101
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Ramšak M, Ramirez DA, Hough LE, Shirts MR, Vidmar S, Eleršič Filipič K, Anderluh G, Jerala R. Programmable de novo designed coiled coil-mediated phase separation in mammalian cells. Nat Commun 2023; 14:7973. [PMID: 38042897 PMCID: PMC10693550 DOI: 10.1038/s41467-023-43742-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Membraneless liquid compartments based on phase-separating biopolymers have been observed in diverse cell types and attributed to weak multivalent interactions predominantly based on intrinsically disordered domains. The design of liquid-liquid phase separated (LLPS) condensates based on de novo designed tunable modules that interact in a well-understood, controllable manner could improve our understanding of this phenomenon and enable the introduction of new features. Here we report the construction of CC-LLPS in mammalian cells, based on designed coiled-coil (CC) dimer-forming modules, where the stability of CC pairs, their number, linkers, and sequential arrangement govern the transition between diffuse, liquid and immobile condensates and are corroborated by coarse-grained molecular simulations. Through modular design, we achieve multiple coexisting condensates, chemical regulation of LLPS, condensate fusion, formation from either one or two polypeptide components or LLPS regulation by a third polypeptide chain. These findings provide further insights into the principles underlying LLPS formation and a design platform for controlling biological processes.
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Affiliation(s)
- Maruša Ramšak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Dominique A Ramirez
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Loren E Hough
- Department of Physics and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Sara Vidmar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Kristina Eleršič Filipič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.
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102
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Moses D, Ginell GM, Holehouse AS, Sukenik S. Intrinsically disordered regions are poised to act as sensors of cellular chemistry. Trends Biochem Sci 2023; 48:1019-1034. [PMID: 37657994 PMCID: PMC10840941 DOI: 10.1016/j.tibs.2023.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
Intrinsically disordered proteins and protein regions (IDRs) are abundant in eukaryotic proteomes and play a wide variety of essential roles. Instead of folding into a stable structure, IDRs exist in an ensemble of interconverting conformations whose structure is biased by sequence-dependent interactions. The absence of a stable 3D structure, combined with high solvent accessibility, means that IDR conformational biases are inherently sensitive to changes in their environment. Here, we argue that IDRs are ideally poised to act as sensors and actuators of cellular physicochemistry. We review the physical principles that underlie IDR sensitivity, the molecular mechanisms that translate this sensitivity to function, and recent studies where environmental sensing by IDRs may play a key role in their downstream function.
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Affiliation(s)
- David Moses
- Department of Chemistry and Biochemistry, University of California, Merced, CA, USA
| | - Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA; Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA; Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA.
| | - Shahar Sukenik
- Department of Chemistry and Biochemistry, University of California, Merced, CA, USA; Quantitative Systems Biology Program, University of California, Merced, CA, USA.
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103
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Wadsworth GM, Zahurancik WJ, Zeng X, Pullara P, Lai LB, Sidharthan V, Pappu RV, Gopalan V, Banerjee PR. RNAs undergo phase transitions with lower critical solution temperatures. Nat Chem 2023; 15:1693-1704. [PMID: 37932412 PMCID: PMC10872781 DOI: 10.1038/s41557-023-01353-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 09/19/2023] [Indexed: 11/08/2023]
Abstract
Co-phase separation of RNAs and RNA-binding proteins drives the biogenesis of ribonucleoprotein granules. RNAs can also undergo phase transitions in the absence of proteins. However, the physicochemical driving forces of protein-free, RNA-driven phase transitions remain unclear. Here we report that various types of RNA undergo phase separation with system-specific lower critical solution temperatures. This entropically driven phase separation is an intrinsic feature of the phosphate backbone that requires Mg2+ ions and is modulated by RNA bases. RNA-only condensates can additionally undergo enthalpically favourable percolation transitions within dense phases. This is enabled by a combination of Mg2+-dependent bridging interactions between phosphate groups and RNA-specific base stacking and base pairing. Phase separation coupled to percolation can cause dynamic arrest of RNAs within condensates and suppress the catalytic activity of an RNase P ribozyme. Our work highlights the need to incorporate RNA-driven phase transitions into models for ribonucleoprotein granule biogenesis.
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Affiliation(s)
- Gable M Wadsworth
- Department of Physics, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Walter J Zahurancik
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Xiangze Zeng
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
- Department of Physics, Hong Kong Baptist University, Hong Kong, China
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Paul Pullara
- Department of Physics, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Lien B Lai
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Vaishnavi Sidharthan
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA.
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| | - Priya R Banerjee
- Department of Physics, The State University of New York at Buffalo, Buffalo, NY, USA.
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104
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Sahin C, Leppert A, Landreh M. Advances in mass spectrometry to unravel the structure and function of protein condensates. Nat Protoc 2023; 18:3653-3661. [PMID: 37907762 DOI: 10.1038/s41596-023-00900-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/09/2023] [Indexed: 11/02/2023]
Abstract
Membrane-less organelles assemble through liquid-liquid phase separation (LLPS) of partially disordered proteins into highly specialized microenvironments. Currently, it is challenging to obtain a clear understanding of the relationship between the structure and function of phase-separated protein assemblies, owing to their size, dynamics and heterogeneity. In this Perspective, we discuss recent advances in mass spectrometry (MS) that offer several promising approaches for the study of protein LLPS. We survey MS tools that have provided valuable insights into other insoluble protein systems, such as amyloids, and describe how they can also be applied to study proteins that undergo LLPS. On the basis of these recent advances, we propose to integrate MS into the experimental workflow for LLPS studies. We identify specific challenges and future opportunities for the analysis of protein condensate structure and function by MS.
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Affiliation(s)
- Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet-Biomedicum, Solna, Sweden.
- Structural Biology and NMR laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Axel Leppert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet-Biomedicum, Solna, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet-Biomedicum, Solna, Sweden.
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
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105
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Basu S, Martínez-Cristóbal P, Frigolé-Vivas M, Pesarrodona M, Lewis M, Szulc E, Bañuelos CA, Sánchez-Zarzalejo C, Bielskutė S, Zhu J, Pombo-García K, Garcia-Cabau C, Zodi L, Dockx H, Smak J, Kaur H, Batlle C, Mateos B, Biesaga M, Escobedo A, Bardia L, Verdaguer X, Ruffoni A, Mawji NR, Wang J, Obst JK, Tam T, Brun-Heath I, Ventura S, Meierhofer D, García J, Robustelli P, Stracker TH, Sadar MD, Riera A, Hnisz D, Salvatella X. Rational optimization of a transcription factor activation domain inhibitor. Nat Struct Mol Biol 2023; 30:1958-1969. [PMID: 38049566 PMCID: PMC10716049 DOI: 10.1038/s41594-023-01159-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 10/23/2023] [Indexed: 12/06/2023]
Abstract
Transcription factors are among the most attractive therapeutic targets but are considered largely 'undruggable' in part due to the intrinsically disordered nature of their activation domains. Here we show that the aromatic character of the activation domain of the androgen receptor, a therapeutic target for castration-resistant prostate cancer, is key for its activity as transcription factor, allowing it to translocate to the nucleus and partition into transcriptional condensates upon activation by androgens. On the basis of our understanding of the interactions stabilizing such condensates and of the structure that the domain adopts upon condensation, we optimized the structure of a small-molecule inhibitor previously identified by phenotypic screening. The optimized compounds had more affinity for their target, inhibited androgen-receptor-dependent transcriptional programs, and had an antitumorigenic effect in models of castration-resistant prostate cancer in cells and in vivo. These results suggest that it is possible to rationally optimize, and potentially even to design, small molecules that target the activation domains of oncogenic transcription factors.
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Affiliation(s)
- Shaon Basu
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Paula Martínez-Cristóbal
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Frigolé-Vivas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mireia Pesarrodona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Michael Lewis
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elzbieta Szulc
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - C Adriana Bañuelos
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Carolina Sánchez-Zarzalejo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stasė Bielskutė
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jiaqi Zhu
- Dartmouth College, Department of Chemistry, Hanover, NH, USA
| | - Karina Pombo-García
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Levente Zodi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Jordann Smak
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Harpreet Kaur
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Cristina Batlle
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Borja Mateos
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mateusz Biesaga
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Albert Escobedo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Lídia Bardia
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Xavier Verdaguer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Barcelona, Spain
| | - Alessandro Ruffoni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nasrin R Mawji
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jun Wang
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jon K Obst
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Teresa Tam
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Facility, Berlin, Germany
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Paul Robustelli
- Dartmouth College, Department of Chemistry, Hanover, NH, USA
| | - Travis H Stracker
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Marianne D Sadar
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Barcelona, Spain.
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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106
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Ganser C, Staples MI, Dowell M, Frazer C, Dainis J, Sircaik S, Bennett RJ. Filamentation and biofilm formation are regulated by the phase-separation capacity of network transcription factors in Candida albicans. PLoS Pathog 2023; 19:e1011833. [PMID: 38091321 PMCID: PMC10718430 DOI: 10.1371/journal.ppat.1011833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
The ability of the fungus Candida albicans to filament and form biofilms contributes to its burden as a leading cause of hospital-acquired infections. Biofilm development involves an interconnected transcriptional regulatory network (TRN) consisting of nine transcription factors (TFs) that bind both to their own regulatory regions and to those of the other network TFs. Here, we show that seven of the nine TFs in the C. albicans biofilm network contain prion-like domains (PrLDs) that have been linked to the ability to form phase-separated condensates. Construction of PrLD mutants in four biofilm TFs reveals that these domains are essential for filamentation and biofilm formation in C. albicans. Moreover, biofilm PrLDs promote the formation of phase-separated condensates in the nuclei of live cells, and PrLD mutations that abolish phase separation (such as the removal of aromatic residues) also prevent biofilm formation. Biofilm TF condensates can selectively recruit other TFs through PrLD-PrLD interactions and can co-recruit RNA polymerase II, implicating condensate formation in the assembly of active transcriptional complexes. Finally, we show that PrLD mutations that block the phase separation of biofilm TFs also prevent filamentation in an in vivo model of gastrointestinal colonization. Together, these studies associate transcriptional condensates with the regulation of filamentation and biofilm formation in C. albicans, and highlight how targeting of PrLD-PrLD interactions could prevent pathogenesis by this species.
