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Alshareedah I, Borcherds WM, Cohen SR, Singh A, Posey AE, Farag M, Bremer A, Strout GW, Tomares DT, Pappu RV, Mittag T, Banerjee PR. Sequence-specific interactions determine viscoelasticity and aging dynamics of protein condensates. bioRxiv 2023:2023.04.06.535902. [PMID: 37066350 PMCID: PMC10104120 DOI: 10.1101/2023.04.06.535902] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Biomolecular condensates are viscoelastic materials. Here, we report results from investigations into molecular-scale determinants of sequence-encoded and age-dependent viscoelasticity of condensates formed by prion-like low-complexity domains (PLCDs). The terminally viscous forms of PLCD condensates are Maxwell fluids. Measured viscoelastic moduli of these condensates are reproducible using a Rouse-Zimm model that accounts for the network-like organization engendered by reversible physical crosslinks among PLCDs in the dense phase. Measurements and computations show that the strengths of aromatic inter-sticker interactions determine the sequence-specific amplitudes of elastic and viscous moduli as well as the timescales over which elastic properties dominate. PLCD condensates also undergo physical aging on sequence-specific timescales. This is driven by mutations to spacer residues that weaken the metastability of terminally viscous phases. The aging of PLCD condensates is accompanied by disorder-to-order transitions, leading to the formation of non-fibrillar, beta-sheet-containing, semi-crystalline, terminally elastic, Kelvin-Voigt solids. Our results suggest that sequence grammars, which refer to the identities of stickers versus spacers in PLCDs, have evolved to afford control over the metastabilities of terminally viscous fluid phases of condensates. This selection can, in some cases, render barriers for conversion from metastable fluids to globally stable solids to be insurmountable on functionally relevant timescales.
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Farag M, Borcherds WM, Bremer A, Mittag T, Pappu RV. Phase separation of protein mixtures is driven by the interplay of homotypic and heterotypic interactions. Nat Commun 2023; 14:5527. [PMID: 37684240 PMCID: PMC10491635 DOI: 10.1038/s41467-023-41274-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Prion-like low-complexity domains (PLCDs) are involved in the formation and regulation of distinct biomolecular condensates that form via phase separation coupled to percolation. Intracellular condensates often encompass numerous distinct proteins with PLCDs. Here, we combine simulations and experiments to study mixtures of PLCDs from two RNA-binding proteins, hnRNPA1 and FUS. Using simulations and experiments, we find that 1:1 mixtures of A1-LCD and FUS-LCD undergo phase separation more readily than either of the PLCDs on their own due to complementary electrostatic interactions. Tie line analysis reveals that stoichiometric ratios of different components and their sequence-encoded interactions contribute jointly to the driving forces for condensate formation. Simulations also show that the spatial organization of PLCDs within condensates is governed by relative strengths of homotypic versus heterotypic interactions. We uncover rules for how interaction strengths and sequence lengths modulate conformational preferences of molecules at interfaces of condensates formed by mixtures of proteins.
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Affiliation(s)
- Mina Farag
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Wade M Borcherds
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Anne Bremer
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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3
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Farag M, Borcherds WM, Bremer A, Mittag T, Pappu RV. Phase Separation in Mixtures of Prion-Like Low Complexity Domains is Driven by the Interplay of Homotypic and Heterotypic Interactions. bioRxiv 2023:2023.03.15.532828. [PMID: 36993212 PMCID: PMC10055064 DOI: 10.1101/2023.03.15.532828] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Prion-like low-complexity domains (PLCDs) are involved in the formation and regulation of distinct biomolecular condensates that form via coupled associative and segregative phase transitions. We previously deciphered how evolutionarily conserved sequence features drive phase separation of PLCDs through homotypic interactions. However, condensates typically encompass a diverse mixture of proteins with PLCDs. Here, we combine simulations and experiments to study mixtures of PLCDs from two RNA binding proteins namely, hnRNPA1 and FUS. We find that 1:1 mixtures of the A1-LCD and FUS-LCD undergo phase separation more readily than either of the PLCDs on their own. The enhanced driving forces for phase separation of mixtures of A1-LCD and FUS-LCD arise partly from complementary electrostatic interactions between the two proteins. This complex coacervation-like mechanism adds to complementary interactions among aromatic residues. Further, tie line analysis shows that stoichiometric ratios of different components and their sequence-encoded interactions jointly contribute to the driving forces for condensate formation. These results highlight how expression levels might be tuned to regulate the driving forces for condensate formation in vivo . Simulations also show that the organization of PLCDs within condensates deviates from expectations based on random mixture models. Instead, spatial organization within condensates will reflect the relative strengths of homotypic versus heterotypic interactions. We also uncover rules for how interaction strengths and sequence lengths modulate conformational preferences of molecules at interfaces of condensates formed by mixtures of proteins. Overall, our findings emphasize the network-like organization of molecules within multicomponent condensates, and the distinctive, composition-specific conformational features of condensate interfaces. Significance Statement Biomolecular condensates are mixtures of different protein and nucleic acid molecules that organize biochemical reactions in cells. Much of what we know about how condensates form comes from studies of phase transitions of individual components of condensates. Here, we report results from studies of phase transitions of mixtures of archetypal protein domains that feature in distinct condensates. Our investigations, aided by a blend of computations and experiments, show that the phase transitions of mixtures are governed by a complex interplay of homotypic and heterotypic interactions. The results point to how expression levels of different protein components can be tuned in cells to modulate internal structures, compositions, and interfaces of condensates, thus affording distinct ways to control the functions of condensates.
