1
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Duewell BR, Wilson NE, Bailey GM, Peabody SE, Hansen SD. Molecular dissection of PI3Kβ synergistic activation by receptor tyrosine kinases, GβGγ, and Rho-family GTPases. eLife 2024; 12:RP88991. [PMID: 38713746 PMCID: PMC11076043 DOI: 10.7554/elife.88991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024] Open
Abstract
Phosphoinositide 3-kinase (PI3K) beta (PI3Kβ) is functionally unique in the ability to integrate signals derived from receptor tyrosine kinases (RTKs), G-protein coupled receptors, and Rho-family GTPases. The mechanism by which PI3Kβ prioritizes interactions with various membrane-tethered signaling inputs, however, remains unclear. Previous experiments did not determine whether interactions with membrane-tethered proteins primarily control PI3Kβ localization versus directly modulate lipid kinase activity. To address this gap in our knowledge, we established an assay to directly visualize how three distinct protein interactions regulate PI3Kβ when presented to the kinase in a biologically relevant configuration on supported lipid bilayers. Using single molecule Total Internal Reflection Fluorescence (TIRF) Microscopy, we determined the mechanism controlling PI3Kβ membrane localization, prioritization of signaling inputs, and lipid kinase activation. We find that auto-inhibited PI3Kβ prioritizes interactions with RTK-derived tyrosine phosphorylated (pY) peptides before engaging either GβGγ or Rac1(GTP). Although pY peptides strongly localize PI3Kβ to membranes, stimulation of lipid kinase activity is modest. In the presence of either pY/GβGγ or pY/Rac1(GTP), PI3Kβ activity is dramatically enhanced beyond what can be explained by simply increasing membrane localization. Instead, PI3Kβ is synergistically activated by pY/GβGγ and pY/Rac1 (GTP) through a mechanism consistent with allosteric regulation.
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Affiliation(s)
- Benjamin R Duewell
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Naomi E Wilson
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Gabriela M Bailey
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Sarah E Peabody
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Scott D Hansen
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of OregonEugeneUnited States
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2
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Duewell BR, Wilson NE, Bailey GM, Peabody SE, Hansen SD. Molecular dissection of PI3Kβ synergistic activation by receptor tyrosine kinases, GβGγ, and Rho-family GTPases. bioRxiv 2023:2023.05.01.538969. [PMID: 37205345 PMCID: PMC10187233 DOI: 10.1101/2023.05.01.538969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The class 1A phosphoinositide 3-kinase (PI3K) beta (PI3Kβ) is functionally unique in the ability to integrate signals derived from receptor tyrosine kinases (RTKs), heterotrimeric guanine nucleotide-binding protein (G-protein)-coupled receptors (GPCRs), and Rho-family GTPases. The mechanism by which PI3Kβ prioritizes interactions with various membrane tethered signaling inputs, however, remains unclear. Previous experiments have not been able to elucidate whether interactions with membrane-tethered proteins primarily control PI3Kβ localization versus directly modulate lipid kinase activity. To address this gap in our understanding of PI3Kβ regulation, we established an assay to directly visualize and decipher how three distinct protein interactions regulate PI3Kβ when presented to the kinase in a biologically relevant configuration on supported lipid bilayers. Using single molecule Total Internal Reflection Fluorescence (TIRF) Microscopy, we determined the mechanism controlling membrane localization of PI3Kβ, prioritization of signaling inputs, and lipid kinase activation. We find that auto-inhibited PI3Kβ prioritizes interactions with RTK-derived tyrosine phosphorylated (pY) peptides before engaging either GβGγ or Rac1(GTP). Although pY peptides strongly localize PI3Kβ to membranes, stimulation of lipid kinase activity is modest. In the presence of either pY/GβGγ or pY/Rac1(GTP), PI3Kβ activity is dramatically enhanced beyond what can be explained by simply increasing the strength of membrane localization. Instead, PI3Kβ is synergistically activated by pY/GβGγ and pY/Rac1(GTP) through a mechanism consistent with allosteric regulation.
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3
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Wills RC, Doyle CP, Zewe JP, Pacheco J, Hansen SD, Hammond GRV. A novel homeostatic mechanism tunes PI(4,5)P2-dependent signaling at the plasma membrane. J Cell Sci 2023; 136:jcs261494. [PMID: 37534432 PMCID: PMC10482388 DOI: 10.1242/jcs.261494] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023] Open
Abstract
The lipid molecule phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P2] controls all aspects of plasma membrane (PM) function in animal cells, from its selective permeability to the attachment of the cytoskeleton. Although disruption of PI(4,5)P2 is associated with a wide range of diseases, it remains unclear how cells sense and maintain PI(4,5)P2 levels to support various cell functions. Here, we show that the PIP4K family of enzymes, which synthesize PI(4,5)P2 via a minor pathway, also function as sensors of tonic PI(4,5)P2 levels. PIP4Ks are recruited to the PM by elevated PI(4,5)P2 levels, where they inhibit the major PI(4,5)P2-synthesizing PIP5Ks. Perturbation of this simple homeostatic mechanism reveals differential sensitivity of PI(4,5)P2-dependent signaling to elevated PI(4,5)P2 levels. These findings reveal that a subset of PI(4,5)P2-driven functions might drive disease associated with disrupted PI(4,5)P2 homeostasis.
