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John LH, Naughton FB, Sansom MSP, Larsen AH. The Role of C2 Domains in Two Different Phosphatases: PTEN and SHIP2. MEMBRANES 2023; 13:408. [PMID: 37103835 PMCID: PMC10146288 DOI: 10.3390/membranes13040408] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/13/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Phosphatase and tensin homologue (PTEN) and SH2-containing inositol 5'-phosphatase 2 (SHIP2) are structurally and functionally similar. They both consist of a phosphatase (Ptase) domain and an adjacent C2 domain, and both proteins dephosphorylate phosphoinositol-tri(3,4,5)phosphate, PI(3,4,5)P3; PTEN at the 3-phophate and SHIP2 at the 5-phosphate. Therefore, they play pivotal roles in the PI3K/Akt pathway. Here, we investigate the role of the C2 domain in membrane interactions of PTEN and SHIP2, using molecular dynamics simulations and free energy calculations. It is generally accepted that for PTEN, the C2 domain interacts strongly with anionic lipids and therefore significantly contributes to membrane recruitment. In contrast, for the C2 domain in SHIP2, we previously found much weaker binding affinity for anionic membranes. Our simulations confirm the membrane anchor role of the C2 domain in PTEN, as well as its necessity for the Ptase domain in gaining its productive membrane-binding conformation. In contrast, we identified that the C2 domain in SHIP2 undertakes neither of these roles, which are generally proposed for C2 domains. Our data support a model in which the main role of the C2 domain in SHIP2 is to introduce allosteric interdomain changes that enhance catalytic activity of the Ptase domain.
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Affiliation(s)
- Laura H. John
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Fiona B. Naughton
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Andreas Haahr Larsen
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
- Department of Neuroscience, University of Copenhagen, 2200 Copenhagen, Denmark
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2
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Atp8a1 deletion increases the proliferative activity of hematopoietic stem cells by impairing PTEN function. Cell Oncol (Dordr) 2023:10.1007/s13402-023-00797-7. [PMID: 36930333 DOI: 10.1007/s13402-023-00797-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2023] [Indexed: 03/18/2023] Open
Abstract
PURPOSE The eukaryotic cell plasma membrane contains several asymmetrically distributed phospholipids, which is maintained by the P4-ATPase flippase complex. Herein, we demonstrated the biological effects and mechanisms of asymmetrical loss in hematopoietic stem cells (HSCs). METHODS An Atp8a1 knockout mouse model was employed, from which the HSC (long-term HSCs and short-term HSCs) population was analyzed to assess their abundance and function. Additionally, competitive bone marrow transplantation and 5-FU stress assays were performed. RNA sequencing was performed on Hematopoietic Stem and Progenitor Cells, and DNA damage was assayed using immunofluorescence staining and comet electrophoresis. The protein abundance for members of key signaling pathways was confirmed using western blotting. RESULTS Atp8a1 deletion resulted in slight hyperleukocytosis, associated with the high proliferation of HSCs and BCR/ABL1 transformed leukemia stem cells (LSCs). Atp8a1 deletion increased the repopulation capability of HSCs with a competitive advantage in reconstitution assay. HSCs without Atp8a1 were more sensitive to 5-FU-induced apoptosis. Moreover, Atp8a1 deletion prevented HSC DNA damage and facilitated DNA repair processes. Genes involved in PI3K-AKT-mTORC1, DNA repair, and AP-1 complex signaling were enriched and elevated in HSCs with Atp8a1 deletion. Furthermore, Atp8a1 deletion caused decreased PTEN protein levels, resulting in the activation of PI3K-AKT-mTORC1 signaling, further increasing the activity of JNK/AP-1 signaling and YAP1 phosphorylation. CONCLUSION We identified the role of Atp8a1 on hematopoiesis and HSCs. Atp8a1 deletion resulted in the loss of phosphatidylserine asymmetry and intracellular signal transduction chaos.
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3
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Kotzampasi DM, Premeti K, Papafotika A, Syropoulou V, Christoforidis S, Cournia Z, Leondaritis G. The orchestrated signaling by PI3Kα and PTEN at the membrane interface. Comput Struct Biotechnol J 2022; 20:5607-5621. [PMID: 36284707 PMCID: PMC9578963 DOI: 10.1016/j.csbj.2022.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/03/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022] Open
Abstract
The oncogene PI3Kα and the tumor suppressor PTEN represent two antagonistic enzymatic activities that regulate the interconversion of the phosphoinositide lipids PI(4,5)P2 and PI(3,4,5)P3 in membranes. As such, they are defining components of phosphoinositide-based cellular signaling and membrane trafficking pathways that regulate cell survival, growth, and proliferation, and are often deregulated in cancer. In this review, we highlight aspects of PI3Kα and PTEN interplay at the intersection of signaling and membrane trafficking. We also discuss the mechanisms of PI3Kα- and PTEN- membrane interaction and catalytic activation, which are fundamental for our understanding of the structural and allosteric implications on signaling at the membrane interface and may aid current efforts in pharmacological targeting of these proteins.
