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Sponholtz MR, Senning EN. The Pleckstrin Homology Domain of PLCδ1 Exhibits Complex Dissociation Properties at the Inner Leaflet of Plasma Membrane Sheets. ACS Chem Neurosci 2021; 12:2072-2078. [PMID: 34048227 DOI: 10.1021/acschemneuro.1c00248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Using total internal reflection fluorescence microscopy, we followed the dissociation of GFP-tagged pleckstrin homology (PH) domains of AKT and PLCδ1 from the plasma membranes of rapidly unroofed cells. We found that the AKT-PH-GFP and PLCδ1-PH-GFP dissociation kinetics can be distinguished by their effective koff values of 0.39 ± 0.05 and 0.56 ± 0.16 s-1, respectively. Furthermore, we identified substantial rebinding events in measurements of PLCδ1-PH-GFP dissociation kinetics. By applying inositol triphosphate (IP3) to samples during the unroofing process, we measured a much larger koff of 1.54 ± 0.42 s-1 for PLCδ1-PH-GFP, indicating that rebinding events are significantly suppressed through competitive action by IP3 for the same PH domain binding site as phosphatidylinositol 4,5-bisphosphate (PIP2). We discuss the complex character of our PLCδ1-PH-GFP fluorescence decays in the context of membrane receptor and ligand theory to address the question of how free PIP2 levels modulate the interaction between membrane-associated proteins and the plasma membrane.
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Affiliation(s)
- Madeline R. Sponholtz
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric N. Senning
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Neuroscience, The University of Texas at Austin, Austin, Texas 78712, United States
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2
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Beber A, Alqabandi M, Prévost C, Viars F, Lévy D, Bassereau P, Bertin A, Mangenot S. Septin‐based readout of PI(4,5)P2 incorporation into membranes of giant unilamellar vesicles. Cytoskeleton (Hoboken) 2018; 76:92-103. [DOI: 10.1002/cm.21480] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/05/2018] [Accepted: 07/10/2018] [Indexed: 01/27/2023]
Affiliation(s)
- Alexandre Beber
- Laboratoire Physico Chimie CurieInstitut Curie, PSL Research University Paris France
- Sorbonne Université Paris France
| | - Maryam Alqabandi
- Laboratoire Physico Chimie CurieInstitut Curie, PSL Research University Paris France
- Sorbonne Université Paris France
| | - Coline Prévost
- Laboratoire Physico Chimie CurieInstitut Curie, PSL Research University Paris France
- Sorbonne Université Paris France
| | - Fanny Viars
- Institut des maladies métaboliques et cardiovasculairesUMR1048, Inserm/Université Paul Sabatier Toulouse France
| | - Daniel Lévy
- Laboratoire Physico Chimie CurieInstitut Curie, PSL Research University Paris France
- Sorbonne Université Paris France
| | - Patricia Bassereau
- Laboratoire Physico Chimie CurieInstitut Curie, PSL Research University Paris France
- Sorbonne Université Paris France
| | - Aurélie Bertin
- Laboratoire Physico Chimie CurieInstitut Curie, PSL Research University Paris France
- Sorbonne Université Paris France
| | - Stéphanie Mangenot
- Laboratoire Physico Chimie CurieInstitut Curie, PSL Research University Paris France
- Sorbonne Université Paris France
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3
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Naughton FB, Kalli AC, Sansom MS. Modes of Interaction of Pleckstrin Homology Domains with Membranes: Toward a Computational Biochemistry of Membrane Recognition. J Mol Biol 2018; 430:372-388. [DOI: 10.1016/j.jmb.2017.12.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 12/08/2017] [Accepted: 12/13/2017] [Indexed: 11/30/2022]
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4
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Herzog FA, Braun L, Schoen I, Vogel V. Improved Side Chain Dynamics in MARTINI Simulations of Protein–Lipid Interfaces. J Chem Theory Comput 2016; 12:2446-58. [DOI: 10.1021/acs.jctc.6b00122] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Florian A. Herzog