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Affiliation(s)
- Rachel C. Wills
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Colleen P. Doyle
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - James P. Zewe
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Jonathan Pacheco
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Scott D. Hansen
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Gerald R. V. Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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4
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Waddell GL, Drew EE, Rupp HP, Hansen SD. Mechanisms controlling membrane recruitment and activation of the autoinhibited SHIP1 inositol 5-phosphatase. J Biol Chem 2023; 299:105022. [PMID: 37423304 PMCID: PMC10448276 DOI: 10.1016/j.jbc.2023.105022] [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: 12/31/2022] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023] Open
Abstract
Signal transduction downstream of growth factor and immune receptor activation relies on the production of phosphatidylinositol-(3,4,5)-trisphosphate (PI(3,4,5)P3) lipids by PI3K. Regulating the strength and duration of PI3K signaling in immune cells, Src homology 2 domain-containing inositol 5-phosphatase 1 (SHIP1) controls the dephosphorylation of PI(3,4,5)P3 to generate phosphatidylinositol-(3,4)-bisphosphate. Although SHIP1 has been shown to regulate neutrophil chemotaxis, B-cell signaling, and cortical oscillations in mast cells, the role that lipid and protein interactions serve in controlling SHIP1 membrane recruitment and activity remains unclear. Using single-molecule total internal reflection fluorescence microscopy, we directly visualized membrane recruitment and activation of SHIP1 on supported lipid bilayers and the cellular plasma membrane. We find that localization of the central catalytic domain of SHIP1 is insensitive to dynamic changes in PI(3,4,5)P3 and phosphatidylinositol-(3,4)-bisphosphate both in vitro and in vivo. Very transient SHIP1 membrane interactions were detected only when membranes contained a combination of phosphatidylserine and PI(3,4,5)P3 lipids. Molecular dissection reveals that SHIP1 is autoinhibited with the N-terminal Src homology 2 domain playing a critical role in suppressing phosphatase activity. Robust SHIP1 membrane localization and relief of autoinhibition can be achieved through interactions with immunoreceptor-derived phosphopeptides presented either in solution or conjugated to a membrane. Overall, this work provides new mechanistic details concerning the dynamic interplay between lipid-binding specificity, protein-protein interactions, and the activation of autoinhibited SHIP1.
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Affiliation(s)
- Grace L Waddell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Emma E Drew
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Henry P Rupp
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Scott D Hansen
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA.
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5
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Harris NJ, Jenkins ML, Nam SE, Rathinaswamy MK, Parson MAH, Ranga-Prasad H, Dalwadi U, Moeller BE, Sheeky E, Hansen SD, Yip CK, Burke JE. Allosteric activation or inhibition of PI3Kγ mediated through conformational changes in the p110γ helical domain. eLife 2023; 12:RP88058. [PMID: 37417733 PMCID: PMC10392983 DOI: 10.7554/elife.88058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023] Open
Abstract
PI3Kγ is a critical immune signaling enzyme activated downstream of diverse cell surface molecules, including Ras, PKCβ activated by the IgE receptor, and Gβγ subunits released from activated GPCRs. PI3Kγ can form two distinct complexes, with the p110γ catalytic subunit binding to either a p101 or p84 regulatory subunit, with these complexes being differentially activated by upstream stimuli. Here, using a combination of cryo electron microscopy, HDX-MS, and biochemical assays, we have identified novel roles of the helical domain of p110γ in regulating lipid kinase activity of distinct PI3Kγ complexes. We defined the molecular basis for how an allosteric inhibitory nanobody potently inhibits kinase activity through rigidifying the helical domain and regulatory motif of the kinase domain. The nanobody did not block either p110γ membrane recruitment or Ras/Gβγ binding, but instead decreased ATP turnover. We also identified that p110γ can be activated by dual PKCβ helical domain phosphorylation leading to partial unfolding of an N-terminal region of the helical domain. PKCβ phosphorylation is selective for p110γ-p84 compared to p110γ-p101, driven by differential dynamics of the helical domain of these different complexes. Nanobody binding prevented PKCβ-mediated phosphorylation. Overall, this work shows an unexpected allosteric regulatory role of the helical domain of p110γ that is distinct between p110γ-p84 and p110γ-p101 and reveals how this can be modulated by either phosphorylation or allosteric inhibitory binding partners. This opens possibilities of future allosteric inhibitor development for therapeutic intervention.
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Affiliation(s)
- Noah J Harris
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Sung-Eun Nam
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, Canada
| | - Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Matthew A H Parson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Harish Ranga-Prasad
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Udit Dalwadi
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, Canada
| | - Brandon E Moeller
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Eleanor Sheeky
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Scott D Hansen
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, Canada
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6
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Waddell GL, Drew EE, Rupp HP, Hansen SD. Mechanisms controlling membrane recruitment and activation of autoinhibited SHIP1. bioRxiv 2023:2023.04.30.538895. [PMID: 37205499 PMCID: PMC10187190 DOI: 10.1101/2023.04.30.538895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Signal transduction downstream of growth factor and immune receptor activation relies on the production of phosphatidylinositol-(3,4,5)-trisphosphate (PI(3,4,5)P 3 ) lipids by phosphoinositide-3-kinase (PI3K). Regulating the strength and duration of PI3K signaling in immune cells, Src homology 2 domain-containing inositol 5-phosphatase 1 (SHIP1) controls the dephosphorylation of PI(3,4,5)P 3 to generate PI(3,4)P 2 . Although SHIP1 has been shown to regulate neutrophil chemotaxis, B-cell signaling, and cortical oscillations in mast cells, the role that lipid and protein interactions serve in controlling SHIP1 membrane recruitment and activity remains unclear. Using single molecule TIRF microscopy, we directly visualized membrane recruitment and activation of SHIP1 on supported lipid bilayers and the cellular plasma membrane. We find that SHIP1's interactions with lipids are insensitive to dynamic changes in PI(3,4,5)P 3 both in vitro and in vivo. Very transient SHIP1 membrane interactions were detected only when membranes contained a combination of phosphatidylserine (PS) and PI(3,4,5)P 3 lipids. Molecular dissection reveals that SHIP1 is autoinhibited with the N-terminal SH2 domain playing a critical role in suppressing phosphatase activity. Robust SHIP1 membrane localization and relief of autoinhibition can be achieved through interactions with immunoreceptor derived phosphopeptides presented either in solution or conjugated to supported membranes. Overall, this work provides new mechanistic details concerning the dynamic interplay between lipid binding specificity, protein-protein interactions, and activation of autoinhibited SHIP1.