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Affiliation(s)
- Danai Maria Kotzampasi
- Biomedical Research Foundation, Academy of Athens, Athens 11527, Greece
- Department of Biology, University of Crete, Heraklion 71500, Greece
| | - Kyriaki Premeti
- Laboratory of Pharmacology, Faculty of Medicine, University of Ioannina, Ioannina 45110, Greece
| | - Alexandra Papafotika
- Laboratory of Biological Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina 45110, Greece
- Biomedical Research Institute, Foundation for Research and Technology, Ioannina 45110, Greece
| | - Vasiliki Syropoulou
- Laboratory of Pharmacology, Faculty of Medicine, University of Ioannina, Ioannina 45110, Greece
| | - Savvas Christoforidis
- Laboratory of Biological Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina 45110, Greece
- Biomedical Research Institute, Foundation for Research and Technology, Ioannina 45110, Greece
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, Athens 11527, Greece
| | - George Leondaritis
- Laboratory of Pharmacology, Faculty of Medicine, University of Ioannina, Ioannina 45110, Greece
- Institute of Biosciences, University Research Center of Ioannina, Ioannina 45110, Greece
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4
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Michalak DJ, Unger B, Lorimer E, Grishaev A, Williams CL, Heinrich F, Lösche M. Structural and biophysical properties of farnesylated KRas interacting with the chaperone SmgGDS-558. Biophys J 2022; 121:3684-3697. [PMID: 35614853 PMCID: PMC9617131 DOI: 10.1016/j.bpj.2022.05.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/02/2022] [Accepted: 05/19/2022] [Indexed: 11/26/2022] Open
Abstract
KRas is a small GTPase and membrane-bound signaling protein. Newly synthesized KRas is post-translationally modified with a membrane-anchoring prenyl group. KRas chaperones are therapeutic targets in cancer due to their participation in trafficking oncogenic KRas to membranes. SmgGDS splice variants are chaperones for small GTPases with basic residues in their hypervariable domain (HVR), including KRas. SmgGDS-607 escorts pre-prenylated small GTPases, while SmgGDS-558 escorts prenylated small GTPases. We provide a structural description of farnesylated and fully processed KRas (KRas-FMe) in complex with SmgGDS-558 and define biophysical properties of this interaction. Surface plasmon resonance measurements on biomimetic model membranes quantified the thermodynamics of the interaction of SmgGDS with KRas, and small-angle x-ray scattering was used to characterize complexes of SmgGDS-558 and KRas-FMe structurally. Structural models were refined using Monte Carlo and molecular dynamics simulations. Our results indicate that SmgGDS-558 interacts with the HVR and the farnesylated C-terminus of KRas-FMe, but not its G-domain. Therefore, SmgGDS-558 interacts differently with prenylated KRas than prenylated RhoA, whose G-domain was found in close contact with SmgGDS-558 in a recent crystal structure. Using immunoprecipitation assays, we show that SmgGDS-558 binds the GTP-bound, GDP-bound, and nucleotide-free forms of farnesylated and fully processed KRas in cells, consistent with SmgGDS-558 not engaging the G-domain of KRas. We found that the dissociation constant, Kd, for KRas-FMe binding to SmgGDS-558 is comparable with that for the KRas complex with PDEδ, a well-characterized KRas chaperone that also does not interact with the KRas G-domain. These results suggest that KRas interacts in similar ways with the two chaperones SmgGDS-558 and PDEδ. Therapeutic targeting of the SmgGDS-558/KRas complex might prove as useful as targeting the PDEδ/KRas complex in KRas-driven cancers.
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Affiliation(s)
- Dennis J Michalak
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Bethany Unger
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Ellen Lorimer
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Alexander Grishaev
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland; Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - Carol L Williams
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland.
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland
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5
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Ohashi Y. Activation Mechanisms of the VPS34 Complexes. Cells 2021; 10:cells10113124. [PMID: 34831348 PMCID: PMC8624279 DOI: 10.3390/cells10113124] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 01/18/2023] Open
Abstract
Phosphatidylinositol-3-phosphate (PtdIns(3)P) is essential for cell survival, and its intracellular synthesis is spatially and temporally regulated. It has major roles in two distinctive cellular pathways, namely, the autophagy and endocytic pathways. PtdIns(3)P is synthesized from phosphatidylinositol (PtdIns) by PIK3C3C/VPS34 in mammals or Vps34 in yeast. Pathway-specific VPS34/Vps34 activity is the consequence of the enzyme being incorporated into two mutually exclusive complexes: complex I for autophagy, composed of VPS34/Vps34-Vps15/Vps15-Beclin 1/Vps30-ATG14L/Atg14 (mammals/yeast), and complex II for endocytic pathways, in which ATG14L/Atg14 is replaced with UVRAG/Vps38 (mammals/yeast). Because of its involvement in autophagy, defects in which are closely associated with human diseases such as cancer and neurodegenerative diseases, developing highly selective drugs that target specific VPS34/Vps34 complexes is an essential goal in the autophagy field. Recent studies on the activation mechanisms of VPS34/Vps34 complexes have revealed that a variety of factors, including conformational changes, lipid physicochemical parameters, upstream regulators, and downstream effectors, greatly influence the activity of these complexes. This review summarizes and highlights each of these influences as well as clarifying key questions remaining in the field and outlining future perspectives.