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Affiliation(s)
- Collin Ganser
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, United States of America
| | - Mae I. Staples
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, United States of America
| | - Maureen Dowell
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, United States of America
| | - Corey Frazer
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, United States of America
| | - Joseph Dainis
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, United States of America
| | - Shabnam Sircaik
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, United States of America
| | - Richard J. Bennett
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, United States of America
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107
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Balasubramanian S, Maharana S, Srivastava A. "Boundary residues" between the folded RNA recognition motif and disordered RGG domains are critical for FUS-RNA binding. J Biol Chem 2023; 299:105392. [PMID: 37890778 PMCID: PMC10687056 DOI: 10.1016/j.jbc.2023.105392] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 09/19/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Fused in sarcoma (FUS) is an abundant RNA-binding protein, which drives phase separation of cellular condensates and plays multiple roles in RNA regulation. The RNA-binding ability of FUS protein is crucial to its cellular function. Here, our molecular simulation study on the FUS-RNA complex provides atomic resolution insights into the observations from biochemical studies and also illuminates our understanding of molecular driving forces that mediate the structure, stability, and interaction of the RNA recognition motif (RRM) and RGG domains of FUS with a stem-loop junction RNA. We observe clear cooperativity and division of labor among the ordered (RRM) and disordered domains (RGG1 and RGG2) of FUS that leads to an organized and tighter RNA binding. Irrespective of the length of RGG2, the RGG2-RNA interaction is confined to the stem-loop junction and the proximal stem regions. On the other hand, the RGG1 interactions are primarily with the longer RNA stem. We find that the C terminus of RRM, which make up the "boundary residues" that connect the folded RRM with the long disordered RGG2 stretch of the protein, plays a critical role in FUS-RNA binding. Our study provides high-resolution molecular insights into the FUS-RNA interactions and forms the basis for understanding the molecular origins of full-length FUS interaction with RNA.
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Affiliation(s)
| | - Shovamayee Maharana
- Department of Molecular and Cell Biology, Indian Institute of Science Bangalore, Bangalore, Karnataka, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bangalore, Karnataka, India.
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108
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Sood A, Zhang B. Preserving condensate structure and composition by lowering sequence complexity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569249. [PMID: 38076908 PMCID: PMC10705451 DOI: 10.1101/2023.11.29.569249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Biological condensates play a vital role in organizing cellular chemistry. They selectively partition biomolecules, preventing unwanted cross-talk and buffering against chemical noise. Intrinsically disordered proteins (IDPs) serve as primary components of these condensates due to their flexibility and ability to engage in multivalent, non-specific interactions, leading to spontaneous aggregation. Theoretical advancements are critical at connecting IDP sequences with condensate emergent properties to establish the so-called molecular grammar. We proposed an extension to the stickers and spacers model, incorporating non-specific pairwise interactions between spacers alongside specific interactions among stickers. Our investigation revealed that while spacer interactions contribute to phase separation and co-condensation, their non-specific nature leads to disorganized condensates. Specific sticker-sticker interactions drive the formation of condensates with well-defined structures and molecular composition. We discussed how evolutionary pressures might emerge to affect these interactions, leading to the prevalence of low complexity domains in IDP sequences. These domains suppress spurious interactions and facilitate the formation of biologically meaningful condensates.
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Affiliation(s)
- Amogh Sood
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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109
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Crabtree MD, Holland J, Pillai AS, Kompella PS, Babl L, Turner NN, Eaton JT, Hochberg GKA, Aarts DGAL, Redfield C, Baldwin AJ, Nott TJ. Ion binding with charge inversion combined with screening modulates DEAD box helicase phase transitions. Cell Rep 2023; 42:113375. [PMID: 37980572 PMCID: PMC10935546 DOI: 10.1016/j.celrep.2023.113375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/14/2023] [Accepted: 10/18/2023] [Indexed: 11/21/2023] Open
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.
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Affiliation(s)
- Michael D Crabtree
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jack Holland
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Arvind S Pillai
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Purnima S Kompella
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Leon Babl
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Noah N Turner
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - James T Eaton
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK; Kavli Insititute of Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Sherrington Rd, Oxford, OX1 3QU, UK
| | - Georg K A Hochberg
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany; Center for Synthetic Microbiology, Philipps University Marburg, Karl-von-Frisch-Straße 14, 35032 Marburg, Germany
| | - Dirk G A L Aarts
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrew J Baldwin
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK; Kavli Insititute of Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Sherrington Rd, Oxford, OX1 3QU, UK.
| | - Timothy J Nott
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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110
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Shi G, Schweizer KS. Theory of the center-of-mass diffusion and viscosity of microstructured and variable sequence copolymer liquids. SOFT MATTER 2023; 19:8893-8910. [PMID: 37955602 DOI: 10.1039/d3sm01193c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Biomolecular condensates formed through the phase separation of proteins and nucleic acids are widely observed, offering a fundamental means of organizing intracellular materials in a membrane-less fashion. Traditionally, these condensates have been regarded as homogeneous isotropic liquids. However, in analogy with some synthetic copolymer systems, our recent theoretical research has demonstrated that model biomolecular condensates can exhibit a microemulsion-like internal structure, contingent upon the specific sequence, inter-chain site-site interactions, and concentrated phase polymer density. Motivated by these considerations, here we present a microscopic dynamical theory for the self-diffusion constant and viscosity of a simpler class of model systems - concentrated unentangled A/B regular multiblock copolymer solutions. Our approach integrates static equilibrium local and microdomain scale structural information obtained from PRISM integral equation theory and the time evolution of the autocorrelation function of monomer scale forces at the center-of-mass level to determine the polymer diffusion constant and viscosity in a weak caging regime far from a glass or gel transition. We focus on regular multi-block systems both for simplicity and for its relevance to synthetic macromolecular science. The impact of sequence and inter-chain attraction strength on the slowing down of copolymer mass transport and flow due to local clustering enhanced collisional friction and emergent microdomain scale ordering are established. Analytic analysis and metrics employed in the study of biomolecular condensates are employed to identify key order parameters that quantity how attractive forces, packing structure, multiblock sequence, and copolymer density determine dynamical slowing down above and below the crossover to a fluctuating polymeric microemulsion state.
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Affiliation(s)
- Guang Shi
- Department of Materials Science, University of Illinois, Urbana, Illinois 61801, USA.
| | - Kenneth S Schweizer
- Department of Materials Science, University of Illinois, Urbana, Illinois 61801, USA.
- Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois 61801, USA
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, USA
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111
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Holland J, Castrejón-Pita AA, Tuinier R, Aarts DGAL, Nott TJ. Surface tension measurement and calculation of model biomolecular condensates. SOFT MATTER 2023; 19:8706-8716. [PMID: 37791635 PMCID: PMC10663989 DOI: 10.1039/d3sm00820g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023]
Abstract
The surface tension of liquid-like protein-rich biomolecular condensates is an emerging physical principle governing the mesoscopic interior organisation of biological cells. In this study, we present a method to evaluate the surface tension of model biomolecular condensates, through straighforward sessile drop measurements of capillary lengths and condensate densities. Our approach bypasses the need for characterizing condensate viscosities, which was required in previously reported techniques. We demonstrate this method using model condensates comprising two mutants of the intrinsically disordered protein Ddx4N. Notably, we uncover a detrimental impact of increased protein net charge on the surface tension of Ddx4N condensates. Furthermore, we explore the application of Scheutjens-Fleer theory, calculating condensate surface tensions through a self-consistent mean-field framework using Flory-Huggins interaction parameters. This relatively simple theory provides semi-quantitative accuracy in predicting Ddx4N condensate surface tensions and enables the evaluation of molecular organisation at condensate surfaces. Our findings shed light on the molecular details of fluid-fluid interfaces in biomolecular condensates.
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Affiliation(s)
- Jack Holland
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK.
- Dept. of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
| | | | - Remco Tuinier
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Dirk G A L Aarts
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK.
| | - Timothy J Nott
- Dept. of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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112
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Davis RB, Supakar A, Ranganath AK, Moosa MM, Banerjee PR. Heterotypic interactions in the dilute phase can drive co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536623. [PMID: 37090622 PMCID: PMC10120661 DOI: 10.1101/2023.04.12.536623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian SWI/SNF complex to oncogenic FET fusion protein condensates. Here, we show that disordered low-complexity domains of multiple SWI/SNF subunits are prion-like with a strong propensity to undergo intracellular phase separation. These PLDs engage in sequence-specific heterotypic interactions with the PLD of FUS in the dilute phase at sub-saturation conditions, leading to the formation of PLD co-condensates. In the dense phase, homotypic and heterotypic PLD interactions are highly cooperative, resulting in the co-mixing of individual PLD phases and forming spatially homogeneous co-condensates. Heterotypic PLD-mediated positive cooperativity in protein-protein interaction networks is likely to play key roles in the co-phase separation of mSWI/SNF complex with transcription factors containing homologous low-complexity domains.
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Affiliation(s)
- Richoo B. Davis
- Department of Physics, University at Buffalo, Buffalo NY 14260, USA
| | - Anushka Supakar
- Department of Biological Sciences, University at Buffalo, Buffalo NY 14260, USA
| | | | | | - Priya R. Banerjee
- Department of Physics, University at Buffalo, Buffalo NY 14260, USA
- Department of Biological Sciences, University at Buffalo, Buffalo NY 14260, USA
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo NY 14260, USA
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113
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Gui T, Fleming C, Manzato C, Bourgeois B, Sirati N, Heuer J, Papadionysiou I, Montfort DIV, Gijzen MV, Smits LMM, Burgering BMT, Madl T, Schuijers J. Targeted perturbation of signaling-driven condensates. Mol Cell 2023; 83:4141-4157.e11. [PMID: 37977121 DOI: 10.1016/j.molcel.2023.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/27/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023]
Abstract
Biomolecular condensates have emerged as a major organizational principle in the cell. However, the formation, maintenance, and dissolution of condensates are still poorly understood. Transcriptional machinery partitions into biomolecular condensates at key cell identity genes to activate these. Here, we report a specific perturbation of WNT-activated β-catenin condensates that disrupts oncogenic signaling. We use a live-cell condensate imaging method in human cancer cells to discover FOXO and TCF-derived peptides that specifically inhibit β-catenin condensate formation on DNA, perturb nuclear β-catenin condensates in cells, and inhibit β-catenin-driven transcriptional activation and colorectal cancer cell growth. We show that these peptides compete with homotypic intermolecular interactions that normally drive condensate formation. Using this framework, we derive short peptides that specifically perturb condensates and transcriptional activation of YAP and TAZ in the Hippo pathway. We propose a "monomer saturation" model in which short interacting peptides can be used to specifically inhibit condensate-associated transcription in disease.