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7
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Harris NJ, Jenkins ML, Nam SE, Rathinaswamy MK, Parson MA, Ranga-Prasad H, Dalwadi U, Moeller BE, Sheekey E, Hansen SD, Yip CK, Burke JE. Allosteric activation or inhibition of PI3Kγ mediated through conformational changes in the p110γ helical domain. bioRxiv 2023:2023.04.12.536585. [PMID: 37090531 PMCID: PMC10120615 DOI: 10.1101/2023.04.12.536585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
PI3Kγ is a critical immune signaling enzyme activated downstream of diverse cell surface molecules, including Ras, PKCβ activated by the IgE receptor, and Gβγ subunits released from activated GPCRs. PI3Kγ can form two distinct complexes, with the p110γ catalytic subunit binding to either a p101 or p84 regulatory subunit, with these complexes being differentially activated by upstream stimuli. Here using a combination of Cryo electron microscopy, HDX-MS, and biochemical assays we have identified novel roles of the helical domain of p110γ in regulating lipid kinase activity of distinct PI3Kγ complexes. We defined the molecular basis for how an allosteric inhibitory nanobody potently inhibits kinase activity through rigidifying the helical domain and regulatory motif of the kinase domain. The nanobody did not block either p110γ membrane recruitment or Ras/Gβγ binding, but instead decreased ATP turnover. We also identified that p110γ can be activated by dual PKCβ helical domain phosphorylation leading to partial unfolding of an N-terminal region of the helical domain. PKCβ phosphorylation is selective for p110γ-p84 compared to p110γ-p101, driven by differential dynamics of the helical domain of these different complexes. Nanobody binding prevented PKCβ mediated phosphorylation. Overall, this works shows an unexpected allosteric regulatory role of the helical domain of p110γ that is distinct between p110γ-p84 and p110γ-p101, and reveals how this can be modulated by either phosphorylation or allosteric inhibitory binding partners. This opens possibilities of future allosteric inhibitor development for therapeutic intervention.
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8
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Rathinaswamy MK, Jenkins ML, Duewell BR, Zhang X, Harris NJ, Evans JT, Stariha JTB, Dalwadi U, Fleming KD, Ranga-Prasad H, Yip CK, Williams RL, Hansen SD, Burke JE. Molecular basis for differential activation of p101 and p84 complexes of PI3Kγ by Ras and GPCRs. Cell Rep 2023; 42:112172. [PMID: 36842083 PMCID: PMC10068899 DOI: 10.1016/j.celrep.2023.112172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/21/2022] [Accepted: 02/13/2023] [Indexed: 02/27/2023] Open
Abstract
Class IB phosphoinositide 3-kinase (PI3Kγ) is activated in immune cells and can form two distinct complexes (p110γ-p84 and p110γ-p101), which are differentially activated by G protein-coupled receptors (GPCRs) and Ras. Using a combination of X-ray crystallography, hydrogen deuterium exchange mass spectrometry (HDX-MS), electron microscopy, molecular modeling, single-molecule imaging, and activity assays, we identify molecular differences between p110γ-p84 and p110γ-p101 that explain their differential membrane recruitment and activation by Ras and GPCRs. The p110γ-p84 complex is dynamic compared with p110γ-p101. While p110γ-p101 is robustly recruited by Gβγ subunits, p110γ-p84 is weakly recruited to membranes by Gβγ subunits alone and requires recruitment by Ras to allow for Gβγ activation. We mapped two distinct Gβγ interfaces on p101 and the p110γ helical domain, with differences in the C-terminal domain of p84 and p101 conferring sensitivity of p110γ-p101 to Gβγ activation. Overall, our work provides key insight into the molecular basis for how PI3Kγ complexes are activated.
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Affiliation(s)
- Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Benjamin R Duewell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA; Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Xuxiao Zhang
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Noah J Harris
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - John T Evans
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Jordan T B Stariha
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Udit Dalwadi
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Harish Ranga-Prasad
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | | | - Scott D Hansen
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA; Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada; Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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9
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Hansen SD, Lee AA, Duewell BR, Groves JT. Membrane-mediated dimerization potentiates PIP5K lipid kinase activity. eLife 2022; 11:73747. [PMID: 35976097 PMCID: PMC9470164 DOI: 10.7554/elife.73747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 08/16/2022] [Indexed: 11/28/2022] Open
Abstract
The phosphatidylinositol 4-phosphate 5-kinase (PIP5K) family of lipid-modifying enzymes generate the majority of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] lipids found at the plasma membrane in eukaryotic cells. PI(4,5)P2 lipids serve a critical role in regulating receptor activation, ion channel gating, endocytosis, and actin nucleation. Here, we describe how PIP5K activity is regulated by cooperative binding to PI(4,5)P2 lipids and membrane-mediated dimerization of the kinase domain. In contrast to constitutively dimeric phosphatidylinositol 5-phosphate 4-kinase (PIP4K, type II PIPK), solution PIP5K exists in a weak monomer–dimer equilibrium. PIP5K monomers can associate with PI(4,5)P2-containing membranes and dimerize in a protein density-dependent manner. Although dispensable for cooperative PI(4,5)P2 binding, dimerization enhances the catalytic efficiency of PIP5K through a mechanism consistent with allosteric regulation. Additionally, dimerization amplifies stochastic variation in the kinase reaction velocity and strengthens effects such as the recently described stochastic geometry sensing. Overall, the mechanism of PIP5K membrane binding creates a broad dynamic range of lipid kinase activities that are coupled to the density of PI(4,5)P2 and membrane-bound kinase.