- Laboratory of Applied Mechanobiology,
Department of Health Sciences and Technology, ETH Zurich, Vladimir-Prelog-Weg
4, 8093 Zurich, Switzerland
| | - Lukas Braun
- Laboratory of Applied Mechanobiology,
Department of Health Sciences and Technology, ETH Zurich, Vladimir-Prelog-Weg
4, 8093 Zurich, Switzerland
| | - Ingmar Schoen
- Laboratory of Applied Mechanobiology,
Department of Health Sciences and Technology, ETH Zurich, Vladimir-Prelog-Weg
4, 8093 Zurich, Switzerland
| | - Viola Vogel
- Laboratory of Applied Mechanobiology,
Department of Health Sciences and Technology, ETH Zurich, Vladimir-Prelog-Weg
4, 8093 Zurich, Switzerland
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5
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Ceccato L, Chicanne G, Nahoum V, Pons V, Payrastre B, Gaits-Iacovoni F, Viaud J. PLIF: A rapid, accurate method to detect and quantitatively assess protein-lipid interactions. Sci Signal 2016; 9:rs2. [PMID: 27025878 DOI: 10.1126/scisignal.aad4337] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Phosphoinositides are a type of cellular phospholipid that regulate signaling in a wide range of cellular and physiological processes through the interaction between their phosphorylated inositol head group and specific domains in various cytosolic proteins. These lipids also influence the activity of transmembrane proteins. Aberrant phosphoinositide signaling is associated with numerous diseases, including cancer, obesity, and diabetes. Thus, identifying phosphoinositide-binding partners and the aspects that define their specificity can direct drug development. However, current methods are costly, time-consuming, or technically challenging and inaccessible to many laboratories. We developed a method called PLIF (for "protein-lipid interaction by fluorescence") that uses fluorescently labeled liposomes and tethered, tagged proteins or peptides to enable fast and reliable determination of protein domain specificity for given phosphoinositides in a membrane environment. We validated PLIF against previously known phosphoinositide-binding partners for various proteins and obtained relative affinity profiles. Moreover, PLIF analysis of the sorting nexin (SNX) family revealed not only that SNXs bound most strongly to phosphatidylinositol 3-phosphate (PtdIns3P or PI3P), which is known from analysis with other methods, but also that they interacted with other phosphoinositides, which had not previously been detected using other techniques. Different phosphoinositide partners, even those with relatively weak binding affinity, could account for the diverse functions of SNXs in vesicular trafficking and protein sorting. Because PLIF is sensitive, semiquantitative, and performed in a high-throughput manner, it may be used to screen for highly specific protein-lipid interaction inhibitors.
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Affiliation(s)
- Laurie Ceccato
- INSERM, U1048 and Université Toulouse 3, I2MC, Avenue Jean Poulhès BP84225, 31432 Toulouse Cedex 04, France
| | - Gaëtan Chicanne
- INSERM, U1048 and Université Toulouse 3, I2MC, Avenue Jean Poulhès BP84225, 31432 Toulouse Cedex 04, France
| | - Virginie Nahoum
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS), 31000 Toulouse, France. Université de Toulouse, UPS (Université Paul Sabatier), IPBS, 31000 Toulouse, France
| | - Véronique Pons
- INSERM, U1048 and Université Toulouse 3, I2MC, Avenue Jean Poulhès BP84225, 31432 Toulouse Cedex 04, France
| | - Bernard Payrastre
- INSERM, U1048 and Université Toulouse 3, I2MC, Avenue Jean Poulhès BP84225, 31432 Toulouse Cedex 04, France. CHU (Centre Hospitalier Universitaire) de Toulouse, Laboratoire d'Hématologie, 31059 Toulouse Cedex 03, France
| | - Frédérique Gaits-Iacovoni
- INSERM, U1048 and Université Toulouse 3, I2MC, Avenue Jean Poulhès BP84225, 31432 Toulouse Cedex 04, France
| | - Julien Viaud
- INSERM, U1048 and Université Toulouse 3, I2MC, Avenue Jean Poulhès BP84225, 31432 Toulouse Cedex 04, France.
