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Moses D, Guadalupe K, Yu F, Flores E, Perez AR, McAnelly R, Shamoon NM, Kaur G, Cuevas-Zepeda E, Merg AD, Martin EW, Holehouse AS, Sukenik S. Structural biases in disordered proteins are prevalent in the cell. Nat Struct Mol Biol 2024; 31:283-292. [PMID: 38177684 PMCID: PMC10873198 DOI: 10.1038/s41594-023-01148-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 10/04/2023] [Indexed: 01/06/2024]
Abstract
Intrinsically disordered proteins and protein regions (IDPs) are prevalent in all proteomes and are essential to cellular function. Unlike folded proteins, IDPs exist in an ensemble of dissimilar conformations. Despite this structural plasticity, intramolecular interactions create sequence-specific structural biases that determine an IDP ensemble's three-dimensional shape. Such structural biases can be key to IDP function and are often measured in vitro, but whether those biases are preserved inside the cell is unclear. Here we show that structural biases in IDP ensembles found in vitro are recapitulated inside human-derived cells. We further reveal that structural biases can change in a sequence-dependent manner due to changes in the intracellular milieu, subcellular localization, and intramolecular interactions with tethered well-folded domains. We propose that the structural sensitivity of IDP ensembles can be leveraged for biological function, can be the underlying cause of IDP-driven pathology or can be used to design disorder-based biosensors and actuators.
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Affiliation(s)
- David Moses
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
- Center for Cellular and Biomolecular Machines, University of California, Merced, Merced, CA, USA
| | - Karina Guadalupe
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
- Center for Cellular and Biomolecular Machines, University of California, Merced, Merced, CA, USA
| | - Feng Yu
- Center for Cellular and Biomolecular Machines, University of California, Merced, Merced, CA, USA
- Quantitative and Systems Biology Program, University of California, Merced, Merced, CA, USA
| | - Eduardo Flores
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
- Center for Cellular and Biomolecular Machines, University of California, Merced, Merced, CA, USA
| | - Anthony R Perez
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
- Center for Cellular and Biomolecular Machines, University of California, Merced, Merced, CA, USA
| | - Ralph McAnelly
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
| | - Nora M Shamoon
- Center for Cellular and Biomolecular Machines, University of California, Merced, Merced, CA, USA
- California State University, Stanislaus, Turlock, CA, USA
| | - Gagandeep Kaur
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
| | | | - Andrea D Merg
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
- Center for Cellular and Biomolecular Machines, University of California, Merced, Merced, CA, USA
| | - Erik W Martin
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
- Dewpoint Therapeutics, Boston, MA, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO, USA
| | - Shahar Sukenik
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA.
- Center for Cellular and Biomolecular Machines, University of California, Merced, Merced, CA, USA.
- Quantitative and Systems Biology Program, University of California, Merced, Merced, CA, USA.
- Health Sciences Research Institute, University of California, Merced, Merced, CA, USA.
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2
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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 2023:2023.10.29.564547. [PMID: 37961106 PMCID: PMC10634935 DOI: 10.1101/2023.10.29.564547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Holehouse A, Emenecker R, Guadalupe K, Shamoon N, Sukenik S. Sequence-ensemble-function relationships for disordered proteins in live cells. Res Sq 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Cuevas-Velazquez CL, Vellosillo T, Guadalupe K, Schmidt HB, Yu F, Moses D, Brophy JAN, Cosio-Acosta D, Das A, Wang L, Jones AM, Covarrubias AA, Sukenik S, Dinneny JR. Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells. Nat Commun 2021; 12:5438. [PMID: 34521831 DOI: 10.1101/2021.02.17.431712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/27/2021] [Indexed: 05/17/2023] Open
Abstract
Cell homeostasis is perturbed when dramatic shifts in the external environment cause the physical-chemical properties inside the cell to change. Experimental approaches for dynamically monitoring these intracellular effects are currently lacking. Here, we leverage the environmental sensitivity and structural plasticity of intrinsically disordered protein regions (IDRs) to develop a FRET biosensor capable of monitoring rapid intracellular changes caused by osmotic stress. The biosensor, named SED1, utilizes the Arabidopsis intrinsically disordered AtLEA4-5 protein expressed in plants under water deficit. Computational modeling and in vitro studies reveal that SED1 is highly sensitive to macromolecular crowding. SED1 exhibits large and near-linear osmolarity-dependent changes in FRET inside living bacteria, yeast, plant, and human cells, demonstrating the broad utility of this tool for studying water-associated stress. This study demonstrates the remarkable ability of IDRs to sense the cellular environment across the tree of life and provides a blueprint for their use as environmentally-responsive molecular tools.