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Affiliation(s)
- Scott D Hansen
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, United States
| | - Albert A Lee
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Benjamin R Duewell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, United States
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
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10
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Kim N(H, Lee A, Rajesh S, Hansen SD, Weiner O, Groves JT. Shape dependent reaction polarization on membranes. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1868] [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: 11/15/2022] Open
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11
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Rathinaswamy MK, Dalwadi U, Fleming KD, Adams C, Stariha JTB, Pardon E, Baek M, Vadas O, DiMaio F, Steyaert J, Hansen SD, Yip CK, Burke JE. Structure of the phosphoinositide 3-kinase (PI3K) p110γ-p101 complex reveals molecular mechanism of GPCR activation. Sci Adv 2021; 7:7/35/eabj4282. [PMID: 34452907 PMCID: PMC8397274 DOI: 10.1126/sciadv.abj4282] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/06/2021] [Indexed: 05/04/2023]
Abstract
The class IB phosphoinositide 3-kinase (PI3K), PI3Kγ, is a master regulator of immune cell function and a promising drug target for both cancer and inflammatory diseases. Critical to PI3Kγ function is the association of the p110γ catalytic subunit to either a p101 or p84 regulatory subunit, which mediates activation by G protein-coupled receptors. Here, we report the cryo-electron microscopy structure of a heterodimeric PI3Kγ complex, p110γ-p101. This structure reveals a unique assembly of catalytic and regulatory subunits that is distinct from other class I PI3K complexes. p101 mediates activation through its Gβγ-binding domain, recruiting the heterodimer to the membrane and allowing for engagement of a secondary Gβγ-binding site in p110γ. Mutations at the p110γ-p101 and p110γ-adaptor binding domain interfaces enhanced Gβγ activation. A nanobody that specifically binds to the p101-Gβγ interface blocks activation, providing a novel tool to study and target p110γ-p101-specific signaling events in vivo.
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Affiliation(s)
- Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Udit Dalwadi
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Carson Adams
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jordan T B Stariha
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Minkyung Baek
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Oscar Vadas
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Scott D Hansen
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
| | - Calvin K Yip
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada.
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
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12
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McKnight LE, Crandall JG, Bailey TB, Banks OGB, Orlandi KN, Truong VN, Donovan DA, Waddell GL, Wiles ET, Hansen SD, Selker EU, McKnight JN. Rapid and inexpensive preparation of genome-wide nucleosome footprints from model and non-model organisms. STAR Protoc 2021; 2:100486. [PMID: 34041500 PMCID: PMC8141940 DOI: 10.1016/j.xpro.2021.100486] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
MNase-seq (micrococcal nuclease sequencing) is used to map nucleosome positions in eukaryotic genomes to study the relationship between chromatin structure and DNA-dependent processes. Current protocols require at least two days to isolate nucleosome-protected DNA fragments. We have developed a streamlined protocol for S. cerevisiae and other fungi which takes only three hours. Modified protocols were developed for wild fungi and mammalian cells. This method for rapidly producing sequencing-ready nucleosome footprints from several organisms makes MNase-seq faster and easier, with less chemical waste. A fast way to prepare micrococcal nuclease nucleosome footprints for MNase-seq Eliminates use of phenol and chloroform and reduces the amount of cells required Adaptable for a variety of organisms
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Affiliation(s)
- Laura E McKnight
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | | | - Thomas B Bailey
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Orion G B Banks
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Kona N Orlandi
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Vi N Truong
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Drake A Donovan
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Grace L Waddell
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Elizabeth T Wiles
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Scott D Hansen
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Jeffrey N McKnight
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
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13
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Hansen SD, Huang WYC, Lee YK, Bieling P, Christensen SM, Groves JT. Stochastic geometry sensing and polarization in a lipid kinase-phosphatase competitive reaction. Proc Natl Acad Sci U S A 2019; 116:15013-15022. [PMID: 31278151 PMCID: PMC6660746 DOI: 10.1073/pnas.1901744116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Phosphorylation reactions, driven by competing kinases and phosphatases, are central elements of cellular signal transduction. We reconstituted a native eukaryotic lipid kinase-phosphatase reaction that drives the interconversion of phosphatidylinositol-4-phosphate [PI(4)P] and phosphatidylinositol-4,5-phosphate [PI(4,5)P2] on membrane surfaces. This system exhibited bistability and formed spatial composition patterns on supported membranes. In smaller confined regions of membrane, rapid diffusion ensures the system remains spatially homogeneous, but the final outcome-a predominantly PI(4)P or PI(4,5)P2 membrane composition-was governed by the size of the reaction environment. In larger confined regions, interplay between the reactions, diffusion, and confinement created a variety of differentially patterned states, including polarization. Experiments and kinetic modeling reveal how these geometric confinement effects arise from a mechanism based on stochastic fluctuations in the copy number of membrane-bound kinases and phosphatases. The underlying requirements for such behavior are unexpectedly simple and likely to occur in natural biological signaling systems.