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Cohen SR, Alshareedah I, Borcherds WM, Farag M, Mittag T, Banerjee PR, Pappu RV. Modified Rouse-Zimm theory for computing sequence-specific viscoelastic properties of biomolecular condensates. Biophys J 2023; 122:206a. [PMID: 36783000 DOI: 10.1016/j.bpj.2022.11.1238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Samuel R Cohen
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA; Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Wade M Borcherds
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mina Farag
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Rohit V Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA; Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO, USA
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Farag M, Bremer A, Borcherds WM, Mittag T, Pappu RV. Complex coacervation contributes to the joint phase behaviors of mixtures of charge-deficient prion-like low-complexity domains. Biophys J 2023; 122:159a. [PMID: 36782740 DOI: 10.1016/j.bpj.2022.11.967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Mina Farag
- Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Anne Bremer
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wade M Borcherds
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rohit V Pappu
- Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
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Alshareedah I, Borcherds WM, Singh A, Cohen SR, Farag M, Pappu RV, Mittag T, Banerjee PR. Uncovering the distinct roles of enthalpy and entropy that give rise to viscoelasticity in biomolecular condensates. Biophys J 2023; 122:207a. [PMID: 36783005 DOI: 10.1016/j.bpj.2022.11.1244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
| | - Wade M Borcherds
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anurag Singh
- Department of Physics, University at Buffalo, Buffalo, NY, USA
| | - Samuel R Cohen
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Mina Farag
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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Borcherds WM, Alshareedah I, Singh A, Das T, Bremer A, Banerjee PR, Pappu RV, Mittag T. A stickers-and-spacers framework explains the viscoelastic and aging properties of biomolecular condensates. Biophys J 2023; 122:296a. [PMID: 36783473 DOI: 10.1016/j.bpj.2022.11.1674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Wade M Borcherds
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Anurag Singh
- Department of Physics, University at Buffalo, Buffalo, NY, USA
| | - Tapojyoti Das
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anne Bremer
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Rohit V Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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Farag M, Cohen SR, Borcherds WM, Bremer A, Mittag T, Pappu RV. Condensates formed by prion-like low-complexity domains have small-world network structures and interfaces defined by expanded conformations. Nat Commun 2022; 13:7722. [PMID: 36513655 PMCID: PMC9748015 DOI: 10.1038/s41467-022-35370-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
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.
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Affiliation(s)
- Mina Farag
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Samuel R Cohen
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Wade M Borcherds
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anne Bremer
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA.
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Bremer A, Posey AE, Borgia MB, Borcherds WM, Farag M, Pappu RV, Mittag T. Quantifying Coexistence Concentrations in Multi-Component Phase-Separating Systems Using Analytical HPLC. Biomolecules 2022; 12:biom12101480. [PMID: 36291688 PMCID: PMC9599810 DOI: 10.3390/biom12101480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/28/2022] Open
Abstract
Over the last decade, evidence has accumulated to suggest that numerous instances of cellular compartmentalization can be explained by the phenomenon of phase separation. This is a process by which a macromolecular solution separates spontaneously into dense and dilute coexisting phases. Semi-quantitative, in vitro approaches for measuring phase boundaries have proven very useful in determining some key features of biomolecular condensates, but these methods often lack the precision necessary for generating quantitative models. Therefore, there is a clear need for techniques that allow quantitation of coexisting dilute and dense phase concentrations of phase-separating biomolecules, especially in systems with more than one type of macromolecule. Here, we report the design and deployment of analytical High-Performance Liquid Chromatography (HPLC) for in vitro separation and quantification of distinct biomolecules that allows us to measure dilute and dense phase concentrations needed to reconstruct coexistence curves in multicomponent mixtures. This approach is label-free, detects lower amounts of material than is accessible with classic UV-spectrophotometers, is applicable to a broad range of macromolecules of interest, is a semi-high-throughput technique, and if needed, the macromolecules can be recovered for further use. The approach promises to provide quantitative insights into the balance of homotypic and heterotypic interactions in multicomponent phase-separating systems.