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Affiliation(s)
- Yohei Ohashi
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Francis Crick Avenue, Cambridge CB2 0QH, UK
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6
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Correa Y, Waldie S, Thépaut M, Micciulla S, Moulin M, Fieschi F, Pichler H, Trevor Forsyth V, Haertlein M, Cárdenas M. SARS-CoV-2 spike protein removes lipids from model membranes and interferes with the capacity of high density lipoprotein to exchange lipids. J Colloid Interface Sci 2021; 602:732-739. [PMID: 34157514 PMCID: PMC8195693 DOI: 10.1016/j.jcis.2021.06.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 01/18/2023]
Abstract
Cholesterol has been shown to affect the extent of coronavirus binding and fusion to cellular membranes. The severity of Covid-19 infection is also known to be correlated with lipid disorders. Furthermore, the levels of both serum cholesterol and high-density lipoprotein (HDL) decrease with Covid-19 severity, with normal levels resuming once the infection has passed. Here we demonstrate that the SARS-CoV-2 spike (S) protein interferes with the function of lipoproteins, and that this is dependent on cholesterol. In particular, the ability of HDL to exchange lipids from model cellular membranes is altered when co-incubated with the spike protein. Additionally, the S protein removes lipids and cholesterol from model membranes. We propose that the S protein affects HDL function by removing lipids from it and remodelling its composition/structure.
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Affiliation(s)
- Yubexi Correa
- Biofilms - Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University, 20506 Malmö, Sweden
| | - Sarah Waldie
- Biofilms - Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University, 20506 Malmö, Sweden; Life Sciences Group, Institut Laue Langevin, Grenoble F-38042, France; Partnership for Structural Biology, Grenoble F-38042, France
| | - Michel Thépaut
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Samantha Micciulla
- Large Scale Structures, Institut Laue Langevin (ILL), Grenoble F-38042, France
| | - Martine Moulin
- Life Sciences Group, Institut Laue Langevin, Grenoble F-38042, France; Partnership for Structural Biology, Grenoble F-38042, France
| | - Franck Fieschi
- Partnership for Structural Biology, Grenoble F-38042, France; Univ. Grenoble Alpes, CNRS, CEA, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria; Graz University of Technology, Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Petersgasse 14, 8010 Graz, Austria
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue Langevin, Grenoble F-38042, France; Partnership for Structural Biology, Grenoble F-38042, France; Faculty of Natural Sciences, Keele University, Staffordshire ST5 5BG, UK.
| | - Michael Haertlein
- Life Sciences Group, Institut Laue Langevin, Grenoble F-38042, France; Partnership for Structural Biology, Grenoble F-38042, France.
| | - Marité Cárdenas
- Biofilms - Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University, 20506 Malmö, Sweden.
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7
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Larsen AH, Sansom MSP. Binding of Ca 2+-independent C2 domains to lipid membranes: A multi-scale molecular dynamics study. Structure 2021; 29:1200-1213.e2. [PMID: 34081910 PMCID: PMC8507603 DOI: 10.1016/j.str.2021.05.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/26/2021] [Accepted: 05/14/2021] [Indexed: 01/17/2023]
Abstract
C2 domains facilitate protein interactions with lipid bilayers in either a Ca2+-dependent or -independent manner. We used molecular dynamics (MD) simulations to explore six Ca2+-independent C2 domains, from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2. In coarse-grained MD simulations these C2 domains formed transient interactions with zwitterionic bilayers, compared with longer-lived interactions with anionic bilayers containing phosphatidylinositol bisphosphate (PIP2). Type I C2 domains bound non-canonically via the front, back, or side of the β sandwich, whereas type II C2 domains bound canonically, via the top loops. C2 domains interacted strongly with membranes containing PIP2, causing bound anionic lipids to cluster around the protein. Binding modes were refined via atomistic simulations. For PTEN and SHIP2, CG simulations of their phosphatase plus C2 domains with PIP2-containing bilayers were also performed, and the roles of the two domains in membrane localization compared. These studies establish a simulation protocol for membrane-recognition proteins. Binding of Ca2+-independent C2 domains to membranes was explored by MD simulation C2 domains from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2 were compared C2 domains formed longer-lived interactions with lipid bilayers containing PIP2 For PTEN and SHIP2, simulations of their phosphatase plus C2 domains were performed
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Affiliation(s)
- Andreas Haahr Larsen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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8
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Gresham IJ, Murdoch TJ, Johnson EC, Robertson H, Webber GB, Wanless EJ, Prescott SW, Nelson ARJ. Quantifying the robustness of the neutron reflectometry technique for structural characterization of polymer brushes. J Appl Crystallogr 2021. [DOI: 10.1107/s160057672100251x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Neutron reflectometry is the foremost technique for in situ determination of the volume fraction profiles of polymer brushes at planar interfaces. However, the subtle features in the reflectometry data produced by these diffuse interfaces challenge data interpretation. Historically, data analyses have used least-squares approaches that do not adequately quantify the uncertainty of the modeled profile and ignore the possibility of other structures that also match the collected data (multimodality). Here, a Bayesian statistical approach is used that permits the structural uncertainty and multimodality to be quantified for polymer brush systems. A free-form model is used to describe the volume fraction profile, minimizing assumptions regarding brush structure, while only allowing physically reasonable profiles to be produced. The model allows the total volume of polymer and the profile monotonicity to be constrained. The rigor of the approach is demonstrated via a round-trip analysis of a simulated system, before it is applied to real data examining the well characterized collapse of a thermoresponsive brush. It is shown that, while failure to constrain the interfacial volume and consider multimodality may result in erroneous structures being derived, carefully constraining the model allows for robust determination of polymer brush compositional profiles. This work highlights that an appropriate combination of flexibility and constraint must be used with polymer brush systems to ensure the veracity of the analysis. The code used in this analysis is provided, enabling the reproduction of the results and the application of the method to similar problems.