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Affiliation(s)
- Tianshu Gui
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands; Oncode Institute, 3721 AL Utrecht, the Netherlands
| | - Cassio Fleming
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Caterina Manzato
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Nafiseh Sirati
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Jasper Heuer
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Ioanna Papadionysiou
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Daniel I van Montfort
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Merel van Gijzen
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Lydia M M Smits
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Boudewijn M T Burgering
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands; Oncode Institute, 3721 AL Utrecht, the Netherlands
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria
| | - Jurian Schuijers
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands; Oncode Institute, 3721 AL Utrecht, the Netherlands.
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114
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Joshi A, Walimbe A, Avni A, Rai SK, Arora L, Sarkar S, Mukhopadhyay S. Single-molecule FRET unmasks structural subpopulations and crucial molecular events during FUS low-complexity domain phase separation. Nat Commun 2023; 14:7331. [PMID: 37957147 PMCID: PMC10643395 DOI: 10.1038/s41467-023-43225-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
Biomolecular condensates formed via phase separation of proteins and nucleic acids are thought to be associated with a wide range of cellular functions and dysfunctions. We dissect critical molecular events associated with phase separation of an intrinsically disordered prion-like low-complexity domain of Fused in Sarcoma by performing single-molecule studies permitting us to access the wealth of molecular information that is skewed in conventional ensemble experiments. Our single-molecule FRET experiments reveal the coexistence of two conformationally distinct subpopulations in the monomeric form. Single-droplet single-molecule FRET studies coupled with fluorescence correlation spectroscopy, picosecond time-resolved fluorescence anisotropy, and vibrational Raman spectroscopy indicate that structural unwinding switches intramolecular interactions into intermolecular contacts allowing the formation of a dynamic network within condensates. A disease-related mutation introduces enhanced structural plasticity engendering greater interchain interactions that can accelerate pathological aggregation. Our findings provide key mechanistic underpinnings of sequence-encoded dynamically-controlled structural unzipping resulting in biological phase separation.
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Affiliation(s)
- Ashish Joshi
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Anuja Walimbe
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Anamika Avni
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sandeep K Rai
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Lisha Arora
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Snehasis Sarkar
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India.
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India.
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India.
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115
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Emenecker RJ, Guadalupe K, Shamoon NM, Sukenik S, Holehouse AS. Sequence-ensemble-function relationships for disordered proteins in live cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.29.564547. [PMID: 37961106 PMCID: PMC10634935 DOI: 10.1101/2023.10.29.564547] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions (IDRs) are ubiquitous across all kingdoms of life and play a variety of essential cellular roles. IDRs exist in a collection of structurally distinct conformers known as an ensemble. An IDR's amino acid sequence determines its ensemble, which in turn can play an important role in dictating molecular function. Yet a clear link connecting IDR sequence, its ensemble properties, and its molecular function in living cells has not been directly established. Here, we set out to test this sequence-ensemble-function paradigm using a novel computational method (GOOSE) that enables the rational design of libraries of IDRs by systematically varying specific sequence properties. Using ensemble FRET, we measured the ensemble dimensions of a library of rationally designed IDRs in human-derived cell lines, revealing how IDR sequence influences ensemble dimensions in situ. Furthermore, we show that the interplay between sequence and ensemble can tune an IDR's ability to sense changes in cell volume - a de novo molecular function for these synthetic sequences. Our results establish biophysical rules for intracellular sequence-ensemble relationships, enable a new route for understanding how IDR sequences map to function in live cells, and set the ground for the design of synthetic IDRs with de novo function.
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Affiliation(s)
- Ryan J. Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Karina Guadalupe
- Department of Chemistry and Biochemistry, University of California, Merced, CA
- Center for Cellular and Biomolecular Machines, University of California, Merced, CA
| | - Nora M. Shamoon
- Center for Cellular and Biomolecular Machines, University of California, Merced, CA
- Quantitative Systems Biology Program, University of California, Merced, CA
| | - Shahar Sukenik
- Department of Chemistry and Biochemistry, University of California, Merced, CA
- Center for Cellular and Biomolecular Machines, University of California, Merced, CA
- Quantitative Systems Biology Program, University of California, Merced, CA
- Health Sciences Research Institute, University of California, Merced, CA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
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116
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Holehouse A, Emenecker R, Guadalupe K, Shamoon N, Sukenik S. Sequence-ensemble-function relationships for disordered proteins in live cells. RESEARCH SQUARE 2023:rs.3.rs-3501110. [PMID: 37986812 PMCID: PMC10659550 DOI: 10.21203/rs.3.rs-3501110/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Intrinsically disordered protein regions (IDRs) are ubiquitous across all kingdoms of life and play a variety of essential cellular roles. IDRs exist in a collection of structurally distinct conformers known as an ensemble. IDR amino acid sequence determines its ensemble, which in turn can play an important role in dictating molecular function. Yet a clear link connecting IDR sequence, its ensemble properties, and its molecular function in living cells has not been systematically established. Here, we set out to test this sequence-ensemble-function paradigm using a novel computational method (GOOSE) that enables the rational design of libraries of IDRs by systematically varying specific sequence properties. Using ensemble FRET, we measured the ensemble dimensions of a library of rationally designed IDRs in human-derived cell lines, revealing how IDR sequence influences ensemble dimensions in situ. Furthermore, we show that the interplay between sequence and ensemble can tune an IDR's ability to sense changes in cell volume - a de novomolecular function for these synthetic sequences. Our results establish biophysical rules for intracellular sequence-ensemble relationships, enable a new route for understanding how IDR sequences map to function in live cells, and set the ground for the design of synthetic IDRs with de novo function.
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117
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do Amaral MJ, Mohapatra S, Passos AR, Lopes da Silva TS, Carvalho RS, da Silva Almeida M, Pinheiro AS, Wegmann S, Cordeiro Y. Copper drives prion protein phase separation and modulates aggregation. SCIENCE ADVANCES 2023; 9:eadi7347. [PMID: 37922348 PMCID: PMC10624353 DOI: 10.1126/sciadv.adi7347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/03/2023] [Indexed: 11/05/2023]
Abstract
Prion diseases are characterized by prion protein (PrP) transmissible aggregation and neurodegeneration, which has been linked to oxidative stress. The physiological function of PrP seems related to sequestering of redox-active Cu2+, and Cu2+ dyshomeostasis is observed in prion disease brain. It is unclear whether Cu2+ contributes to PrP aggregation, recently shown to be mediated by PrP condensation. This study indicates that Cu2+ promotes PrP condensation in live cells at the cell surface and in vitro through copartitioning. Molecularly, Cu2+ inhibited PrP β-structure and hydrophobic residues exposure. Oxidation, induced by H2O2, triggered liquid-to-solid transition of PrP:Cu2+ condensates and promoted amyloid-like PrP aggregation. In cells, overexpression of PrPC initially protected against Cu2+ cytotoxicity but led to PrPC aggregation upon extended copper exposure. Our data suggest that PrP condensates function as a buffer for copper that prevents copper toxicity but can transition into PrP aggregation at prolonged oxidative stress.
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Affiliation(s)
- Mariana Juliani do Amaral
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | | | - Aline Ribeiro Passos
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | | | | | - Marcius da Silva Almeida
- Plataforma Avançada de Biomoléculas, Centro Nacional de Biologia Estrutural e Bioimagem, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anderson Sá Pinheiro
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Susanne Wegmann
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | - Yraima Cordeiro
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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118
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Johnson CN, Sojitra KA, Sohn EJ, Moreno-Romero AK, Baudin A, Xu X, Mittal J, Libich DS. Insights into Molecular Diversity within the FET Family: Unraveling Phase Separation of the N-Terminal Low Complexity Domain from RNA-Binding Protein EWS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.564484. [PMID: 37961424 PMCID: PMC10634919 DOI: 10.1101/2023.10.27.564484] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The FET family proteins, which includes FUS, EWS, and TAF15, are RNA chaperones instrumental in processes such as mRNA maturation, transcriptional regulation, and the DNA damage response. These proteins have clinical significance: chromosomal rearrangements in FET proteins are implicated in Ewing family tumors and related sarcomas. Furthermore, point mutations in FUS and TAF15 are associated with neurodegenerative conditions like amyotrophic lateral sclerosis and frontotemporal lobar dementia. The fusion protein EWS::FLI1, the causative mutation of Ewing sarcoma, arises from a genomic translocation that fuses the low-complexity domain (LCD) of EWS (EWSLCD) with the DNA binding domain of the ETS transcription factor FLI1. This fusion not only alters transcriptional programs but also hinders native EWS functions like splicing. However, the precise function of the intrinsically disordered EWSLCD is still a topic of active investigation. Due to its flexible nature, EWSLCD can form transient interactions with itself and other biomolecules, leading to the formation of biomolecular condensates through phase separation - a mechanism thought to be central to the oncogenicity of EWS::FLI1. In our study, we used paramagnetic relaxation enhancement NMR, analytical ultracentrifugation, light microscopy, and all-atom molecular dynamics (MD) simulations to better understand the self-association and phase separation tendencies of EWSLCD. Our aim was to elucidate the molecular events that underpin EWSLCD-mediated biomolecular condensation. Our NMR data suggest tyrosine residues primarily drive the interactions vital for EWSLCD phase separation. Moreover, a higher density and proximity of tyrosine residues amplify the likelihood of condensate formation. Atomistic MD simulations and hydrodynamic experiments revealed that the tyrosine-rich N and C-termini tend to populate compact conformations, establishing unique contact networks, that are connected by a predominantly extended, tyrosine-depleted, linker region. MD simulations provide critical input on the relationship between contacts formed within a single molecule (intramolecular) and inside the condensed phase (intermolecular), and changes in protein conformations upon condensation. These results offer deeper insights into the condensate-forming abilities of the FET proteins and highlights unique structural and functional nuances between EWS and its counterparts, FUS and TAF15.