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Affiliation(s)
- Scott D Hansen
- Department of Chemistry, University of California, Berkeley, CA 94720;
- California Institute for Quantitative Biosciences, Berkeley, CA 94720
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
| | - William Y C Huang
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Young Kwang Lee
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Peter Bieling
- California Institute for Quantitative Biosciences, Berkeley, CA 94720
| | | | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, CA 94720;
- California Institute for Quantitative Biosciences, Berkeley, CA 94720
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14
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McAffee DB, Low-Nam ST, Lin JJY, Alvarez SA, Hansen SD, Groves JT. Single pMHC:TCR Binding Events Precipitate LAT Assemblies Capable of Spatially Decoupling from the Originating Ligand. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.2858] [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: 10/27/2022] Open
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15
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Low-Nam ST, Lin JJY, McAffee DB, Alvarez SA, Hansen SD, Roybal KT, Groves JT. Beyond the TCR, Antigen Discrimination in T Cells Continues in the LAT:GRB2:SOS Protein Condensate. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.2856] [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: 11/24/2022] Open
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16
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Bieling P, Hansen SD, Akin O, Li TD, Hayden CC, Fletcher DA, Mullins RD. WH2 and proline-rich domains of WASP-family proteins collaborate to accelerate actin filament elongation. EMBO J 2017; 37:102-121. [PMID: 29141912 PMCID: PMC5753033 DOI: 10.15252/embj.201797039] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 02/04/2023] Open
Abstract
WASP‐family proteins are known to promote assembly of branched actin networks by stimulating the filament‐nucleating activity of the Arp2/3 complex. Here, we show that WASP‐family proteins also function as polymerases that accelerate elongation of uncapped actin filaments. When clustered on a surface, WASP‐family proteins can drive branched actin networks to grow much faster than they could by direct incorporation of soluble monomers. This polymerase activity arises from the coordinated action of two regulatory sequences: (i) a WASP homology 2 (WH2) domain that binds actin, and (ii) a proline‐rich sequence that binds profilin–actin complexes. In the absence of profilin, WH2 domains are sufficient to accelerate filament elongation, but in the presence of profilin, proline‐rich sequences are required to support polymerase activity by (i) bringing polymerization‐competent actin monomers in proximity to growing filament ends, and (ii) promoting shuttling of actin monomers from profilin–actin complexes onto nearby WH2 domains. Unoccupied WH2 domains transiently associate with free filament ends, preventing their growth and dynamically tethering the branched actin network to the WASP‐family proteins that create it. Collaboration between WH2 and proline‐rich sequences thus strikes a balance between filament growth and tethering. Our work expands the number of critical roles that WASP‐family proteins play in the assembly of branched actin networks to at least three: (i) promoting dendritic nucleation; (ii) linking actin networks to membranes; and (iii) accelerating filament elongation.
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Affiliation(s)
- Peter Bieling
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA, USA .,Department of Bioengineering & Biophysics Program, University of California, Berkeley, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Scott D Hansen
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Orkun Akin
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Tai-De Li
- Department of Bioengineering & Biophysics Program, University of California, Berkeley, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Daniel A Fletcher
- Department of Bioengineering & Biophysics Program, University of California, Berkeley, CA, USA .,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - R Dyche Mullins
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
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17
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Smith AAA, Autzen HE, Laursen T, Wu V, Yen M, Hall A, Hansen SD, Cheng Y, Xu T. Controlling Styrene Maleic Acid Lipid Particles through RAFT. Biomacromolecules 2017; 18:3706-3713. [DOI: 10.1021/acs.biomac.7b01136] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anton A. A. Smith
- Chemistry,
Materials Science and Engineering UC Berkeley, Berkeley, California 94720, United States
- Science
and Technology, Aarhus University, 8000 Aarhus, Denmark
| | - Henriette E. Autzen
- Science
and Technology, Aarhus University, 8000 Aarhus, Denmark
- Biochemistry
and Biophysics, UCSF, San Francisco, California 94143, United States
| | - Tomas Laursen
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Vincent Wu
- Chemistry,
Materials Science and Engineering UC Berkeley, Berkeley, California 94720, United States
| | - Max Yen
- Chemistry,
Materials Science and Engineering UC Berkeley, Berkeley, California 94720, United States
| | - Aaron Hall
- Chemistry,
Materials Science and Engineering UC Berkeley, Berkeley, California 94720, United States
| | - Scott D. Hansen
- California
Institute for Quantitative Biosciences (QB3), UC Berkeley, Berkeley, California 94720, United States
| | - Yifan Cheng
- Biochemistry
and Biophysics, UCSF, San Francisco, California 94143, United States
| | - Ting Xu
- Chemistry,
Materials Science and Engineering UC Berkeley, Berkeley, California 94720, United States
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18
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Huang WY, Yan Q, Lin WC, Chung JK, Hansen SD, Christensen SM, Tu HL, Kuriyan J, Groves JT. Protein Assembly on Membrane Surface alters the Dynamical Spectrum of Downstream Signaling Reactions. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.534] [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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19
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Hansen SD, Huang WY, Kwang Lee Y, Groves JT. Stochastic Fluctuation Sensing in a Bistable Phosphatidylinositol-Based Reaction Diffusion System. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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20
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Kwang Lee Y, Low-Nam S, Hansen SD, Alvrez S, Yue Monatrice Lam H, Groves JT. Single Molecule Assays of Full Length SOS on Membranes using Crude Cell Lysates. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.3148] [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: 11/16/2022] Open
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21
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Hansen SD, Mullins RD. Lamellipodin promotes actin assembly by clustering Ena/VASP proteins and tethering them to actin filaments. eLife 2015; 4. [PMID: 26295568 PMCID: PMC4543927 DOI: 10.7554/elife.06585] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 07/27/2015] [Indexed: 11/16/2022] Open
Abstract