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Affiliation(s)
- Anne Bremer
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ammon E. Posey
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Madeleine B. Borgia
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Wade M. Borcherds
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mina Farag
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Correspondence: (R.V.P.); (T.M.)
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Correspondence: (R.V.P.); (T.M.)
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Mittag T, Bremer A, Farag M, Borcherds WM, Pappu RV. Phase behavior of intrinsically disordered prion‐like domains. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.0i193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tanja Mittag
- Structural BiologySt. Jude Children's Research HospitalMemphisTN
| | - Anne Bremer
- Structural BiologySt. Jude Children's Research HospitalMemphisTN
| | - Mina Farag
- Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS)Washington University in St LouisSt. LouisMO
| | | | - Rohit V. Pappu
- Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS)Washington University in St LouisSt. LouisMO
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11
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Bremer A, Farag M, Borcherds WM, Peran I, Martin EW, Pappu RV, Mittag T. Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains. Nat Chem 2022; 14:196-207. [PMID: 34931046 PMCID: PMC8818026 DOI: 10.1038/s41557-021-00840-w] [Citation(s) in RCA: 143] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 10/19/2021] [Indexed: 12/20/2022]
Abstract
Prion-like low-complexity domains (PLCDs) have distinctive sequence grammars that determine their driving forces for phase separation. Here we uncover the physicochemical underpinnings of how evolutionarily conserved compositional biases influence the phase behaviour of PLCDs. We interpret our results in the context of the stickers-and-spacers model for the phase separation of associative polymers. We find that tyrosine is a stronger sticker than phenylalanine, whereas arginine is a context-dependent auxiliary sticker. In contrast, lysine weakens sticker-sticker interactions. Increasing the net charge per residue destabilizes phase separation while also weakening the strong coupling between single-chain contraction in dilute phases and multichain interactions that give rise to phase separation. Finally, glycine and serine residues act as non-equivalent spacers, and thus make the glycine versus serine contents an important determinant of the driving forces for phase separation. The totality of our results leads to a set of rules that enable comparative estimates of composition-specific driving forces for PLCD phase separation.
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Affiliation(s)
- Anne Bremer
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mina Farag
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St Louis, St Louis, MO, USA
| | - Wade M Borcherds
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ivan Peran
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Erik W Martin
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St Louis, St Louis, MO, USA.
| | - Tanja Mittag
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA.
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12
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Bremer A, Farag M, Borcherds WM, Peran I, Martin EW, Pappu RV, Mittag T. Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains. Nat Chem 2022; 14:196-207. [PMID: 34931046 DOI: 10.1101/2021.01.01.425046] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 10/19/2021] [Indexed: 05/25/2023]
Abstract
Prion-like low-complexity domains (PLCDs) have distinctive sequence grammars that determine their driving forces for phase separation. Here we uncover the physicochemical underpinnings of how evolutionarily conserved compositional biases influence the phase behaviour of PLCDs. We interpret our results in the context of the stickers-and-spacers model for the phase separation of associative polymers. We find that tyrosine is a stronger sticker than phenylalanine, whereas arginine is a context-dependent auxiliary sticker. In contrast, lysine weakens sticker-sticker interactions. Increasing the net charge per residue destabilizes phase separation while also weakening the strong coupling between single-chain contraction in dilute phases and multichain interactions that give rise to phase separation. Finally, glycine and serine residues act as non-equivalent spacers, and thus make the glycine versus serine contents an important determinant of the driving forces for phase separation. The totality of our results leads to a set of rules that enable comparative estimates of composition-specific driving forces for PLCD phase separation.
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Affiliation(s)
- Anne Bremer
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mina Farag
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St Louis, St Louis, MO, USA
| | - Wade M Borcherds
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ivan Peran
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Erik W Martin
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St Louis, St Louis, MO, USA.
| | - Tanja Mittag
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA.
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13
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Bremer A, Farag M, Borcherds WM, Pappu RV, Mittag T. Hidden Complexities in the Phase Behavior of Low-Complexity Disordered Proteins. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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14
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Borcherds WM, Bremer A, Farag M, Peran I, Martin EW, Pappu RV, Mittag T. Exploring the Effects of Increased Charge Content on the Phase Behavior of a Protein Low Complexity Domain. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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15
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Fenton MJ, Borcherds WM, Daughdrill GW, Chen L, Chen J. MDMX Acidic Domain Requires the WF Motif for the Initiation of the Secondary Interaction with the P53DBD. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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16
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Levy R, Borcherds WM, He F, Daughdrill GW, Chen J. Protein Disorder Regulates the DNA Binding Specificity of p53. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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17
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Abstract
Protein disorder is a pervasive phenomenon in biology and a natural consequence of polymer evolution that facilitates cell signaling by organizing sites for posttranslational modifications and protein-protein interactions into arrays of short linear motifs that can be rearranged by RNA splicing. Disordered proteins are missing the long-range nonpolar interactions that form tertiary structures, but they often contain regions with residual secondary structure that are stabilized by protein binding. NMR spectroscopy is uniquely suited to detect residual secondary structure in a disordered protein and it can provide atomic resolution data on the structure and dynamics of disordered protein interaction sites. Here we describe how backbone chemical shifts are used for assigning residual secondary structure in disordered proteins and discuss some of the tools available for estimating secondary structure populations with a focus on disordered proteins containing different levels of alpha helical secondary structure which are stabilized by protein binding.