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Affiliation(s)
- Courtney N Johnson
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Kandarp A Sojitra
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Erich J Sohn
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Alma K Moreno-Romero
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Antoine Baudin
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Xiaoping Xu
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843, United States
| | - David S Libich
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
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119
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Sekiyama N, Kobayashi R, Kodama TS. Toward a high-resolution mechanism of intrinsically disordered protein self-assembly. J Biochem 2023; 174:391-398. [PMID: 37488093 DOI: 10.1093/jb/mvad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/02/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
Membraneless organelles formed via the self-assembly of intrinsically disordered proteins (IDPs) play a crucial role in regulating various physiological functions. Elucidating the mechanisms behind IDP self-assembly is of great interest not only from a biological perspective but also for understanding how amino acid mutations in IDPs contribute to the development of neurodegenerative diseases and other disorders. Currently, two proposed mechanisms explain IDP self-assembly: (1) the sticker-and-spacer framework, which considers amino acid residues as beads to simulate the intermolecular interactions, and (2) the cross-β hypothesis, which focuses on the β-sheet interactions between the molecular surfaces constructed by multiple residues. This review explores the advancement of new models that provide higher resolution insights into the IDP self-assembly mechanism based on new findings obtained from structural studies of IDPs.
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Affiliation(s)
- Naotaka Sekiyama
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ryoga Kobayashi
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takashi S Kodama
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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120
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Patil A, Strom AR, Paulo JA, Collings CK, Ruff KM, Shinn MK, Sankar A, Cervantes KS, Wauer T, St Laurent JD, Xu G, Becker LA, Gygi SP, Pappu RV, Brangwynne CP, Kadoch C. A disordered region controls cBAF activity via condensation and partner recruitment. Cell 2023; 186:4936-4955.e26. [PMID: 37788668 PMCID: PMC10792396 DOI: 10.1016/j.cell.2023.08.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 07/16/2023] [Accepted: 08/24/2023] [Indexed: 10/05/2023]
Abstract
Intrinsically disordered regions (IDRs) represent a large percentage of overall nuclear protein content. The prevailing dogma is that IDRs engage in non-specific interactions because they are poorly constrained by evolutionary selection. Here, we demonstrate that condensate formation and heterotypic interactions are distinct and separable features of an IDR within the ARID1A/B subunits of the mSWI/SNF chromatin remodeler, cBAF, and establish distinct "sequence grammars" underlying each contribution. Condensation is driven by uniformly distributed tyrosine residues, and partner interactions are mediated by non-random blocks rich in alanine, glycine, and glutamine residues. These features concentrate a specific cBAF protein-protein interaction network and are essential for chromatin localization and activity. Importantly, human disease-associated perturbations in ARID1B IDR sequence grammars disrupt cBAF function in cells. Together, these data identify IDR contributions to chromatin remodeling and explain how phase separation provides a mechanism through which both genomic localization and functional partner recruitment are achieved.
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Affiliation(s)
- Ajinkya Patil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Amy R Strom
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Clayton K Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kiersten M Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Min Kyung Shinn
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Akshay Sankar
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kasey S Cervantes
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tobias Wauer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA
| | - Jessica D St Laurent
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Department of Obstetrics and Gynecology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Grace Xu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lindsay A Becker
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Chevy Chase, MD 21044, USA; Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544, USA.
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 21044, USA.
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121
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Kang WB, Bao L, Zhang K, Guo J, Zhu BC, Tang QY, Ren WT, Zhu G. Multi-scale molecular simulation of random peptide phase separation and its extended-to-compact structure transition driven by hydrophobic interactions. SOFT MATTER 2023; 19:7944-7954. [PMID: 37815389 DOI: 10.1039/d3sm00633f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Intrinsically disordered proteins (IDPs) often undergo liquid-liquid phase separation (LLPS) and form membraneless organelles or protein condensates. One of the core problems is how do electrostatic repulsion and hydrophobic interactions in peptides regulate the phase separation process? To answer this question, this study uses random peptides composed of positively charged arginine (Arg, R) and hydrophobic isoleucine (Ile, I) as the model systems, and conduct large-scale simulations using all atom and coarse-grained model multi-scale simulation methods. In this article, we investigate the phase separation of different sequences using a coarse-grained model. It is found that the stronger the electrostatic repulsion in the system, the more extended the single-chain structure, and the more likely the system forms a low-density homogeneous phase. In contrast, the stronger the hydrophobic effect of the system, the more compact the single-chain structure, the easier phase separation, and the higher the critical temperature of phase separation. Overall, by taking the random polypeptides composed of two types of amino acid residues as model systems, this study discusses the relationship between the protein sequence and phase behaviour, and provides theoretical insights into the interactions within or between proteins. It is expected to provide essential physical information for the sequence design of functional IDPs, as well as data to support the diagnosis and treatment of the LLPS-associated diseases.
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Affiliation(s)
- Wen Bin Kang
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
| | - Lei Bao
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
| | - Kai Zhang
- School of Physics, Nanjing University, Nanjing 210093, China
| | - Jia Guo
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
| | - Ben Chao Zhu
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
| | - Qian-Yuan Tang
- Department of Physics, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Wei Tong Ren
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Gen Zhu
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
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122
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Pesce F, Bremer A, Tesei G, Hopkins JB, Grace CR, Mittag T, Lindorff-Larsen K. Design of intrinsically disordered protein variants with diverse structural properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.22.563461. [PMID: 37961110 PMCID: PMC10634714 DOI: 10.1101/2023.10.22.563461] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered proteins (IDPs) perform a wide range of functions in biology, suggesting that the ability to design IDPs could help expand the repertoire of proteins with novel functions. Designing IDPs with specific structural or functional properties has, however, been difficult, in part because determining accurate conformational ensembles of IDPs generally requires a combination of computational modelling and experiments. Motivated by recent advancements in efficient physics-based models for simulations of IDPs, we have developed a general algorithm for designing IDPs with specific structural properties. We demonstrate the power of the algorithm by generating variants of naturally occurring IDPs with different levels of compaction and that vary more than 100 fold in their propensity to undergo phase separation, even while keeping a fixed amino acid composition. We experimentally tested designs of variants of the low-complexity domain of hnRNPA1 and find high accuracy in our computational predictions, both in terms of single-chain compaction and propensity to undergo phase separation. We analyze the sequence features that determine changes in compaction and propensity to phase separate and find an overall good agreement with previous findings for naturally occurring sequences. Our general, physics-based method enables the design of disordered sequences with specified conformational properties. Our algorithm thus expands the toolbox for protein design to include also the most flexible proteins and will enable the design of proteins whose functions exploit the many properties afforded by protein disorder.
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Affiliation(s)
- Francesco Pesce
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anne Bremer
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Giulio Tesei
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jesse B. Hopkins
- BioCAT, Department of Physics, Illinois Institute of Technology, Chicago, IL, USA
| | - Christy R. Grace
- 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
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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123
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Dar F, Cohen SR, Mitrea DM, Phillips AH, Nagy G, Leite WC, Stanley CB, Choi JM, Kriwacki RW, Pappu RV. Biomolecular condensates form spatially inhomogeneous network fluids. RESEARCH SQUARE 2023:rs.3.rs-3419423. [PMID: 37886520 PMCID: PMC10602126 DOI: 10.21203/rs.3.rs-3419423/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The functions of biomolecular condensates are thought to be influenced by their material properties, and these are in turn determined by the multiscale structural features within condensates. However, structural characterizations of condensates are challenging, and hence rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and bespoke coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that mimic nucleolar granular components (GCs). We show that facsimiles of GCs are network fluids featuring spatial inhomogeneities across hierarchies of length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights, extracted from a combination of approaches, suggest that condensates formed by multivalent proteins share features with network fluids formed by associative systems such as patchy or hairy colloids.
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Affiliation(s)
- Furqan Dar
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
- These authors contributed equally: Furqan Dar, Samuel R. Cohen, and Jeong-Mo Choi
| | - Samuel R. Cohen
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA
- These authors contributed equally: Furqan Dar, Samuel R. Cohen, and Jeong-Mo Choi
| | - Diana M. Mitrea
- Dewpoint Therapeutics Inc., 451 D Street, Boston, MA 02210, USA
| | - Aaron H. Phillips
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Gergely Nagy
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Wellington C. Leite
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Christopher B. Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - Jeong-Mo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
- These authors contributed equally: Furqan Dar, Samuel R. Cohen, and Jeong-Mo Choi
| | - Richard W. Kriwacki
- 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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124
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Poudyal M, Patel K, Gadhe L, Sawner AS, Kadu P, Datta D, Mukherjee S, Ray S, Navalkar A, Maiti S, Chatterjee D, Devi J, Bera R, Gahlot N, Joseph J, Padinhateeri R, Maji SK. Intermolecular interactions underlie protein/peptide phase separation irrespective of sequence and structure at crowded milieu. Nat Commun 2023; 14:6199. [PMID: 37794023 PMCID: PMC10550955 DOI: 10.1038/s41467-023-41864-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) has emerged as a crucial biological phenomenon underlying the sequestration of macromolecules (such as proteins and nucleic acids) into membraneless organelles in cells. Unstructured and intrinsically disordered domains are known to facilitate multivalent interactions driving protein LLPS. We hypothesized that LLPS could be an intrinsic property of proteins/polypeptides but with distinct phase regimes irrespective of their sequence and structure. To examine this, we studied many (a total of 23) proteins/polypeptides with different structures and sequences for LLPS study in the presence and absence of molecular crowder, polyethylene glycol (PEG-8000). We showed that all proteins and even highly charged polypeptides (under study) can undergo liquid condensate formation, however with different phase regimes and intermolecular interactions. We further demonstrated that electrostatic, hydrophobic, and H-bonding or a combination of such intermolecular interactions plays a crucial role in individual protein/peptide LLPS.
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Affiliation(s)
- Manisha Poudyal
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Komal Patel
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, IIT Bombay, Powai, Mumbai, 400076, India
| | - Laxmikant Gadhe
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Ajay Singh Sawner
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Debalina Datta
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Semanti Mukherjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Soumik Ray
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Siddhartha Maiti
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
- Department of Bioengineering, VIT Bhopal University, Bhopal-Indore Highway, Kothrikalan, Sehore, Madhya Pradesh, 466114, India
| | - Debdeep Chatterjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Jyoti Devi
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Riya Bera
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Nitisha Gahlot
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Jennifer Joseph
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, IIT Bombay, Powai, Mumbai, 400076, India.