Enabled/Vasodilator (Ena/VASP) proteins promote actin filament assembly at multiple locations, including: leading edge membranes, focal adhesions, and the surface of intracellular pathogens. One important Ena/VASP regulator is the mig-10/Lamellipodin/RIAM family of adaptors that promote lamellipod formation in fibroblasts and drive neurite outgrowth and axon guidance in neurons. To better understand how MRL proteins promote actin network formation we studied the interactions between Lamellipodin (Lpd), actin, and VASP, both in vivo and in vitro. We find that Lpd binds directly to actin filaments and that this interaction regulates its subcellular localization and enhances its effect on VASP polymerase activity. We propose that Lpd delivers Ena/VASP proteins to growing barbed ends and increases their polymerase activity by tethering them to filaments. This interaction represents one more pathway by which growing actin filaments produce positive feedback to control localization and activity of proteins that regulate their assembly. DOI:http://dx.doi.org/10.7554/eLife.06585.001 Actin—the most abundant protein in most eukaryotic cells—assembles into a network of filaments that spans the length and breadth of the cell. Like the skeleton of an animal, this ‘actin cytoskeleton’ gives the cell its shape and strength, and enables the cell to actively move through its environment. To start moving, many cells begin assembling actin filaments next to the cell membrane. The growth of these filaments pushes the membrane forward and creates a two-dimensional structure called a ‘lamellipod’, which explores the space around the cell and steers its movement. The actin filaments in a lamellipod are dynamic and undergo repeated cycles of assembly and disassembly. These processes are tightly regulated by a variety of other proteins. Members of the Ena/VASP protein family, for example, collect the building blocks of an actin filament and rapidly stack them in place on the fast-growing end of a filament. The activities of Ena/VASP proteins play an especially important role in creating lamellipodial actin networks and in driving cell movement. Previous work showed that a protein called Lamellipodin binds to Ena/VASP proteins and helps recruit them to the cell membrane. However, it was unclear whether Lamellipodin could affect the activity of Ena/VASP proteins or their interaction with the actin filaments. Hansen and Mullins have now analyzed the interactions between Ena/VASP, Lamellipodin and actin. The experiments demonstrate that Lamellipodin does not simply tether Ena/VASP proteins to the membrane but also binds directly to actin filaments, via a binding site that is distinct from the site that contacts Ena/VASP. Further experiments with purified proteins revealed that Lamellipodin could interact with both actin filaments and Ena/VASP proteins at the same time. Hansen and Mullins also found that purified Lamellipodin interacted with VASP proteins to form clustered protein complexes, and that together with the tethering of actin filaments to the membrane, this clustering greatly increased VASP's ability to lengthen actin filaments. By visualizing Lamellipodin tagged with a green fluorescent protein in living cells, Hansen and Mullins then showed that its interaction with actin filaments was sufficient to localize Lamellipodin to the cell membrane. Finally, since Lamellipodin interacts with a multitude of signaling molecules in addition to Ena/VASP proteins, the next big challenge is to understand how Lamellipodin itself is regulated. Future studies could also explore how cells harness the power of the actin cytoskeleton to carry out these essential activities. DOI:http://dx.doi.org/10.7554/eLife.06585.002
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Affiliation(s)
- Scott D Hansen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco School of Medicine, San Francisco, United States
| | - R Dyche Mullins
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco School of Medicine, San Francisco, United States
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22
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Iversen L, Tu HL, Lin WC, Christensen SM, Abel SM, Iwig J, Wu HJ, Gureasko J, Rhodes C, Petit RS, Hansen SD, Thill P, Yu CH, Stamou D, Chakraborty AK, Kuriyan J, Groves JT. Molecular kinetics. Ras activation by SOS: allosteric regulation by altered fluctuation dynamics. Science 2014; 345:50-4. [PMID: 24994643 DOI: 10.1126/science.1250373] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual SOS molecules catalyzing nucleotide exchange in H-Ras. Single-molecule kinetic traces revealed that SOS samples a broad distribution of turnover rates through stochastic fluctuations between distinct, long-lived (more than 100 seconds), functional states. The expected allosteric activation of SOS by Ras-guanosine triphosphate (GTP) was conspicuously absent in the mean rate. However, fluctuations into highly active states were modulated by Ras-GTP. This reveals a mechanism in which functional output may be determined by the dynamical spectrum of rates sampled by a small number of enzymes, rather than the ensemble average.
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Affiliation(s)
- Lars Iversen
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hsiung-Lin Tu
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wan-Chen Lin
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sune M Christensen
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Steven M Abel
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Jeff Iwig
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hung-Jen Wu
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jodi Gureasko
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher Rhodes
- Department of Mechanical Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rebecca S Petit
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Scott D Hansen
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Peter Thill
- Department of Chemistry, MIT, Cambridge, MA 02139, USA
| | - Cheng-Han Yu
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Dimitrios Stamou
- Department of Chemistry and Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Department of Chemistry, MIT, Cambridge, MA 02139, USA. Department of Biological Engineering, MIT, Cambridge, MA 02139, USA. Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA. Department of Physics, MIT, Cambridge, MA 02139, USA. Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
| | - John Kuriyan
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jay T Groves
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. Mechanobiology Institute, National University of Singapore, Singapore. Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Berkeley Education Alliance for Research in Singapore, 1 Create Way, CREATE tower level 11, University Town, Singapore 138602.
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23
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Pokutta S, Choi HJ, Ahlsen G, Hansen SD, Weis WI. Structural and thermodynamic characterization of cadherin·β-catenin·α-catenin complex formation. J Biol Chem 2014; 289:13589-601. [PMID: 24692547 DOI: 10.1074/jbc.m114.554709] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The classical cadherin·β-catenin·α-catenin complex mediates homophilic cell-cell adhesion and mechanically couples the actin cytoskeletons of adjacent cells. Although α-catenin binds to β-catenin and to F-actin, β-catenin significantly weakens the affinity of α-catenin for F-actin. Moreover, α-catenin self-associates into homodimers that block β-catenin binding. We investigated quantitatively and structurally αE- and αN-catenin dimer formation, their interaction with β-catenin and the cadherin·β-catenin complex, and the effect of the α-catenin actin-binding domain on β-catenin association. The two α-catenin variants differ in their self-association properties: at physiological temperatures, αE-catenin homodimerizes 10× more weakly than does αN-catenin but is kinetically trapped in its oligomeric state. Both αE- and αN-catenin bind to β-catenin with a Kd of 20 nM, and this affinity is increased by an order of magnitude when cadherin is bound to β-catenin. We describe the crystal structure of a complex representing the full β-catenin·αN-catenin interface. A three-dimensional model of the cadherin·β-catenin·α-catenin complex based on these new structural data suggests mechanisms for the enhanced stability of the ternary complex. The C-terminal actin-binding domain of α-catenin has no influence on the interactions with β-catenin, arguing against models in which β-catenin weakens actin binding by stabilizing inhibitory intramolecular interactions between the actin-binding domain and the rest of α-catenin.