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Richens JL, Lane JS, Bramble JP, O'Shea P. The electrical interplay between proteins and lipids in membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1828-36. [DOI: 10.1016/j.bbamem.2015.03.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/16/2015] [Accepted: 03/18/2015] [Indexed: 11/17/2022]
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Modulated mechanism of phosphatidylserine on the catalytic activity of Naja naja atra phospholipase A2 and Notechis scutatus scutatus notexin. Toxicon 2014; 92:113-22. [PMID: 25449100 DOI: 10.1016/j.toxicon.2014.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/01/2014] [Accepted: 10/09/2014] [Indexed: 11/24/2022]
Abstract
Phosphatidylserine (PS) externalization is a hallmark for apoptotic death of cells. Previous studies showed that Naja naja atra phospholipase A2 (NnaPLA2) and Notechis scutatus scutatus notexin induced apoptosis of human cancer cells. However, NnaPLA2 and notexin did not markedly disrupt the integrity of cellular membrane as evidenced by membrane permeability of propidium iodide. These findings reflected that the ability of NnaPLA2 and notexin to hydrolyze membrane phospholipids may be affected by PS externalization. To address that question, this study investigated the membrane-interacted mode and catalytic activity of NnaPLA2 and notexin toward outer leaflet (phosphatidylcholine/sphingomyelin/cholesterol, PC/SM/Chol) and inner leaflet (phosphatidylserine/phosphatidylethanolamine/cholesterol, PS/PE/Chol) of plasma membrane-mimicking vesicles. PS incorporation promoted enzymatic activity of NnaPLA2 and notexin on PC and PC/SM vesicles, but suppressed NnaPLA2 and notexin activity on PC/SM/Chol and PE/Chol vesicles. PS incorporation increased the membrane fluidity of PC vesicles but reduced membrane fluidity of PC/SM, PC/SM/Chol and PE/Chol vesicles. PS increased the phospholipid order of all the tested vesicles. Moreover, PS incorporation did not greatly alter the binding affinity of notexin and NnaPLA2 with phospholipid vesicles. Acrylamide quenching studies and trinitrophenylation of Lys residues revealed that membrane-bound mode of notexin and NnaPLA2 varied with the targeted membrane compositions. The fine structure of catalytic site in NnaPLA2 and notexin in all the tested vesicles showed different changes. Collectively, the present data suggest that membrane-inserted PS modulates PLA2 interfacial activity via its effects on membrane structure and membrane-bound mode of NnaPLA2 and notexin, and membrane compositions determine the effect of PS on PLA2 activity.
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Tanio M, Nishimura K. Analysis of the phospholipase C-δ1 pleckstrin homology domain using native polyacrylamide gel electrophoresis. Anal Biochem 2012; 431:106-14. [DOI: 10.1016/j.ab.2012.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 09/04/2012] [Accepted: 09/10/2012] [Indexed: 10/27/2022]
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9
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Goñi FM, Montes LR, Alonso A. Phospholipases C and sphingomyelinases: Lipids as substrates and modulators of enzyme activity. Prog Lipid Res 2012; 51:238-66. [DOI: 10.1016/j.plipres.2012.03.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 03/23/2012] [Accepted: 03/26/2012] [Indexed: 11/30/2022]
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10
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Tokuda N, Kawai K, Lee YH, Ikegami T, Yamaguchi S, Yagisawa H, Fukui Y, Tuzi S. Membrane-induced alteration of the secondary structure in the SWAP-70 pleckstrin homology domain. J Biochem 2012; 151:391-401. [DOI: 10.1093/jb/mvr146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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11
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Rous sarcoma virus gag has no specific requirement for phosphatidylinositol-(4,5)-bisphosphate for plasma membrane association in vivo or for liposome interaction in vitro. J Virol 2011; 85:10851-60. [PMID: 21813603 DOI: 10.1128/jvi.00760-11] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The MA domain of the retroviral Gag protein mediates interactions with the plasma membrane, which is the site of productive virus release. HIV-1 MA has a phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P₂] binding pocket; depletion of this phospholipid from the plasma membrane compromises Gag membrane association and virus budding. We used multiple methods to examine the possible role of PI(4,5)P₂ in Gag-membrane interaction of the alpharetrovirus Rous sarcoma virus (RSV). In contrast to HIV-1, which was tested in parallel, neither membrane localization of RSV Gag-GFP nor release of virus-like particles was affected by phosphatase-mediated depletion of PI(4,5)P₂ in transfected avian cells. In liposome flotation experiments, RSV Gag required acidic lipids for binding but showed no specificity for PI(4,5)P₂. Mono-, di-, and triphosphorylated phosphatidylinositol phosphate (PIP) species as well as high concentrations of phosphatidylserine (PS) supported similar levels of flotation. A mutation that increases the overall charge of RSV MA also enhanced Gag membrane binding. Contrary to previous reports, we found that high concentrations of PS, in the absence of PIPs, also strongly promoted HIV-1 Gag flotation. Taken together, we interpret these results to mean that RSV Gag membrane association is driven by electrostatic interactions and not by any specific association with PI(4,5)P₂.