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125
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Kotha SR, Staller MV. Clusters of acidic and hydrophobic residues can predict acidic transcriptional activation domains from protein sequence. Genetics 2023; 225:iyad131. [PMID: 37462277 PMCID: PMC10550315 DOI: 10.1093/genetics/iyad131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/03/2023] [Indexed: 10/06/2023] Open
Abstract
Transcription factors activate gene expression in development, homeostasis, and stress with DNA binding domains and activation domains. Although there exist excellent computational models for predicting DNA binding domains from protein sequence, models for predicting activation domains from protein sequence have lagged, particularly in metazoans. We recently developed a simple and accurate predictor of acidic activation domains on human transcription factors. Here, we show how the accuracy of this human predictor arises from the clustering of aromatic, leucine, and acidic residues, which together are necessary for acidic activation domain function. When we combine our predictor with the predictions of convolutional neural network (CNN) models trained in yeast, the intersection is more accurate than individual models, emphasizing that each approach carries orthogonal information. We synthesize these findings into a new set of activation domain predictions on human transcription factors.
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Affiliation(s)
- Sanjana R Kotha
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA
| | - Max Valentín Staller
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
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126
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Welles RM, Sojitra KA, Garabedian MV, Xia B, Wang W, Guan M, Regy RM, Gallagher ER, Hammer DA, Mittal J, Good MC. Determinants of Disordered Protein Co-Assembly Into Discrete Condensed Phases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.10.532134. [PMID: 36945618 PMCID: PMC10028963 DOI: 10.1101/2023.03.10.532134] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Cells harbor numerous mesoscale membraneless compartments that house specific biochemical processes and perform distinct cellular functions. These protein and RNA-rich bodies are thought to form through multivalent interactions among proteins and nucleic acids resulting in demixing via liquid-liquid phase separation (LLPS). Proteins harboring intrinsically disordered regions (IDRs) predominate in membraneless organelles. However, it is not known whether IDR sequence alone can dictate the formation of distinct condensed phases. We identified a pair of IDRs capable of forming spatially distinct condensates when expressed in cells. When reconstituted in vitro, these model proteins do not co-partition, suggesting condensation specificity is encoded directly in the polypeptide sequences. Through computational modeling and mutagenesis, we identified the amino acids and chain properties governing homotypic and heterotypic interactions that direct selective condensation. These results form the basis of physicochemical principles that may direct subcellular organization of IDRs into specific condensates and reveal an IDR code that can guide construction of orthogonal membraneless compartments.
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127
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Zytkiewicz E, Shkel IA, Cheng X, Rupanya A, McClure K, Karim R, Yang S, Yang F, Record MT. Quantifying Amide-Aromatic Interactions at Molecular and Atomic Levels: Experimentally Determined Enthalpic and Entropic Contributions to Interactions of Amide sp 2O, N, C and sp 3C Unified Atoms with Naphthalene sp 2C Atoms in Water. Biochemistry 2023; 62:2841-2853. [PMID: 37695675 DOI: 10.1021/acs.biochem.3c00367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
In addition to amide hydrogen bonds and the hydrophobic effect, interactions involving π-bonded sp2 atoms of amides, aromatics, and other groups occur in protein self-assembly processes including folding, oligomerization, and condensate formation. These interactions also occur in aqueous solutions of amide and aromatic compounds, where they can be quantified. Previous analysis of thermodynamic coefficients quantifying net-favorable interactions of amide compounds with other amides and aromatics revealed that interactions of amide sp2O with amide sp2N unified atoms (presumably C═O···H-N hydrogen bonds) and amide/aromatic sp2C (lone pair π, n-π*) are particularly favorable. Sp3C-sp3C (hydrophobic), sp3C-sp2C (hydrophobic, CH-π), sp2C-sp2C (hydrophobic, π-π), and sp3C-sp2N interactions are favorable, sp2C-sp2N interactions are neutral, while sp2O-sp2O and sp2N-sp2N self-interactions and sp2O-sp3C interactions are unfavorable. Here, from determinations of favorable effects of 14 amides on naphthalene solubility at 10, 25, and 45 °C, we dissect amide-aromatic interaction free energies into enthalpic and entropic contributions and find these vary systematically with amide composition. Analysis of these results yields enthalpic and entropic contributions to intrinsic strengths of interactions of amide sp2O, sp2N, sp2C, and sp3C unified atoms with aromatic sp2C atoms. For each interaction, enthalpic and entropic contributions have the same sign and are much larger in magnitude than the interaction free energy itself. The amide sp2O-aromatic sp2C interaction is enthalpy-driven and entropically unfavorable, consistent with direct chemical interaction (e.g., lone pair-π), while amide sp3C- and sp2C-aromatic sp2C interactions are entropy-driven and enthalpically unfavorable, consistent with hydrophobic effects. These findings are relevant for interactions involving π-bonded sp2 atoms in protein processes.
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Affiliation(s)
- Emily Zytkiewicz
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Irina A Shkel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Xian Cheng
- Biophysics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Anuchit Rupanya
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kate McClure
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Rezwana Karim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Sumin Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Felix Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - M Thomas Record
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Biophysics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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128
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Negri ML, D'Annunzio S, Vitali G, Zippo A. May the force be with you: Nuclear condensates function beyond transcription control: Potential nongenetic functions of nuclear condensates in physiological and pathological conditions. Bioessays 2023; 45:e2300075. [PMID: 37530178 DOI: 10.1002/bies.202300075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
Over the past decade, research has revealed biomolecular condensates' relevance in diverse cellular functions. Through a phase separation process, they concentrate macromolecules in subcompartments shaping the cellular organization and physiology. In the nucleus, biomolecular condensates assemble relevant biomolecules that orchestrate gene expression. We here hypothesize that chromatin condensates can also modulate the nongenetic functions of the genome, including the nuclear mechanical properties. The importance of chromatin condensates is supported by the genetic evidence indicating that mutations in their members are causative of a group of rare Mendelian diseases named chromatinopathies (CPs). Despite a broad spectrum of clinical features and the perturbations of the epigenetic machinery characterizing the CPs, recent findings highlighted negligible changes in gene expression. These data argue in favor of possible noncanonical functions of chromatin condensates in regulating the genome's spatial organization and, consequently, the nuclear mechanics. In this review, we discuss how condensates may impact nuclear mechanical properties, thus affecting the cellular response to mechanical cues and, eventually, cell fate and identity. Chromatin condensates organize macromolecules in the nucleus orchestrating the transcription regulation and mutations in their members are responsible for rare diseases named chromatinopathies. We argue that chromatin condensates, in concert with the nuclear lamina, may also govern the nuclear mechanical properties affecting the cellular response to external cues.
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Affiliation(s)
- Maria Luce Negri
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Sarah D'Annunzio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giulia Vitali
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessio Zippo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
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129
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Linsenmeier M, Faltova L, Morelli C, Capasso Palmiero U, Seiffert C, Küffner AM, Pinotsi D, Zhou J, Mezzenga R, Arosio P. The interface of condensates of the hnRNPA1 low-complexity domain promotes formation of amyloid fibrils. Nat Chem 2023; 15:1340-1349. [PMID: 37749234 PMCID: PMC10533390 DOI: 10.1038/s41557-023-01289-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/05/2023] [Indexed: 09/27/2023]
Abstract
The maturation of liquid-like protein condensates into amyloid fibrils has been associated with several neurodegenerative diseases. However, the molecular mechanisms underlying this liquid-to-solid transition have remained largely unclear. Here we analyse the amyloid formation mediated by condensation of the low-complexity domain of hnRNPA1, a protein involved in amyotrophic lateral sclerosis. We show that phase separation and fibrillization are connected but distinct processes that are modulated by different regions of the protein sequence. By monitoring the spatial and temporal evolution of amyloid formation we demonstrate that the formation of fibrils does not occur homogeneously inside the droplets but is promoted at the interface of the condensates. We further show that coating the interface of the droplets with surfactant molecules inhibits fibril formation. Our results reveal that the interface of biomolecular condensates of hnRNPA1 promotes fibril formation, therefore suggesting interfaces as a potential novel therapeutic target against the formation of aberrant amyloids mediated by condensation.
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Affiliation(s)
- Miriam Linsenmeier
- Department of Chemistry and Applied Sciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Sciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Chiara Morelli
- Department of Chemistry and Applied Sciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Sciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Charlotte Seiffert
- Department of Chemistry and Applied Sciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Andreas M Küffner
- Department of Chemistry and Applied Sciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Dorothea Pinotsi
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zurich, Switzerland
| | - Jiangtao Zhou
- Department for Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Raffaele Mezzenga
- Department for Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Sciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland.
- Bringing Materials to Life Initiative, ETH Zurich, Zurich, Switzerland.
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130
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Hazra M, Levy Y. Cross-Talk of Cation-π Interactions with Electrostatic and Aromatic Interactions: A Salt-Dependent Trade-off in Biomolecular Condensates. J Phys Chem Lett 2023; 14:8460-8469. [PMID: 37721444 PMCID: PMC10544028 DOI: 10.1021/acs.jpclett.3c01642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
Biomolecular condensates are essential for cellular functionality, yet the complex interplay among the diverse molecular interactions that mediate their formation remains poorly understood. Here, using coarse-grained molecular dynamics simulations, we address the contribution of cation-π interactions to the stability of condensates formed via liquid-liquid phase separation. We found greater stabilization of up to 80% via cation-π interactions in condensates formed from peptides with higher aromatic residue content or less charge clustering. The contribution of cation-π interactions to droplet stability increases with increasing ionic strength, suggesting a trade-off between cation-π and electrostatic interactions. Cation-π interactions, therefore, can compensate for reduced electrostatic interactions, such as occurs at higher salt concentrations and in sequences with less charged residue content or clustering. Designing condensates with desired biophysical characteristics therefore requires quantification not only of the individual interactions but also cross-talks involving charge-charge, π-π, and cation-π interactions.
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Affiliation(s)
- Milan
Kumar Hazra
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot 76100, Israel
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131
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Flores-Solis D, Lushpinskaia IP, Polyansky AA, Changiarath A, Boehning M, Mirkovic M, Walshe J, Pietrek LM, Cramer P, Stelzl LS, Zagrovic B, Zweckstetter M. Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II. Nat Commun 2023; 14:5979. [PMID: 37749095 PMCID: PMC10519987 DOI: 10.1038/s41467-023-41633-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 09/10/2023] [Indexed: 09/27/2023] Open
Abstract
Eukaryotic gene regulation and pre-mRNA transcription depend on the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. Due to its highly repetitive, intrinsically disordered sequence, the CTD enables clustering and phase separation of Pol II. The molecular interactions that drive CTD phase separation and Pol II clustering are unclear. Here, we show that multivalent interactions involving tyrosine impart temperature- and concentration-dependent self-coacervation of the CTD. NMR spectroscopy, molecular ensemble calculations and all-atom molecular dynamics simulations demonstrate the presence of diverse tyrosine-engaging interactions, including tyrosine-proline contacts, in condensed states of human CTD and other low-complexity proteins. We further show that the network of multivalent interactions involving tyrosine is responsible for the co-recruitment of the human Mediator complex and CTD during phase separation. Our work advances the understanding of the driving forces of CTD phase separation and thus provides the basis to better understand CTD-mediated Pol II clustering in eukaryotic gene transcription.