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9
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Van QN, López CA, Tonelli M, Taylor T, Niu B, Stanley CB, Bhowmik D, Tran TH, Frank PH, Messing S, Alexander P, Scott D, Ye X, Drew M, Chertov O, Lösche M, Ramanathan A, Gross ML, Hengartner NW, Westler WM, Markley JL, Simanshu DK, Nissley DV, Gillette WK, Esposito D, McCormick F, Gnanakaran S, Heinrich F, Stephen AG. Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane. Proc Natl Acad Sci U S A 2020; 117:24258-24268. [PMID: 32913056 PMCID: PMC7533834 DOI: 10.1073/pnas.2006504117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The small GTPase KRAS is localized at the plasma membrane where it functions as a molecular switch, coupling extracellular growth factor stimulation to intracellular signaling networks. In this process, KRAS recruits effectors, such as RAF kinase, to the plasma membrane where they are activated by a series of complex molecular steps. Defining the membrane-bound state of KRAS is fundamental to understanding the activation of RAF kinase and in evaluating novel therapeutic opportunities for the inhibition of oncogenic KRAS-mediated signaling. We combined multiple biophysical measurements and computational methodologies to generate a consensus model for authentically processed, membrane-anchored KRAS. In contrast to the two membrane-proximal conformations previously reported, we identify a third significantly populated state using a combination of neutron reflectivity, fast photochemical oxidation of proteins (FPOP), and NMR. In this highly populated state, which we refer to as "membrane-distal" and estimate to comprise ∼90% of the ensemble, the G-domain does not directly contact the membrane but is tethered via its C-terminal hypervariable region and carboxymethylated farnesyl moiety, as shown by FPOP. Subsequent interaction of the RAF1 RAS binding domain with KRAS does not significantly change G-domain configurations on the membrane but affects their relative populations. Overall, our results are consistent with a directional fly-casting mechanism for KRAS, in which the membrane-distal state of the G-domain can effectively recruit RAF kinase from the cytoplasm for activation at the membrane.
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Affiliation(s)
- Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - Troy Taylor
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Ben Niu
- National Mass Spectrometry Resource, Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Debsindhu Bhowmik
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Timothy H Tran
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Peter H Frank
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Simon Messing
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Patrick Alexander
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Daniel Scott
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Xiaoying Ye
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Matt Drew
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Oleg Chertov
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Mathias Lösche
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Arvind Ramanathan
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
| | - Michael L Gross
- National Mass Spectrometry Resource, Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - William M Westler
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - John L Markley
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - Dhirendra K Simanshu
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Dwight V Nissley
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - William K Gillette
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Dominic Esposito
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Frank McCormick
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702;
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702;
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10
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Soubias O, Pant S, Heinrich F, Zhang Y, Roy NS, Li J, Jian X, Yohe ME, Randazzo PA, Lösche M, Tajkhorshid E, Byrd RA. Membrane surface recognition by the ASAP1 PH domain and consequences for interactions with the small GTPase Arf1. SCIENCE ADVANCES 2020; 6:6/40/eabd1882. [PMID: 32998886 PMCID: PMC7527224 DOI: 10.1126/sciadv.abd1882] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/04/2020] [Indexed: 05/05/2023]
Abstract
Adenosine diphosphate-ribosylation factor (Arf) guanosine triphosphatase-activating proteins (GAPs) are enzymes that need to bind to membranes to catalyze the hydrolysis of guanosine triphosphate (GTP) bound to the small GTP-binding protein Arf. Binding of the pleckstrin homology (PH) domain of the ArfGAP With SH3 domain, ankyrin repeat and PH domain 1 (ASAP1) to membranes containing phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is key for maximum GTP hydrolysis but not fully understood. By combining nuclear magnetic resonance, neutron reflectometry, and molecular dynamics simulation, we show that binding of multiple PI(4,5)P2 molecules to the ASAP1 PH domain (i) triggers a functionally relevant allosteric conformational switch and (ii) maintains the PH domain in a well-defined orientation, allowing critical contacts with an Arf1 mimic to occur. Our model provides a framework to understand how binding of the ASAP1 PH domain to PI(4,5)P2 at the membrane may play a role in the regulation of ASAP1.
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Affiliation(s)
- Olivier Soubias
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- NIST Center for Neutron Research, Gaithersburg, MD 20878, USA
| | - Yue Zhang
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Neeladri Sekhar Roy
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jess Li
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marielle E Yohe
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
- NIST Center for Neutron Research, Gaithersburg, MD 20878, USA
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - R Andrew Byrd
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA.