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Affiliation(s)
- Cesar L Cuevas-Velazquez
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico.
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico.
| | - Tamara Vellosillo
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Karina Guadalupe
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA
- Chemistry and Chemical Biology Program, University of California, Merced, CA, 95343, USA
| | - Hermann Broder Schmidt
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Feng Yu
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA
- Quantitative Systems Biology Program, University of California, Merced, CA, 95343, USA
| | - David Moses
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA
- Chemistry and Chemical Biology Program, University of California, Merced, CA, 95343, USA
| | - Jennifer A N Brophy
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Dante Cosio-Acosta
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
| | - Alakananda Das
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Lingxin Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | | | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico.
| | - Shahar Sukenik
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA.
- Chemistry and Chemical Biology Program, University of California, Merced, CA, 95343, USA.
- Quantitative Systems Biology Program, University of California, Merced, CA, 95343, USA.
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
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Cuevas-Velazquez CL, Vellosillo T, Guadalupe K, Schmidt HB, Yu F, Moses D, Brophy JAN, Cosio-Acosta D, Das A, Wang L, Jones AM, Covarrubias AA, Sukenik S, Dinneny JR. Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells. Nat Commun 2021; 12:5438. [PMID: 34521831 PMCID: PMC8440526 DOI: 10.1038/s41467-021-25736-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/27/2021] [Indexed: 12/15/2022] Open
Abstract
Cell homeostasis is perturbed when dramatic shifts in the external environment cause the physical-chemical properties inside the cell to change. Experimental approaches for dynamically monitoring these intracellular effects are currently lacking. Here, we leverage the environmental sensitivity and structural plasticity of intrinsically disordered protein regions (IDRs) to develop a FRET biosensor capable of monitoring rapid intracellular changes caused by osmotic stress. The biosensor, named SED1, utilizes the Arabidopsis intrinsically disordered AtLEA4-5 protein expressed in plants under water deficit. Computational modeling and in vitro studies reveal that SED1 is highly sensitive to macromolecular crowding. SED1 exhibits large and near-linear osmolarity-dependent changes in FRET inside living bacteria, yeast, plant, and human cells, demonstrating the broad utility of this tool for studying water-associated stress. This study demonstrates the remarkable ability of IDRs to sense the cellular environment across the tree of life and provides a blueprint for their use as environmentally-responsive molecular tools.
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Affiliation(s)
- Cesar L Cuevas-Velazquez
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico.
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico.
| | - Tamara Vellosillo
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Karina Guadalupe
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA
- Chemistry and Chemical Biology Program, University of California, Merced, CA, 95343, USA
| | - Hermann Broder Schmidt
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Feng Yu
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA
- Quantitative Systems Biology Program, University of California, Merced, CA, 95343, USA
| | - David Moses
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA
- Chemistry and Chemical Biology Program, University of California, Merced, CA, 95343, USA
| | - Jennifer A N Brophy
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Dante Cosio-Acosta
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
| | - Alakananda Das
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Lingxin Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | | | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico.
| | - Shahar Sukenik
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA.
- Chemistry and Chemical Biology Program, University of California, Merced, CA, 95343, USA.
- Quantitative Systems Biology Program, University of California, Merced, CA, 95343, USA.
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
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Moses D, Guadalupe K, Sukenik S. Probing the Hidden Sensitivity of Intrinsically Disordered Proteins to Their Chemical Environment. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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7
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Guadalupe K, Mendoza J. Stability of Hsp60 from Helicobacter Pylori: Effect of GTP Binding. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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