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12
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Influence of membrane curvature on the structure of the membrane-associated pleckstrin homology domain of phospholipase C-δ1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:2575-83. [DOI: 10.1016/j.bbamem.2009.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 10/09/2009] [Accepted: 10/13/2009] [Indexed: 12/25/2022]
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13
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Psachoulia E, Sansom MSP. Interactions of the pleckstrin homology domain with phosphatidylinositol phosphate and membranes: characterization via molecular dynamics simulations. Biochemistry 2008; 47:4211-20. [PMID: 18341295 DOI: 10.1021/bi702319k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of interaction of pleckstrin homology (PH) domains with phosphatidylinositol 4,5-bisphosphate (PIP 2)-containing lipid bilayers remains uncertain. While crystallographic studies have emphasized PH-inositol 1,4,5-trisphosphate (IP 3) interactions, biophysical studies indicate a degree of less specific protein-bilayer interactions. We have used molecular dynamics simulations to characterize the interactions of the PH domain from phospholipase C-delta1 with IP 3 and with PIP 2, the latter in lipid bilayers and in detergent micelles. Simulations of the PH domain in water reveal a reduction in protein flexibility when IP 3 is bound. Simulations of the PH domain bound to PIP 2 in lipid bilayers indicate a tightening of ligand-protein interactions relative to the PH-IP 3 complex, alongside formation of H-bonds between PH side chains and lipid (PC) headgroups, and a degree of penetration of hydrophobic side chains into the core of the bilayer. Comparison with simulations of the PH-bound domain to a PC bilayer in the absence of PIP 2 suggests that the presence of PIP 2 increases the extent of PH-membrane interactions. Thus, comparative molecular dynamics simulations reveal how a PI-binding domain undergoes changes in conformational dynamics on binding to a PIP 2-containing membrane and how interactions additional to those with the PI headgroup are formed.
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Affiliation(s)
- Emi Psachoulia
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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Saitô H, Naito A. NMR studies on fully hydrated membrane proteins, with emphasis on bacteriorhodopsin as a typical and prototype membrane protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3145-61. [PMID: 17964534 DOI: 10.1016/j.bbamem.2007.08.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Revised: 08/24/2007] [Accepted: 08/29/2007] [Indexed: 11/30/2022]
Abstract
The 3D structures or dynamic feature of fully hydrated membrane proteins are very important at ambient temperature, in relation to understanding their biological activities, although their data, especially from the flexible portions such as surface regions, are unavailable from X-ray diffraction or cryoelectron microscope at low temperature. In contrast, high-resolution solid-state NMR spectroscopy has proved to be a very convenient alternative means to be able to reveal their dynamic structures. To clarify this problem, we describe here how we are able to reveal such structures and dynamic features, based on intrinsic probes from high-resolution solid-state NMR studies on bacteriorhodopsin (bR) as a typical membrane protein in 2D crystal, regenerated preparation in lipid bilayer and detergents. It turned out that their dynamic features are substantially altered upon their environments where bR is present. We further review NMR applications to study structure and dynamics of a variety of membrane proteins, including sensory rhodopsin, rhodopsin, photoreaction centers, diacylglycerol kinases, etc.
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Affiliation(s)
- Hazime Saitô
- Center for Quantum Life Sciences, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
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15
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Drin G, Scarlata S. Stimulation of phospholipase Cbeta by membrane interactions, interdomain movement, and G protein binding--how many ways can you activate an enzyme? Cell Signal 2007; 19:1383-92. [PMID: 17524618 PMCID: PMC1963342 DOI: 10.1016/j.cellsig.2007.04.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Accepted: 04/08/2007] [Indexed: 11/19/2022]
Abstract
Signaling proteins are usually composed of one or more conserved structural domains. These domains are usually regulatory in nature by binding to specific activators or effectors, or species that regulate cellular location, etc. Inositol-specific mammalian phospholipase C (PLC) enzymes are multidomain proteins whose activities are controlled by regulators, such as G proteins, as well as membrane interactions. One of these domains has been found to bind membranes, regulators, and activate the catalytic region. The recently solved structure of a major region of PLC-beta2 together with the structure of PLC-delta1 and a wealth of biochemical studies poises the system towards an understanding of the mechanism through which their regulations occurs.
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Affiliation(s)
- Guillaume Drin
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS et Université de Nice-Sophia Antipolis, 06560 Valbonne, France
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