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Affiliation(s)
- David Flores-Solis
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 35075, Göttingen, Germany
| | - Irina P Lushpinskaia
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 35075, Göttingen, Germany
| | - Anton A Polyansky
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Campus Vienna Biocenter 5, 1030, Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Arya Changiarath
- Faculty of Biology, Johannes Gutenberg University Mainz (JGU), Gresemundweg 2, 55128, Mainz, Germany
- KOMET1, Institute of Physics, Johannes Gutenberg University Mainz (JGU), Staudingerweg 9, 55099, Mainz, Germany
| | - Marc Boehning
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany
| | - Milana Mirkovic
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Campus Vienna Biocenter 5, 1030, Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - James Walshe
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany
| | - Lisa M Pietrek
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Strasße 3, 60438, Frankfurt am Main, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany
| | - Lukas S Stelzl
- Faculty of Biology, Johannes Gutenberg University Mainz (JGU), Gresemundweg 2, 55128, Mainz, Germany
- KOMET1, Institute of Physics, Johannes Gutenberg University Mainz (JGU), Staudingerweg 9, 55099, Mainz, Germany
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Bojan Zagrovic
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Campus Vienna Biocenter 5, 1030, Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 35075, Göttingen, Germany.
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany.
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132
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Khandwala CB, Sarkar P, Schmidt HB, Ma M, Kinnebrew M, Pusapati GV, Patel BB, Tillo D, Lebensohn AM, Rohatgi R. Direct ionic stress sensing and mitigation by the transcription factor NFAT5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.23.559074. [PMID: 37886503 PMCID: PMC10602047 DOI: 10.1101/2023.09.23.559074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Homeostatic control of intracellular ionic strength is essential for protein, organelle and genome function, yet mechanisms that sense and enable adaptation to ionic stress remain poorly understood in animals. We find that the transcription factor NFAT5 directly senses solution ionic strength using a C-terminal intrinsically disordered region. Both in intact cells and in a purified system, NFAT5 forms dynamic, reversible biomolecular condensates in response to increasing ionic strength. This self-associative property, conserved from insects to mammals, allows NFAT5 to accumulate in the nucleus and activate genes that restore cellular ion content. Mutations that reduce condensation or those that promote aggregation both reduce NFAT5 activity, highlighting the importance of optimally tuned associative interactions. Remarkably, human NFAT5 alone is sufficient to reconstitute a mammalian transcriptional response to ionic or hypertonic stress in yeast. Thus NFAT5 is both the sensor and effector of a cell-autonomous ionic stress response pathway in animal cells.
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Affiliation(s)
- Chandni B. Khandwala
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Parijat Sarkar
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - H. Broder Schmidt
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mengxiao Ma
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maia Kinnebrew
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ganesh V. Pusapati
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bhaven B. Patel
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Desiree Tillo
- Center for Cancer Research Genomics Core, National Cancer Institute, National Institutes of Health, NIH, Building 37, RM 2056B, Bethesda, MD, 20892, USA
| | - Andres M. Lebensohn
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NIH, Building 37, RM 2056B, Bethesda, MD, 20892, USA
| | - Rajat Rohatgi
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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133
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Mukherjee S, Schäfer LV. Thermodynamic forces from protein and water govern condensate formation of an intrinsically disordered protein domain. Nat Commun 2023; 14:5892. [PMID: 37735186 PMCID: PMC10514047 DOI: 10.1038/s41467-023-41586-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) can drive a multitude of cellular processes by compartmentalizing biological cells via the formation of dense liquid biomolecular condensates, which can function as membraneless organelles. Despite its importance, the molecular-level understanding of the underlying thermodynamics of this process remains incomplete. In this study, we use atomistic molecular dynamics simulations of the low complexity domain (LCD) of human fused in sarcoma (FUS) protein to investigate the contributions of water and protein molecules to the free energy changes that govern LLPS. Both protein and water components are found to have comparably sizeable thermodynamic contributions to the formation of FUS condensates. Moreover, we quantify the counteracting effects of water molecules that are released into the bulk upon condensate formation and the waters retained within the protein droplets. Among the various factors considered, solvation entropy and protein interaction enthalpy are identified as the most important contributions, while solvation enthalpy and protein entropy changes are smaller. These results provide detailed molecular insights on the intricate thermodynamic interplay between protein- and solvation-related forces underlying the formation of biomolecular condensates.
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Affiliation(s)
- Saumyak Mukherjee
- Center for Theoretical Chemistry, Ruhr University Bochum, D-44780, Bochum, Germany
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Ruhr University Bochum, D-44780, Bochum, Germany.
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134
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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: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [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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135
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Riback JA, Eeftens JM, Lee DSW, Quinodoz SA, Donlic A, Orlovsky N, Wiesner L, Beckers L, Becker LA, Strom AR, Rana U, Tolbert M, Purse BW, Kleiner R, Kriwacki R, Brangwynne CP. Viscoelasticity and advective flow of RNA underlies nucleolar form and function. Mol Cell 2023; 83:3095-3107.e9. [PMID: 37683610 PMCID: PMC11089468 DOI: 10.1016/j.molcel.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 04/20/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
The nucleolus is the largest biomolecular condensate and facilitates transcription, processing, and assembly of ribosomal RNA (rRNA). Although nucleolar function is thought to require multiphase liquid-like properties, nucleolar fluidity and its connection to the highly coordinated transport and biogenesis of ribosomal subunits are poorly understood. Here, we use quantitative imaging, mathematical modeling, and pulse-chase nucleotide labeling to examine nucleolar material properties and rRNA dynamics. The mobility of rRNA is several orders of magnitude slower than that of nucleolar proteins, with rRNA steadily moving away from the transcriptional sites in a slow (∼1 Å/s), radially directed fashion. This constrained but directional mobility, together with polymer physics-based calculations, suggests that nascent rRNA forms an entangled gel, whose constant production drives outward flow. We propose a model in which progressive maturation of nascent rRNA reduces its initial entanglement, fluidizing the nucleolar periphery to facilitate the release of assembled pre-ribosomal particles.
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Affiliation(s)
- Joshua A Riback
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Jorine M Eeftens
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Daniel S W Lee
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Sofia A Quinodoz
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Anita Donlic
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Natalia Orlovsky
- Department of Molecular Biology, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Lennard Wiesner
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Lien Beckers
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Lindsay A Becker
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Amy R Strom
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Ushnish Rana
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Michele Tolbert
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Byron W Purse
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Ralph Kleiner
- Department of Chemistry, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Richard Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, Princeton, NJ 08544, USA; Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544, USA.
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136
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Lipiński WP, Zehnder J, Abbas M, Güntert P, Spruijt E, Wiegand T. Fibrils Emerging from Droplets: Molecular Guiding Principles behind Phase Transitions of a Short Peptide-Based Condensate Studied by Solid-State NMR. Chemistry 2023; 29:e202301159. [PMID: 37310801 DOI: 10.1002/chem.202301159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/15/2023]
Abstract
Biochemical reactions occurring in highly crowded cellular environments require different means of control to ensure productivity and specificity. Compartmentalization of reagents by liquid-liquid phase separation is one of these means. However, extremely high local protein concentrations of up to 400 mg/ml can result in pathological aggregation into fibrillar amyloid structures, a phenomenon that has been linked to various neurodegenerative diseases. Despite its relevance, the process of liquid-to-solid transition inside condensates is still not well understood at the molecular level. We thus herein use small peptide derivatives that can undergo both liquid-liquid and subsequent liquid-to-solid phase transition as model systems to study both processes. Using solid-state nuclear magnetic resonance (NMR) and transmission electron microscopy (TEM), we compare the structure of condensed states of leucine, tryptophan and phenylalanine containing derivatives, distinguishing between liquid-like condensates, amorphous aggregates and fibrils, respectively. A structural model for the fibrils formed by the phenylalanine derivative was obtained by an NMR-based structure calculation. The fibrils are stabilised by hydrogen bonds and side-chain π-π interactions, which are likely much less pronounced or absent in the liquid and amorphous state. Such noncovalent interactions are equally important for the liquid-to-solid transition of proteins, particularly those related to neurodegenerative diseases.
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Affiliation(s)
- Wojciech P Lipiński
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Johannes Zehnder
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Manzar Abbas
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Peter Güntert
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- Institute of Biophysical Chemistry Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji-shi, 192-0397, Tokyo, Japan
| | - Evan Spruijt
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Thomas Wiegand
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
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137
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Nicy, Collepardo-Guevara R, Joseph JA, Wales DJ. Energy landscapes and heat capacity signatures for peptides correlate with phase separation propensity. QRB DISCOVERY 2023; 4:e7. [PMID: 37771761 PMCID: PMC10523320 DOI: 10.1017/qrd.2023.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/09/2023] [Accepted: 07/17/2023] [Indexed: 09/30/2023] Open
Abstract
Phase separation plays an important role in the formation of membraneless compartments within the cell and intrinsically disordered proteins with low-complexity sequences can drive this compartmentalisation. Various intermolecular forces, such as aromatic-aromatic and cation-aromatic interactions, promote phase separation. However, little is known about how the ability of proteins to phase separate under physiological conditions is encoded in their energy landscapes and this is the focus of the present investigation. Our results provide a first glimpse into how the energy landscapes of minimal peptides that contain - and cation- interactions differ from the peptides that lack amino acids with such interactions. The peaks in the heat capacity () as a function of temperature report on alternative low-lying conformations that differ significantly in terms of their enthalpic and entropic contributions. The analysis and subsequent quantification of frustration of the energy landscape suggest that the interactions that promote phase separation lead to features (peaks or inflection points) at low temperatures in . More features may occur for peptides containing residues with better phase separation propensity and the energy landscape is more frustrated for such peptides. Overall, this work links the features in the underlying single-molecule potential energy landscapes to their collective phase separation behaviour and identifies quantities ( and frustration metric) that can be utilised in soft material design.