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Affiliation(s)
- Sabine Pokutta
- From the Departments of Structural Biology and Molecular and Cellular Physiology, Stanford University, Stanford, California 94305
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24
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Lin WC, Iversen L, Tu HL, Christensen SM, Hansen SD, Hwang WY, Groves JT. Oligomerization of H-Ras on Membrane Surfaces. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3951] [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: 10/23/2022] Open
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25
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Hansen SD, Kwiatkowski AV, Ouyang CY, Liu H, Pokutta S, Watkins SC, Volkmann N, Hanein D, Weis WI, Mullins RD, Nelson WJ. αE-catenin actin-binding domain alters actin filament conformation and regulates binding of nucleation and disassembly factors. Mol Biol Cell 2013; 24:3710-20. [PMID: 24068324 PMCID: PMC3842997 DOI: 10.1091/mbc.e13-07-0388] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
αE-catenin regulates transitions in actin organization between cell migration and cell–cell adhesion by controlling barbed-end polymerization of unbranched actin filaments and inhibiting Arp2/3 complex and cofilin regulation of actin filament branching and disassembly. The actin-binding protein αE-catenin may contribute to transitions between cell migration and cell–cell adhesion that depend on remodeling the actin cytoskeleton, but the underlying mechanisms are unknown. We show that the αE-catenin actin-binding domain (ABD) binds cooperatively to individual actin filaments and that binding is accompanied by a conformational change in the actin protomer that affects filament structure. αE-catenin ABD binding limits barbed-end growth, especially in actin filament bundles. αE-catenin ABD inhibits actin filament branching by the Arp2/3 complex and severing by cofilin, both of which contact regions of the actin protomer that are structurally altered by αE-catenin ABD binding. In epithelial cells, there is little correlation between the distribution of αE-catenin and the Arp2/3 complex at developing cell–cell contacts. Our results indicate that αE-catenin binding to filamentous actin favors assembly of unbranched filament bundles that are protected from severing over more dynamic, branched filament arrays.
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Affiliation(s)
- Scott D Hansen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, School of Medicine, San Francisco, CA 94158 Department of Biology, Stanford University, Stanford, CA 94305 Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261 Bioinformatics and Systems Biology Program, Sanford Burnham Medical Research Institute, La Jolla, CA 92037 Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305 Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
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26
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Abstract
The actin cytoskeleton is essential to all eukaryotic cells. In addition to playing important structural roles, assembly of actin into filaments powers diverse cellular processes, including cell motility, cytokinesis, and endocytosis. Actin polymerization is tightly regulated by its numerous cofactors, which control spatial and temporal assembly of actin as well as the physical properties of these filaments. Development of an in vitro model of actin polymerization from purified components has allowed for great advances in determining the effects of these proteins on the actin cytoskeleton. Here we describe how to use the pyrene actin assembly assay to determine the effect of a protein on the kinetics of actin assembly, either directly or as mediated by proteins such as nucleation or capping factors. Secondly, we show how fluorescently labeled phalloidin can be used to visualize the filaments that are created in vitro to give insight into how proteins regulate actin filament structure. Finally, we describe a method for visualizing dynamic assembly and disassembly of single actin filaments and fluorescently labeled actin binding proteins using total internal reflection fluorescence (TIRF) microscopy.
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Affiliation(s)
- Scott D Hansen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
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27
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Abstract
Now that many genomes have been sequenced, a central concern of cell biology is to understand how the proteins they encode work together to create living matter. In vitro studies form an essential part of this program because understanding cellular functions of biological molecules often requires isolating them and reconstituting their activities. In particular, many elements of the actin cytoskeleton were first discovered by biochemical methods and their cellular functions deduced from in vitro experiments. We highlight recent advances that have come from in vitro studies, beginning with studies of actin filaments, and ending with multi-component reconstitutions of complex actin-based processes, including force-generation and cell spreading. We describe both scientific results and the technical innovations that made them possible.
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Affiliation(s)
- R Dyche Mullins
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94110, United States.
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28
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Mouneimne G, Hansen SD, Selfors LM, Petrak L, Hickey MM, Gallegos LL, Simpson KJ, Lim J, Gertler FB, Hartwig JH, Mullins RD, Brugge JS. Differential remodeling of actin cytoskeleton architecture by profilin isoforms leads to distinct effects on cell migration and invasion. Cancer Cell 2012; 22:615-30. [PMID: 23153535 PMCID: PMC3500527 DOI: 10.1016/j.ccr.2012.09.027] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 09/06/2012] [Accepted: 09/28/2012] [Indexed: 01/17/2023]
Abstract
Dynamic actin cytoskeletal reorganization is integral to cell motility. Profilins are well-characterized regulators of actin polymerization; however, functional differences among coexpressed profilin isoforms are not well defined. Here, we demonstrate that profilin-1 and profilin-2 differentially regulate membrane protrusion, motility, and invasion; these processes are promoted by profilin-1 and suppressed by profilin-2. Compared to profilin-1, profilin-2 preferentially drives actin polymerization by the Ena/VASP protein, EVL. Profilin-2 and EVL suppress protrusive activity and cell motility by an actomyosin contractility-dependent mechanism. Importantly, EVL or profilin-2 downregulation enhances invasion in vitro and in vivo. In human breast cancer, lower EVL expression correlates with high invasiveness and poor patient outcome. We propose that profilin-2/EVL-mediated actin polymerization enhances actin bundling and suppresses breast cancer cell invasion.