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11
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Treece BW, Heinrich F, Ramanathan A, Lösche M. Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results. J Chem Theory Comput 2020; 16:3408-3419. [DOI: 10.1021/acs.jctc.0c00136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Bradley W. Treece
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- The NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Arvind Ramanathan
- Data Science and Learning, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- The NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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12
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Pond MP, Eells R, Treece BW, Heinrich F, Lösche M, Roux B. Membrane Anchoring of Hck Kinase via the Intrinsically Disordered SH4-U and Length Scale Associated with Subcellular Localization. J Mol Biol 2019; 432:2985-2997. [PMID: 31877324 DOI: 10.1016/j.jmb.2019.11.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/21/2022]
Abstract
Src family kinases (SFKs) are a group of nonreceptor tyrosine kinases that are characterized by their involvement in critical signal transduction pathways. SFKs are often found attached to membranes, but little is known about the conformation of the protein in this environment. Here, solution nuclear magnetic resonance (NMR), neutron reflectometry (NR), and molecular dynamics (MD) simulations were employed to study the membrane interactions of the intrinsically disordered SH4 and Unique domains of the Src family kinase Hck. Through development of a procedure to combine the information from the different techniques, we were able produce a first-of-its-kind atomically detailed structural ensemble of a membrane-bound intrinsically disordered protein. Evaluation of the model demonstrated its consistency with previous work and provided insight into how SFK Unique domains act to differentiate the family members from one another. Fortuitously, the position of the ensemble on the membrane allowed the model to be combined with configurations of the multidomain Hck kinase previously determined from small-angle solution X-ray scattering to produce full-length models of membrane-anchored Hck. The resulting models allowed us to estimate that the kinase active site is positioned about 65 ± 35 Å away from the membrane surface, offering the first estimations of the length scale associated with the concept of SFK subcellular localization.
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Affiliation(s)
- Matthew P Pond
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, IL, 60637, USA
| | - Rebecca Eells
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Bradley W Treece
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213, USA; Center for Neutron Research, NIST, Gaithersburg, MD, 20899, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213, USA; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA; Center for Neutron Research, NIST, Gaithersburg, MD, 20899, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, IL, 60637, USA.
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13
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Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, Hong L, Katsaras J, Kelman Z, Kharlampieva E, Kneller GR, Kovalevsky A, Krueger S, Langan P, Lieberman R, Liu Y, Losche M, Lyman E, Mao Y, Marino J, Mattos C, Meilleur F, Moody P, Nickels JD, O'Dell WB, O'Neill H, Perez-Salas U, Peters J, Petridis L, Sokolov AP, Stanley C, Wagner N, Weinrich M, Weiss K, Wymore T, Zhang Y, Smith JC. Neutron scattering in the biological sciences: progress and prospects. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1129-1168. [PMID: 30605130 DOI: 10.1107/s2059798318017503] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.
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Affiliation(s)
- Rana Ashkar
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - Hassina Z Bilheux
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Robert Briber
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - David J E Callaway
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Xiaolin Cheng
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
| | - Xiang Qiang Chu
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mark Dadmun
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Paul Fenimore
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Frank Gabel
- Institut Laue-Langevin, Université Grenoble Alpes, CEA, CNRS, IBS, 38042 Grenoble, France
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick Herberle
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Liang Hong
- Department of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - John Katsaras
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Eugenia Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS, Université d'Orléans, Chateau de la Source, Avenue du Parc Floral, Orléans, France
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Paul Langan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Raquel Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yun Liu
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mathias Losche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, DE 19716, USA
| | - Yimin Mao
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Peter Moody
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, England
| | - Jonathan D Nickels
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Hugh O'Neill
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Ursula Perez-Salas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Loukas Petridis
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - Alexei P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Christopher Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Norman Wagner
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Michael Weinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Kevin Weiss
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Troy Wymore
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Yang Zhang
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Jeremy C Smith
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
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14
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Kawanabe A, Hashimoto M, Nishizawa M, Nishizawa K, Narita H, Yonezawa T, Jinno Y, Sakata S, Nakagawa A, Okamura Y. The hydrophobic nature of a novel membrane interface regulates the enzyme activity of a voltage-sensing phosphatase. eLife 2018; 7:41653. [PMID: 30484774 PMCID: PMC6298786 DOI: 10.7554/elife.41653] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 11/28/2018] [Indexed: 01/24/2023] Open
Abstract
Voltage-sensing phosphatases (VSP) contain a voltage sensor domain (VSD) similar to that of voltage-gated ion channels but lack a pore-gate domain. A VSD in a VSP regulates the cytoplasmic catalytic region (CCR). However, the mechanisms by which the VSD couples to the CCR remain elusive. Here we report a membrane interface (named ‘the hydrophobic spine’), which is essential for the coupling of the VSD and CCR. Our molecular dynamics simulations suggest that the hydrophobic spine of Ciona intestinalis VSP (Ci-VSP) provides a hinge-like motion for the CCR through the loose membrane association of the phosphatase domain. Electrophysiological experiments indicate that the voltage-dependent phosphatase activity of Ci-VSP depends on the hydrophobicity and presence of an aromatic ring in the hydrophobic spine. Analysis of conformational changes in the VSD and CCR suggests that the VSP has two states with distinct enzyme activities and that the second transition depends on the hydrophobic spine.