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Affiliation(s)
- Nicy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Department of Physics, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Jerelle A. Joseph
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - David J. Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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138
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Wilson C, Lewis KA, Fitzkee NC, Hough LE, Whitten ST. ParSe 2.0: A web tool to identify drivers of protein phase separation at the proteome level. Protein Sci 2023; 32:e4756. [PMID: 37574757 PMCID: PMC10464302 DOI: 10.1002/pro.4756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
We have developed an algorithm, ParSe, which accurately identifies from the primary sequence those protein regions likely to exhibit physiological phase separation behavior. Originally, ParSe was designed to test the hypothesis that, for flexible proteins, phase separation potential is correlated to hydrodynamic size. While our results were consistent with that idea, we also found that many different descriptors could successfully differentiate between three classes of protein regions: folded, intrinsically disordered, and phase-separating intrinsically disordered. Consequently, numerous combinations of amino acid property scales can be used to make robust predictions of protein phase separation. Built from that finding, ParSe 2.0 uses an optimal set of property scales to predict domain-level organization and compute a sequence-based prediction of phase separation potential. The algorithm is fast enough to scan the whole of the human proteome in minutes on a single computer and is equally or more accurate than other published predictors in identifying proteins and regions within proteins that drive phase separation. Here, we describe a web application for ParSe 2.0 that may be accessed through a browser by visiting https://stevewhitten.github.io/Parse_v2_FASTA to quickly identify phase-separating proteins within large sequence sets, or by visiting https://stevewhitten.github.io/Parse_v2_web to evaluate individual protein sequences.
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Affiliation(s)
- Colorado Wilson
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
- Present address:
Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular BiophysicsUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Karen A. Lewis
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
| | - Nicholas C. Fitzkee
- Department of ChemistryMississippi State UniversityMississippi StateMississippiUSA
| | - Loren E. Hough
- Department of PhysicsUniversity of Colorado BoulderBoulderColoradoUSA
- BioFrontiers InstituteUniversity of Colorado BoulderBoulderColoradoUSA
| | - Steven T. Whitten
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
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139
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Ho W, Huang H, Huang J. IFF: Identifying key residues in intrinsically disordered regions of proteins using machine learning. Protein Sci 2023; 32:e4739. [PMID: 37498545 PMCID: PMC10443345 DOI: 10.1002/pro.4739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/21/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023]
Abstract
Conserved residues in protein homolog sequence alignments are structurally or functionally important. For intrinsically disordered proteins or proteins with intrinsically disordered regions (IDRs), however, alignment often fails because they lack a steric structure to constrain evolution. Although sequences vary, the physicochemical features of IDRs may be preserved in maintaining function. Therefore, a method to retrieve common IDR features may help identify functionally important residues. We applied unsupervised contrastive learning to train a model with self-attention neuronal networks on human IDR orthologs. Parameters in the model were trained to match sequences in ortholog pairs but not in other IDRs. The trained model successfully identifies previously reported critical residues from experimental studies, especially those with an overall pattern (e.g., multiple aromatic residues or charged blocks) rather than short motifs. This predictive model can be used to identify potentially important residues in other proteins, improving our understanding of their functions. The trained model can be run directly from the Jupyter Notebook in the GitHub repository using Binder (mybinder.org). The only required input is the primary sequence. The training scripts are available on GitHub (https://github.com/allmwh/IFF). The training datasets have been deposited in an Open Science Framework repository (https://osf.io/jk29b).
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Affiliation(s)
- Wen‐Lin Ho
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Hsuan‐Cheng Huang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Jie‐rong Huang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
- Department of Life Sciences and Institute of Genome SciencesNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
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140
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Ray S, Mason TO, Boyens-Thiele L, Farzadfard A, Larsen JA, Norrild RK, Jahnke N, Buell AK. Mass photometric detection and quantification of nanoscale α-synuclein phase separation. Nat Chem 2023; 15:1306-1316. [PMID: 37337111 DOI: 10.1038/s41557-023-01244-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/19/2023] [Indexed: 06/21/2023]
Abstract
Protein liquid-liquid phase separation can lead to disease-related amyloid fibril formation. The mechanisms of conversion of monomeric protein into condensate droplets and of the latter into fibrils remain elusive. Here, using mass photometry, we demonstrate that the Parkinson's disease-related protein, α-synuclein, can form dynamic nanoscale clusters at physiologically relevant, sub-saturated concentrations. Nanoclusters nucleate in bulk solution and promote amyloid fibril formation of the dilute-phase monomers upon ageing. Their formation is instantaneous, even under conditions where macroscopic assemblies appear only after several days. The slow growth of the nanoclusters can be attributed to a kinetic barrier, probably due to an interfacial penalty from the charged C terminus of α-synuclein. Our findings reveal that α-synuclein phase separation occurs at much wider ranges of solution conditions than reported so far. Importantly, we establish mass photometry as a promising methodology to detect and quantify nanoscale precursors of phase separation. We also demonstrate its general applicability by probing the existence of nanoclusters of a non-amyloidogenic protein, Ddx4n1.
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Affiliation(s)
- Soumik Ray
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas O Mason
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Lars Boyens-Thiele
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Azad Farzadfard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jacob Aunstrup Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Rasmus K Norrild
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Nadin Jahnke
- Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
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141
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Qin S, Zhou HX. Atomistic modeling of liquid-liquid phase equilibrium explains dependence of critical temperature on γ-crystallin sequence. Commun Biol 2023; 6:886. [PMID: 37644195 PMCID: PMC10465548 DOI: 10.1038/s42003-023-05270-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
Liquid-liquid phase separation of protein solutions has regained heightened attention for its biological importance and pathogenic relevance. Coarse-grained models are limited when explaining residue-level effects on phase equilibrium. Here we report phase diagrams for γ-crystallins using atomistic modeling. The calculations were made possible by combining our FMAP method for computing chemical potentials and Brownian dynamics simulations for configurational sampling of dense protein solutions, yielding the binodal and critic temperature (Tc). We obtain a higher Tc for a known high-Tc γ-crystallin, γF, than for a low-Tc paralog, γB. The difference in Tc is corroborated by a gap in second virial coefficient. Decomposition of inter-protein interactions reveals one amino-acid substitution between γB and γF, from Ser to Trp at position 130, as the major contributor to the difference in Tc. This type of analysis enables us to link phase equilibrium to amino-acid sequence and to design mutations for altering phase equilibrium.
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Affiliation(s)
- Sanbo Qin
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA.
- Department of Physics, University of Illinois Chicago, Chicago, IL, 60607, USA.
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142
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Lesage P, Maxwell PH. A prion-like domain in Gag capsid protein drives retrotransposon particle assembly and mobility. Proc Natl Acad Sci U S A 2023; 120:e2311419120. [PMID: 37590432 PMCID: PMC10466094 DOI: 10.1073/pnas.2311419120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023] Open
Affiliation(s)
- Pascale Lesage
- Université Paris Cité, Institut de Recherche Saint Louis, Inserm, U944, CNRS, UMR7212, Paris75010, France
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143
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Zhang Y, Li S, Gong X, Chen J. Accurate Simulation of Coupling between Protein Secondary Structure and Liquid-Liquid Phase Separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554378. [PMID: 37662293 PMCID: PMC10473686 DOI: 10.1101/2023.08.22.554378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Intrinsically disordered proteins (IDPs) frequently mediate liquid-liquid phase separation (LLPS) that underlies the formation of membraneless organelles. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding sequence-specific phase separation of IDPs. However, the widely-used Cα-only models are severely limited in capturing the peptide nature of IDPs, including backbone-mediated interactions and effects of secondary structures, in LLPS. Here, we describe a hybrid resolution (HyRes) protein model for accurate description of the backbone and transient secondary structures in LLPS. With an atomistic backbone and coarse-grained side chains, HyRes accurately predicts the residue helical propensity and chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for direct simulation of spontaneous phase separation, and at the same time accurate enough to resolve the effects of single mutations. HyRes simulations also successfully predict increased beta-sheet formation in the condensate, consistent with available experimental data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate LLPS propensity. The simulations successfully recapitulate the effect of these mutants on the helicity and LLPS propensity of TDP-43 CR. Analyses reveal that the balance between backbone and sidechain-mediated interactions, but not helicity itself, actually determines LLPS propensity. We believe that the HyRes model represents an important advance in the molecular simulation of LLPS and will help elucidate the coupling between IDP transient secondary structures and phase separation.
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Affiliation(s)
| | | | - Xiping Gong
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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144
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Lalmansingh JM, Keeley AT, Ruff KM, Pappu RV, Holehouse AS. SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins. J Chem Theory Comput 2023; 19:5609-5620. [PMID: 37463458 PMCID: PMC11188088 DOI: 10.1021/acs.jctc.3c00190] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Conformational heterogeneity is a defining hallmark of intrinsically disordered proteins and protein regions (IDRs). The functions of IDRs and the emergent cellular phenotypes they control are associated with sequence-specific conformational ensembles. Simulations of conformational ensembles that are based on atomistic and coarse-grained models are routinely used to uncover the sequence-specific interactions that may contribute to IDR functions. These simulations are performed either independently or in conjunction with data from experiments. Functionally relevant features of IDRs can span a range of length scales. Extracting these features requires analysis routines that quantify a range of properties. Here, we describe a new analysis suite simulation analysis of unfolded regions of proteins (SOURSOP), an object-oriented and open-source toolkit designed for the analysis of simulated conformational ensembles of IDRs. SOURSOP implements several analysis routines motivated by principles in polymer physics, offering a unique collection of simple-to-use functions to characterize IDR ensembles. As an extendable framework, SOURSOP supports the development and implementation of new analysis routines that can be easily packaged and shared.
