synthetic Biology Centre for Doctoral Training (EPSRC grant EP/L016494/1) for support. G.K.A.H. is support by the Max Planck Society. Funding Information: M.D.C. and T.J.N. thank Micron Oxford for microscopy support and M. Maj for support with flow cytometry experiments. T.J.N. thanks F. Barr and members of the Barr group for the gift of HeLa cells and support with tissue culture. We thank M. Krishnan for discussions on charge-inversion and seeing the significance of this mechanism in our data. We thank the Engineering and Physical Sciences Research Council (EPSRC) (EP/R029849/1) and the Wellcome Institutional Strategic Support Fund, John Fell Fund, and Edward Penley Abraham Cephalosporin Fund at the University of Oxford for funding the 950 MHz NMR facility. A.J.B. is supported by ERC grant 101002859. For the purpose of open access, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission. Funding for this work came from a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant 202320/Z/16/Z) awarded to T.J.N. T.J.N. and M.D.C. thank New College, Oxford, for support. L.B. thanks Studienstiftung des deutschen Volkes, and J.H. acknowledges the Synthetic Biology Centre for Doctoral Training (EPSRC grant EP/L016494/1) for support. G.K.A.H. is support by the Max Planck Society. Conceptualization, M.D.C. and T.J.N.; methodology, M.D.C. and A.J.B.; resources, J.T.E. D.G.A.L.A. and C.R.; data curation, C.R.; investigation, M.D.C. J.H. A.S.P. P.S.K. L.B. N.N.T. and T.J.N.; formal analysis, M.D.C. J.H. A.S.P. A.J.B. and T.J.N.; visualization, M.D.C. A.J.B. and T.J.N.; writing – original draft, M.D.C.; writing – review & editing, J.H. G.K.A.H. D.G.A.L.A. A.J.B. and T.J.N.; funding acquisition, T.J.N.; supervision, T.J.N. The authors declare no competing interests. Publisher Copyright: © 2023 The Authors

PY - 2023/11/28

Y1 - 2023/11/28

N2 - Membraneless organelles, or biomolecular condensates, enable cells to compartmentalize material and processes into unique biochemical environments. While specific, attractive molecular interactions are known to stabilize biomolecular condensates, repulsive interactions, and the balance between these opposing forces, are largely unexplored. Here, we demonstrate that repulsive and attractive electrostatic interactions regulate condensate stability, internal mobility, interfaces, and selective partitioning of molecules both in vitro and in cells. We find that signaling ions, such as calcium, alter repulsions between model Ddx3 and Ddx4 condensate proteins by directly binding to negatively charged amino acid sidechains and effectively inverting their charge, in a manner fundamentally dissimilar to electrostatic screening. Using a polymerization model combined with generalized stickers and spacers, we accurately quantify and predict condensate stability over a wide range of pH, salt concentrations, and amino acid sequences. Our model provides a general quantitative treatment for understanding how charge and ions reversibly control condensate stability.

AB - Membraneless organelles, or biomolecular condensates, enable cells to compartmentalize material and processes into unique biochemical environments. While specific, attractive molecular interactions are known to stabilize biomolecular condensates, repulsive interactions, and the balance between these opposing forces, are largely unexplored. Here, we demonstrate that repulsive and attractive electrostatic interactions regulate condensate stability, internal mobility, interfaces, and selective partitioning of molecules both in vitro and in cells. We find that signaling ions, such as calcium, alter repulsions between model Ddx3 and Ddx4 condensate proteins by directly binding to negatively charged amino acid sidechains and effectively inverting their charge, in a manner fundamentally dissimilar to electrostatic screening. Using a polymerization model combined with generalized stickers and spacers, we accurately quantify and predict condensate stability over a wide range of pH, salt concentrations, and amino acid sequences. Our model provides a general quantitative treatment for understanding how charge and ions reversibly control condensate stability.

KW - intrinsically disordered protein

KW - phase transition

KW - multivalent ions

KW - ion binding

KW - transition temperature

KW - net charge

KW - membraneless organelles

KW - biomolecular condensates

KW - RNA helicase

KW - Ca2+

UR - http://www.scopus.com/inward/record.url?scp=85177226897&partnerID=8YFLogxK

U2 - 10.1016/j.celrep.2023.113375

DO - 10.1016/j.celrep.2023.113375

M3 - Article

SN - 2211-1247

VL - 42

JO - Cell Reports

JF - Cell Reports

IS - 11

M1 - 113375

ER -

Ion binding with charge inversion combined with screening modulates DEAD box helicase phase transitions

Abstract

Keywords

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