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Affiliation(s)
- Akira Kawanabe
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masaki Hashimoto
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | | | | | - Hirotaka Narita
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Tomoko Yonezawa
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuka Jinno
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Souhei Sakata
- Department of Physiology, Division of Life Sciences, Faculty of Medicine, Osaka Medical College, Osaka, Japan
| | | | - Yasushi Okamura
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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15
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Leitner MG, Hobiger K, Mavrantoni A, Feuer A, Oberwinkler J, Oliver D, Halaszovich CR. A126 in the active site and TI167/168 in the TI loop are essential determinants of the substrate specificity of PTEN. Cell Mol Life Sci 2018; 75:4235-4250. [PMID: 29987362 PMCID: PMC6182344 DOI: 10.1007/s00018-018-2867-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 06/19/2018] [Accepted: 07/03/2018] [Indexed: 01/16/2023]
Abstract
PTEN prevents tumor genesis by antagonizing the PI3 kinase/Akt pathway through D3 site phosphatase activity toward PI(3,4)P2 and PI(3,4,5)P3. The structural determinants of this important specificity remain unknown. Interestingly, PTEN shares remarkable homology to voltage-sensitive phosphatases (VSPs) that dephosphorylate D5 and D3 sites of PI(4,5)P2, PI(3,4)P2, and PI(3,4,5)P3. Since the catalytic center of PTEN and VSPs differ markedly only in TI/gating loop and active site motif, we wondered whether these differences explained the variation of their substrate specificity. Therefore, we introduced mutations into PTEN to mimic corresponding sequences of VSPs and studied phosphatase activity in living cells utilizing engineered, voltage switchable PTENCiV, a Ci-VSP/PTEN chimera that retains D3 site activity of the native enzyme. Substrate specificity of this enzyme was analyzed with whole-cell patch clamp in combination with total internal reflection fluorescence microscopy and genetically encoded phosphoinositide sensors. In PTENCiV, mutating TI167/168 in the TI loop into the corresponding ET pair of VSPs induced VSP-like D5 phosphatase activity toward PI(3,4,5)P3, but not toward PI(4,5)P2. Combining TI/ET mutations with an A126G exchange in the active site removed major sequence variations between PTEN and VSPs and resulted in D5 activity toward PI(4,5)P2 and PI(3,4,5)P3 of PTENCiV. This PTEN mutant thus fully reproduced the substrate specificity of native VSPs. Importantly, the same combination of mutations also induced D5 activity toward PI(3,4,5)P3 in native PTEN demonstrating that the same residues determine the substrate specificity of the tumor suppressor in living cells. Reciprocal mutations in VSPs did not alter their substrate specificity, but reduced phosphatase activity. In summary, A126 in the active site and TI167/168 in the TI loop are essential determinants of PTEN's substrate specificity, whereas additional features might contribute to the enzymatic activity of VSPs.
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Affiliation(s)
- Michael G Leitner
- Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstr. 1-2, 35037, Marburg, Germany
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Kirstin Hobiger
- Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstr. 1-2, 35037, Marburg, Germany
| | - Angeliki Mavrantoni
- Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstr. 1-2, 35037, Marburg, Germany
| | - Anja Feuer
- Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstr. 1-2, 35037, Marburg, Germany
| | - Johannes Oberwinkler
- Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstr. 1-2, 35037, Marburg, Germany
| | - Dominik Oliver
- Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstr. 1-2, 35037, Marburg, Germany
- DFG Research Training Group GRK 2213, Membrane Plasticity in Tissue Development and Remodeling, Philipps-University Marburg, 35043, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), Universities of Marburg and Giessen, Marburg/Giessen, Germany
| | - Christian R Halaszovich
- Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstr. 1-2, 35037, Marburg, Germany.
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16
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Combining scattering and computer simulation for the study of biomolecular soft interfaces. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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17
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Fricano-Kugler CJ, Getz SA, Williams MR, Zurawel AA, DeSpenza T, Frazel PW, Li M, O’Malley AJ, Moen EL, Luikart BW. Nuclear Excluded Autism-Associated Phosphatase and Tensin Homolog Mutations Dysregulate Neuronal Growth. Biol Psychiatry 2018; 84:265-277. [PMID: 29373119 PMCID: PMC5984669 DOI: 10.1016/j.biopsych.2017.11.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/01/2017] [Accepted: 11/16/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Phosphatase and tensin homolog (PTEN) negatively regulates downstream protein kinase B signaling, resulting in decreased cellular growth and proliferation. PTEN is mutated in a subset of children with autism spectrum disorder (ASD); however, the mechanism by which specific point mutations alter PTEN function is largely unknown. Here, we assessed how ASD-associated single-nucleotide variations in PTEN (ASD-PTEN) affect function. METHODS We used viral-mediated molecular substitution of human PTEN into Pten knockout mouse neurons and assessed neuronal morphology to determine the functional impact of ASD-PTEN. We employed molecular cloning to examine how PTEN's stability, subcellular localization, and catalytic activity affect neuronal growth. RESULTS We identified a set of ASD-PTEN mutations displaying altered lipid phosphatase function and subcellular localization. We demonstrated that wild-type PTEN can rescue the neuronal hypertrophy, while PTEN H93R, F241S, D252G, W274L, N276S, and D326N failed to rescue this hypertrophy. A subset of these mutations lacked nuclear localization, prompting us to examine the role of nuclear PTEN in regulating neuronal growth. We found that nuclear PTEN alone is sufficient to regulate soma size. Furthermore, forced localization of the D252G and W274L mutations into the nucleus partially restores regulation of soma size. CONCLUSIONS ASD-PTEN mutations display decreased stability, catalytic activity, and/or altered subcellular localization. Mutations lacking nuclear localization uncover a novel mechanism whereby lipid phosphatase activity in the nucleus can regulate mammalian target of rapamycin signaling and neuronal growth.