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Affiliation(s)
- Jared M. Lalmansingh
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alex T. Keeley
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana-Champaign, IL 61801, USA
| | - Kiersten M. Ruff
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alex S. Holehouse
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
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145
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Mohanty P, Shenoy J, Rizuan A, Mercado-Ortiz JF, Fawzi NL, Mittal J. A synergy between site-specific and transient interactions drives the phase separation of a disordered, low-complexity domain. Proc Natl Acad Sci U S A 2023; 120:e2305625120. [PMID: 37579155 PMCID: PMC10450430 DOI: 10.1073/pnas.2305625120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is involved in key processes in RNA metabolism and is frequently implicated in many neurodegenerative diseases, including amyotrophic lateral sclerosis and frontotemporal dementia. The prion-like, disordered C-terminal domain (CTD) of TDP-43 is aggregation-prone, can undergo liquid-liquid phase separation (LLPS) in isolation, and is critical for phase separation (PS) of the full-length protein under physiological conditions. While a short conserved helical region (CR, spanning residues 319-341) promotes oligomerization and is essential for LLPS, aromatic residues in the flanking disordered regions (QN-rich, IDR1/2) are also found to play a critical role in PS and aggregation. Compared with other phase-separating proteins, TDP-43 CTD has a notably distinct sequence composition including many aliphatic residues such as methionine and leucine. Aliphatic residues were previously suggested to modulate the apparent viscosity of the resulting phases, but their direct contribution toward CTD phase separation has been relatively ignored. Using multiscale simulations coupled with in vitro saturation concentration (csat) measurements, we identified the importance of aromatic residues while also suggesting an essential role for aliphatic methionine residues in promoting single-chain compaction and LLPS. Surprisingly, NMR experiments showed that transient interactions involving phenylalanine and methionine residues in the disordered flanking regions can directly enhance site-specific, CR-mediated intermolecular association. Overall, our work highlights an underappreciated mode of biomolecular recognition, wherein both transient and site-specific hydrophobic interactions act synergistically to drive the oligomerization and phase separation of a disordered, low-complexity domain.
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Affiliation(s)
- Priyesh Mohanty
- Artie McFerrinDepartment of Chemical Engineering, Texas A&M University, College Station, TX77843
| | - Jayakrishna Shenoy
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI02912
| | - Azamat Rizuan
- Artie McFerrinDepartment of Chemical Engineering, Texas A&M University, College Station, TX77843
| | - José F. Mercado-Ortiz
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI02912
| | - Nicolas L. Fawzi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI02912
| | - Jeetain Mittal
- Artie McFerrinDepartment of Chemical Engineering, Texas A&M University, College Station, TX77843
- Department of Chemistry, Texas A&M University, College Station, TX77843
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX77843
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146
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Tortora MMC, Brennan LD, Karpen G, Jost D. HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation. Proc Natl Acad Sci U S A 2023; 120:e2211855120. [PMID: 37549295 PMCID: PMC10438847 DOI: 10.1073/pnas.2211855120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 06/28/2023] [Indexed: 08/09/2023] Open
Abstract
The spatial segregation of pericentromeric heterochromatin (PCH) into distinct, membrane-less nuclear compartments involves the binding of Heterochromatin Protein 1 (HP1) to H3K9me2/3-rich genomic regions. While HP1 exhibits liquid-liquid phase separation properties in vitro, its mechanistic impact on the structure and dynamics of PCH condensate formation in vivo remains largely unresolved. Here, using a minimal theoretical framework, we systematically investigate the mutual coupling between self-interacting HP1-like molecules and the chromatin polymer. We reveal that the specific affinity of HP1 for H3K9me2/3 loci facilitates coacervation in nucleo and promotes the formation of stable PCH condensates at HP1 levels far below the concentration required to observe phase separation in purified protein assays in vitro. These heterotypic HP1-chromatin interactions give rise to a strong dependence of the nucleoplasmic HP1 density on HP1-H3K9me2/3 stoichiometry, consistent with the thermodynamics of multicomponent phase separation. The dynamical cross talk between HP1 and the viscoelastic chromatin scaffold also leads to anomalously slow equilibration kinetics, which strongly depend on the genomic distribution of H3K9me2/3 domains and result in the coexistence of multiple long-lived, microphase-separated PCH compartments. The morphology of these complex coacervates is further found to be governed by the dynamic establishment of the underlying H3K9me2/3 landscape, which may drive their increasingly abnormal, aspherical shapes during cell development. These findings compare favorably to 4D microscopy measurements of HP1 condensate formation in live Drosophila embryos and suggest a general quantitative model of PCH formation based on the interplay between HP1-based phase separation and chromatin polymer mechanics.
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Affiliation(s)
- Maxime M. C. Tortora
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 69007Lyon, France
| | - Lucy D. Brennan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Gary Karpen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of BioEngineering and BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 69007Lyon, France
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147
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Alston JJ, Soranno A. Condensation Goes Viral: A Polymer Physics Perspective. J Mol Biol 2023; 435:167988. [PMID: 36709795 PMCID: PMC10368797 DOI: 10.1016/j.jmb.2023.167988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
The past decade has seen a revolution in our understanding of how the cellular environment is organized, where an incredible body of work has provided new insights into the role played by membraneless organelles. These rapid advancements have been made possible by an increasing awareness of the peculiar physical properties that give rise to such bodies and the complex biology that enables their function. Viral infections are not extraneous to this. Indeed, in host cells, viruses can harness existing membraneless compartments or, even, induce the formation of new ones. By hijacking the cellular machinery, these intracellular bodies can assist in the replication, assembly, and packaging of the viral genome as well as in the escape of the cellular immune response. Here, we provide a perspective on the fundamental polymer physics concepts that may help connect and interpret the different observed phenomena, ranging from the condensation of viral genomes to the phase separation of multicomponent solutions. We complement the discussion of the physical basis with a description of biophysical methods that can provide quantitative insights for testing and developing theoretical and computational models.
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Affiliation(s)
- Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA.
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148
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Kaddis Maldonado R, Lambert GS, Rice BL, Sudol M, Flanagan JM, Parent LJ. The Rous sarcoma virus Gag Polyprotein Forms Biomolecular Condensates Driven by Intrinsically-disordered Regions. J Mol Biol 2023; 435:168182. [PMID: 37328094 PMCID: PMC10527454 DOI: 10.1016/j.jmb.2023.168182] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
Biomolecular condensates (BMCs) play important roles incellular structures includingtranscription factories, splicing speckles, and nucleoli. BMCs bring together proteins and other macromolecules, selectively concentrating them so that specific reactions can occur without interference from the surrounding environment. BMCs are often made up of proteins that contain intrinsically disordered regions (IDRs), form phase-separated spherical puncta, form liquid-like droplets that undergo fusion and fission, contain molecules that are mobile, and are disrupted with phase-dissolving drugs such as 1,6-hexanediol. In addition to cellular proteins, many viruses, including influenza A, SARS-CoV-2, and human immunodeficiency virus type 1 (HIV-1) encode proteins that undergo phase separation and rely on BMC formation for replication. In prior studies of the retrovirus Rous sarcoma virus (RSV), we observed that the Gag protein forms discrete spherical puncta in the nucleus, cytoplasm, and at the plasma membrane that co-localize with viral RNA and host factors, raising the possibility that RSV Gag forms BMCs that participate in the intracellular phase of the virion assembly pathway. In our current studies, we found that Gag contains IDRs in the N-terminal (MAp2p10) and C-terminal (NC) regions of the protein and fulfills many criteria of BMCs. Although the role of BMC formation in RSV assembly requires further study, our results suggest the biophysical properties of condensates are required for the formation of Gag complexes in the nucleus and the cohesion of these complexes as they traffic through the nuclear pore, into the cytoplasm, and to the plasma membrane, where the final assembly and release of virus particles occurs.
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Affiliation(s)
- Rebecca Kaddis Maldonado
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA; Department of Microbiology & Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Gregory S Lambert
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Breanna L Rice
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Malgorzata Sudol
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - John M Flanagan
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Leslie J Parent
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA; Department of Microbiology & Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
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149
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Alston JJ, Soranno A, Holehouse AS. Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.06.552128. [PMID: 37609146 PMCID: PMC10441348 DOI: 10.1101/2023.08.06.552128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Intrinsically disordered regions (IDRs) are critical for cellular function, yet often appear to lack sequence conservation when assessed by multiple sequence alignments. This raises the question of if and how function can be encoded and preserved in these regions despite massive sequence variation. To address this question, we have applied coarse-grained molecular dynamics simulations to investigate non-specific RNA binding of coronavirus nucleocapsid proteins. Coronavirus nucleocapsid proteins consist of multiple interspersed disordered and folded domains that bind RNA. We focussed here on the first two domains of coronavirus nucleocapsid proteins, the disordered N-terminal domain (NTD) followed by the folded RNA binding domain (RBD). While the NTD is highly variable across evolution, the RBD is structurally conserved. This combination makes the NTD-RBD a convenient model system to explore the interplay between an IDR adjacent to a folded domain, and how changes in IDR sequence can influence molecular recognition of a partner. Our results reveal a surprising degree of sequence-specificity encoded by both the composition and the precise order of the amino acids in the NTD. The presence of an NTD can - depending on the sequence - either suppress or enhance RNA binding. Despite this sensitivity, large-scale variation in NTD sequences is possible while certain sequence features are retained. Consequently, a conformationally-conserved fuzzy RNA:protein complex is found across nucleocapsid protein orthologs, despite large-scale changes in both NTD sequence and RBD surface chemistry. Taken together, these insights shed light on the ability of disordered regions to preserve functional characteristics despite their sequence variability.
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150
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Saha D, Jana B. Decoupling of Interactions between Model-Charged Peptides Reveals Key Factors Responsible for Liquid-Liquid Phase Separation. J Phys Chem B 2023; 127:6656-6667. [PMID: 37480340 DOI: 10.1021/acs.jpcb.3c03087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Liquid-liquid phase separation (LLPS) by disordered proteins has been shown to govern biological processes and cause numerous diseases. Therefore, a deeper understanding of the interactions and their variation with external factors is key to modulating the LLPS behavior of different systems and protecting proteins from pathological aggregation. In this context, we have looked at interactions between similarly charged peptides to understand the molecular features that may drive or prevent condensate formation under various conditions. We have studied dimer formation for model peptides where charged and noncharged amino acids have been placed alternatively. Using arginine and glutamic acid as the charged residues and varying the other residues with glycine, alanine, and proline to alter hydrophobicity, we have obtained the free-energy surface (FES) for the dimer formation for these systems under high salt concentration at two different temperatures using all-atom molecular dynamics simulations and the well-tempered metadynamics method. Our results indicate that a combination of effects such as hydrophobicity, arginine-arginine interactions, or water release from the solvation shell makes dimerization free energy more favorable for the positively charged peptides with lower flexibility. For the negatively charged peptides, the crucial role of water has been found in governing the FES. Systems having charged residues and phenylalanine in the peptide sequence also have been studied at high salt concentrations using unbiased simulations. In this case, only the positively charged peptides were found to aggregate through temperature-dependent hydrophobic and cation-π interactions. Overall, our study indicates that the negatively charged peptides are more likely to remain in the dilute phase under various conditions compared to the positively charged systems. The findings from our study would be helpful in designing and controlling systems to obtain LLPS behavior for therapeutic usage.
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Affiliation(s)
- Debasis Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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