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Affiliation(s)
- Ghassan Mouneimne
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Scott D. Hansen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Laura M. Selfors
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Lara Petrak
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Michele M. Hickey
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Lisa L. Gallegos
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Kaylene J. Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, 3002
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3050
| | - James Lim
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Frank B. Gertler
- The Koch Institute for integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - John H. Hartwig
- Division of Translational Medicine at Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
| | - R. Dyche Mullins
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Joan S. Brugge
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- Corresponding author: , Phone: 617 432 3974, Fax: 617 432 3969
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29
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Rozelle DK, Hansen SD, Kaplan KB. Chromosome passenger complexes control anaphase duration and spindle elongation via a kinesin-5 brake. J Cell Biol 2011; 193:285-94. [PMID: 21482719 PMCID: PMC3080259 DOI: 10.1083/jcb.201011002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 03/14/2011] [Indexed: 02/03/2023] Open
Abstract
During mitosis, chromosome passenger complexes (CPCs) exhibit a well-conserved association with the anaphase spindle and have been implicated in spindle stability. However, their precise effect on the spindle is not clear. In this paper, we show, in budding yeast, that a CPC consisting of CBF3, Bir1, and Sli15, but not Ipl1, is required for normal spindle elongation. CPC mutants slow spindle elongation through the action of the bipolar kinesins Cin8 and Kip1. The same CPC mutants that slow spindle elongation also result in the enrichment of Cin8 and Kip1 at the spindle midzone. Together, these findings argue that CPCs function to organize the spindle midzone and potentially switch motors between force generators and molecular brakes. We also find that slowing spindle elongation delays the mitotic exit network (MEN)-dependent release of Cdc14, thus delaying spindle breakdown until a minimal spindle size is reached. We propose that these CPC- and MEN-dependent mechanisms are important for coordinating chromosome segregation with spindle breakdown and mitotic exit.
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Affiliation(s)
- Daniel K Rozelle
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
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30
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Abstract
Visualization of VASP tetramers interacting with static and growing actin filaments in vitro by TIRF microscopy leads to a new model for VASP-mediated actin filament assembly. Ena/VASP proteins regulate the actin cytoskeleton during cell migration and morphogenesis and promote assembly of both filopodial and lamellipodial actin networks. To understand the molecular mechanisms underlying their cellular functions we used total internal reflection fluorescence microscopy to visualize VASP tetramers interacting with static and growing actin filaments in vitro. We observed multiple filament binding modes: (1) static side binding, (2) side binding with one-dimensional diffusion, and (3) processive barbed end tracking. Actin monomers antagonize side binding but promote high affinity (Kd = 9 nM) barbed end attachment. In low ionic strength buffers, VASP tetramers are weakly processive (Koff = 0.69 s−1) polymerases that deliver multiple actin monomers per barbed end–binding event and effectively antagonize filament capping. In higher ionic strength buffers, VASP requires profilin for effective polymerase and anti-capping activity. Based on our observations, we propose a mechanism that accounts for all three binding modes and provides a model for how VASP promotes actin filament assembly.
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Affiliation(s)
- Scott D Hansen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco School of Medicine, San Francisco, CA 94158, USA
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31
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Gillis AN, Thomas S, Hansen SD, Kaplan KB. A novel role for the CBF3 kinetochore-scaffold complex in regulating septin dynamics and cytokinesis. J Cell Biol 2005; 171:773-84. [PMID: 16330709 PMCID: PMC2171293 DOI: 10.1083/jcb.200507017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2005] [Accepted: 10/24/2005] [Indexed: 11/29/2022] Open
Abstract
In budding yeast, the kinetochore scaffold complex centromere binding factor 3 (CBF3) is required to form kinetochores on centromere DNA and to allow proper chromosome segregation. We have previously shown that SKP1 and SGT1 balance the assembly and turnover of CBF3 complexes, a cycle that we suggest is independent of its role in chromosome segregation (Rodrigo-Brenni, M.C., S. Thomas, D.C. Bouck, and K.B. Kaplan. 2004. Mol. Biol. Cell. 15:3366-3378). We provide evidence that this cycle contributes to a second, kinetochore-independent function of CBF3. In this study, we show that inhibiting the assembly of CBF3 causes disorganized septins and defects in cell polarity that give rise to cytokinesis failures. Specifically, we show that septin ring separation and disassembly is delayed in anaphase, suggesting that CBF3 regulates septin dynamics. Only mutations that affect the CBF3 cycle, and not mutants in outer kinetochore subunits, cause defects in septins. These results demonstrate a novel role for CBF3 in regulating cytokinesis, a role that is reminiscent of passenger proteins. Consistent with this possibility, we find that CBF3 interacts with Bir1p, the homologue of the passenger protein Survivin. Mutants in Bir1p similarly affect septin organization, leading us to propose that CBF3 and Bir1p act as passenger proteins to coordinate chromosome segregation with cytokinesis.
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Affiliation(s)
- Amethyst N Gillis
- The Section of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
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32
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Sennels S, Biering-Sørensen F, Andersen OT, Hansen SD. Functional neuromuscular stimulation controlled by surface electromyographic signals produced by volitional activation of the same muscle: adaptive removal of the muscle response from the recorded EMG-signal. IEEE Trans Rehabil Eng 1997; 5:195-206. [PMID: 9184905 DOI: 10.1109/86.593293] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In order to use the volitional electromyography (EMG) as a control signal for the stimulation of the same muscle, it is necessary to eliminate the stimulation artifacts and the muscle responses caused by the stimulation. The stimulation artifacts, caused by the electric field in skin and tissue generated by the stimulation current, are relatively easy to eliminate by shutting down the EMG-amplifier at the onset of the stimulation pulses. The muscle response is a nonstationary signal, therefore, an adaptive linear prediction filter is proposed. The filter is implemented and for three filter lengths tested on both simulated and real data. The filter performance is compared with a conventional fixed comb filter. The simulations indicate that the adaptive filter is relatively insensitive to variations in amplitude of the muscle responses, and for all filter lengths produces a good filtering. For variations in shape of the muscle responses and for real data, an increased filter performance can be achieved by increasing the filter length. Using a filter length of up to seven stimulation periods, it is possible to reduce real muscle responses to a level comparable with the background noise. Using the shut-down circuit and the adaptive filter both the stimulation artifacts and the muscle responses can be effectively eliminated from the EMG signal from a stimulated muscle. It is therefore possible to extract the volitional EMG from a partly paralyzed muscle and use it for controlling the stimulation of the same muscle.
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Affiliation(s)
- S Sennels
- Department of Mathematical Modeling, Technical University of Denmark, Lyngby, Denmark
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