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Affiliation(s)
- Catherine J. Fricano-Kugler
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, Lebanon, New Hampshire 03756
| | - Stephanie A. Getz
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, Lebanon, New Hampshire 03756
| | - Michael R. Williams
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, Lebanon, New Hampshire 03756
| | - Ashley A. Zurawel
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, Lebanon, New Hampshire 03756
| | - Tyrone DeSpenza
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, Lebanon, New Hampshire 03756
| | - Paul W. Frazel
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, Lebanon, New Hampshire 03756
| | - Meijie Li
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, Lebanon, New Hampshire 03756
| | - Alistair J. O’Malley
- The Dartmouth Institute for Health Policy and Clinical Practice, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA,Department of Biomedical Data Science, The Dartmouth Institute for Health Policy and Clinical Practice, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Erika L. Moen
- The Dartmouth Institute for Health Policy and Clinical Practice, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Bryan W. Luikart
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, Lebanon, New Hampshire 03756,Corresponding Author-
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18
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Mattauch S, Koutsioubas A, Rücker U, Korolkov D, Fracassi V, Daemen J, Schmitz R, Bussmann K, Suxdorf F, Wagener M, Kämmerling P, Kleines H, Fleischhauer-Fuß L, Bednareck M, Ossoviy V, Nebel A, Stronciwilk P, Staringer S, Gödel M, Richter A, Kusche H, Kohnke T, Ioffe A, Babcock E, Salhi Z, Bruckel T. The high-intensity reflectometer of the Jülich Centre for Neutron Science: MARIA. J Appl Crystallogr 2018; 51:646-654. [PMID: 29896056 PMCID: PMC5988004 DOI: 10.1107/s1600576718006994] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 05/08/2018] [Indexed: 11/30/2022] Open
Abstract
MARIA (magnetism reflectometer with high incident angle) is a world class vertical sample reflectometer dedicated to the investigation of thin films in the fields of magnetism, soft matter and biology. The elliptical vertically focusing guide allows one to measure small samples with a typical size of 1 × 1 cm very efficiently. The double-bounce polarizer and the in situ pumped 3He SEOP (spin-exchange optical pumping) neutron spin filter cell for analysing the polarization of the reflected neutron beam can be moved into the beam in seconds. The polarized flux of MARIA amounts to 5 × 107 n (s cm2)-1 at the sample position with a horizontally collimated beam of 3 mrad, a wavelength of λ = 4.5 Å and a wavelength resolution of Δλ/λ = 10%. In the non-polarized mode a flux of 1.2 × 108 n (s cm2)-1 is achieved in this configuration. MARIA is also capable of grazing-incidence small-angle neutron scattering measurements, using a pinhole collimation with two four-segment slits and an absorber that prevents the focusing of the elliptical guide in the vertical direction.
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Affiliation(s)
- Stefan Mattauch
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Alexandros Koutsioubas
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Ulrich Rücker
- Jülich Centre for Neutron Science JCNS and Peter Grünberg Institut PGI, JARA-FIT, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Denis Korolkov
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | | | - Jos Daemen
- ZEA-1, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Ralf Schmitz
- ZEA-1, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Klaus Bussmann
- Jülich Centre for Neutron Science JCNS and Peter Grünberg Institut PGI, JARA-FIT, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Frank Suxdorf
- ZEA-2, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | | | | | - Harald Kleines
- ZEA-2, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | | | | | - Vladimir Ossoviy
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Andreas Nebel
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Peter Stronciwilk
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Simon Staringer
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Marko Gödel
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Alfred Richter
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Harald Kusche
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Thomas Kohnke
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Alexander Ioffe
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Earl Babcock
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Zahir Salhi
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Thomas Bruckel
- Jülich Centre for Neutron Science JCNS and Peter Grünberg Institut PGI, JARA-FIT, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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19
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A pathogenic role for germline PTEN variants which accumulate into the nucleus. Eur J Hum Genet 2018; 26:1180-1187. [PMID: 29706633 DOI: 10.1038/s41431-018-0155-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/27/2018] [Accepted: 03/30/2018] [Indexed: 11/08/2022] Open
Abstract
The PTEN gene encodes a master regulator protein that exerts essential functions both in the cytoplasm and in the nucleus. PTEN is mutated in the germline of both patients with heterogeneous tumor syndromic diseases, categorized as PTEN hamartoma tumor syndrome (PHTS), and a group affected with autism spectrum disorders (ASD). Previous studies have unveiled the functional heterogeneity of PTEN variants found in both patient cohorts, making functional studies necessary to provide mechanistic insights related to their pathogenicity. Here, we have functionally characterized a PTEN missense variant [c.49C>G; p.(Gln17Glu); Q17E] associated to both PHTS and ASD patients. The PTEN Q17E variant displayed partially reduced PIP3-catalytic activity and normal stability in cells, as shown using S. cerevisiae and mammalian cell experimental models. Remarkably, PTEN Q17E accumulated in the nucleus, in a process involving the PTEN N-terminal nuclear localization sequence. The analysis of additional germline-associated PTEN N-terminal variants illustrated the existence of a PTEN N-terminal region whose targeting in disease causes PTEN nuclear accumulation, in parallel with defects in PIP3-catalytic activity in cells. Our findings highlight the frequent occurrence of PTEN gene mutations targeting PTEN N-terminus whose pathogenicity may be related, at least in part, with the retention of PTEN in the nucleus. This could be important for the implementation of precision therapies for patients with alterations in the PTEN pathway.