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Affiliation(s)
- Wade M Borcherds
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, United States.
| | - Gary W Daughdrill
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, United States.
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18
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Poosapati A, Gregory E, Borcherds WM, Chemes LB, Daughdrill GW. Uncoupling the Folding and Binding of an Intrinsically Disordered Protein. J Mol Biol 2018; 430:2389-2402. [PMID: 29890118 DOI: 10.1016/j.jmb.2018.05.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/31/2018] [Accepted: 05/31/2018] [Indexed: 01/29/2023]
Abstract
The relationship between helical stability and binding affinity was examined for the intrinsically disordered transactivation domain of the myeloblastosis oncoprotein, c-Myb, and its ordered binding partner, KIX. A series of c-Myb mutants was designed to either increase or decrease helical stability without changing the binding interface with KIX. This included a complimentary series of A, G, P, and V mutants at three non-interacting sites. We were able to use the glycine mutants as a reference state and show a strong correlation between binding affinity and helical stability. The intrinsic helicity of c-Myb is 21%, and helicity values of the mutants ranged from 8% to 28%. The c-Myb helix is divided into two conformationally distinct segments. The N-terminal segment, from K291-L301, has an average helicity greater than 60% and the C-terminal segment, from S304-L315, has an average helicity less than 10%. We observed different effects on binding when these two segments were mutated. Mutants in the N-terminal segment that increased helicity had no effect on the binding affinity to KIX, while helix destabilizing glycine and proline mutants reduced binding affinity by more than 1 kcal/mol. Mutants that either increased or decreased helical stability in the C-terminal segment had almost no effect on binding. However, several of the mutants reveal the presence of multiple conformations accessible in the bound state based on changes in enthalpy and linkage analysis of binding free energies. These results may explain the high level of sequence identity (>90%), even at non-interacting sites, for c-Myb homologues.
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Affiliation(s)
- Anusha Poosapati
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA; Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
| | - Emily Gregory
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA; Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
| | - Wade M Borcherds
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA; Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
| | - Lucia B Chemes
- Instituto de Investigaciones Biotecnológicas IIB-INTECH, Universidad Nacional de San Martín, Buenos Aires, CP1650, Argentina.
| | - Gary W Daughdrill
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA; Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
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Borcherds WM, Daughdrill GW, Mishall K, Wu H. Crossing the Entropic Barrier to Coupled Folding and Binding. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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Daughdrill GW, Borcherds WM, Wu H. Disorder predictors also predict backbone dynamics for a family of disordered proteins. PLoS One 2011; 6:e29207. [PMID: 22195023 PMCID: PMC3240651 DOI: 10.1371/journal.pone.0029207] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 11/22/2011] [Indexed: 01/04/2023] Open
Abstract
Several algorithms have been developed that use amino acid sequences to predict whether or not a protein or a region of a protein is disordered. These algorithms make accurate predictions for disordered regions that are 30 amino acids or longer, but it is unclear whether the predictions can be directly related to the backbone dynamics of individual amino acid residues. The nuclear Overhauser effect between the amide nitrogen and hydrogen (NHNOE) provides an unambiguous measure of backbone dynamics at single residue resolution and is an excellent tool for characterizing the dynamic behavior of disordered proteins. In this report, we show that the NHNOE values for several members of a family of disordered proteins are highly correlated with the output from three popular algorithms used to predict disordered regions from amino acid sequence. This is the first test between an experimental measure of residue specific backbone dynamics and disorder predictions. The results suggest that some disorder predictors can accurately estimate the backbone dynamics of individual amino acids in a long disordered region.
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Affiliation(s)
- Gary W Daughdrill
- Department of Cell Biology, Microbiology and Molecular Biology and Center for Drug Discovery and Innovation, University of South Florida, Tampa, Florida, United States of America.
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Pine AT, Mishall KM, Borcherds WM, Wu H, Daughdrill GW. Structural Basis for the Dynamic Behavior of a Family of Disordered Proteins. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Borcherds WM, Wu H, Pine AT, Mishall KM, Daughdrill GW. Evolution of Structure and Dynamics for a Family of Disordered Proteins. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.3036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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