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Protein⁻Phospholipid Interaction Motifs: A Focus on Phosphatidic Acid. Biomolecules 2018; 8:biom8020020. [PMID: 29690573 PMCID: PMC6022864 DOI: 10.3390/biom8020020] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/16/2018] [Accepted: 04/16/2018] [Indexed: 12/12/2022] Open
Abstract
Cellular membranes are composed of thousands of different lipids usually maintained within a narrow range of concentrations. In addition to their well-known structural and metabolic roles, signaling functions for many lipids have also emerged over the last two decades. The latter largely depend on the ability of particular classes of lipids to interact specifically with a great variety of proteins and to regulate their localization and activity. Among these lipids, phosphatidic acid (PA) plays a unique role in a large repertoire of cellular activities, most likely in relation to its unique biophysical properties. However, until recently, only incomplete information was available to model the interaction between PA and its protein partners. The development of new liposome-based assays as well as molecular dynamic simulation are now providing novel information. We will review the different factors that have shown to modulate the capacity of PA to interact with specific domains in target proteins.
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21
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Cai J, Li R, Xu X, Zhang L, Lian R, Fang L, Huang Y, Feng X, Liu X, Li X, Zhu X, Zhang H, Wu J, Zeng M, Song E, He Y, Yin Y, Li J, Li M. CK1α suppresses lung tumour growth by stabilizing PTEN and inducing autophagy. Nat Cell Biol 2018; 20:465-478. [PMID: 29593330 DOI: 10.1038/s41556-018-0065-8] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/14/2018] [Indexed: 12/19/2022]
Abstract
The contribution of autophagy to cancer development remains controversial, largely owing to the fact that autophagy can be tumour suppressive or oncogenic in different biological contexts. Here, we show that in non-small-cell lung cancer (NSCLC), casein kinase 1 alpha 1 (CK1α) suppresses tumour growth by functioning as an autophagy inducer to activate an autophagy-regulating, tumour-suppressive PTEN/AKT/FOXO3a/Atg7 axis. Specifically, CK1α bound the C-terminal tail of PTEN and enhanced both PTEN stability and activity by competitively antagonizing NEDD4-1-induced PTEN polyubiquitination and abrogating PTEN phosphorylation, thereby inhibiting AKT activity and activating FOXO3a-induced transcription of Atg7. Notably, blocking CK1α-induced Atg7-dependent autophagy cooperates with oncogenic HRasV12 to initiate tumorigenesis of lung epithelial cells. An association of a CK1α-modulated autophagic program with the anti-neoplastic activities of the CK1α/PTEN/FOXO3a/Atg7 axis was demonstrated in xenografted tumour models and human NSCLC specimens. This provides insights into the biological and potentially clinical significance of autophagy in NSCLC.
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MESH Headings
- A549 Cells
- Animals
- Autophagy
- Autophagy-Related Protein 7/genetics
- Autophagy-Related Protein 7/metabolism
- Carcinoma, Non-Small-Cell Lung/enzymology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Casein Kinase Ialpha/genetics
- Casein Kinase Ialpha/metabolism
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Enzyme Stability
- Female
- Forkhead Box Protein O3/genetics
- Forkhead Box Protein O3/metabolism
- Gene Expression Regulation, Neoplastic
- Genes, ras
- HCT116 Cells
- HEK293 Cells
- Humans
- Lung Neoplasms/enzymology
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Mice, Inbred BALB C
- Mice, Nude
- Nedd4 Ubiquitin Protein Ligases/metabolism
- PTEN Phosphohydrolase/genetics
- PTEN Phosphohydrolase/metabolism
- Phosphorylation
- Protein Binding
- Protein Interaction Domains and Motifs
- Proto-Oncogene Proteins c-akt/metabolism
- Signal Transduction
- Time Factors
- Tumor Burden
- Ubiquitination
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Affiliation(s)
- Junchao Cai
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou, China
| | - Rong Li
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaonan Xu
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Sun Yat-sen University, Guangzhou, China
| | - Le Zhang
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Rong Lian
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Lishan Fang
- The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Yongbo Huang
- State Key Laboratory of Respiratory Diseases and Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xianming Feng
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Ximeng Liu
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Xu Li
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Xun Zhu
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Heng Zhang
- Neurosurgery Intensive Care Unit, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jueheng Wu
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Musheng Zeng
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Erwei Song
- Department of Breast Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yukai He
- Department of Medicine and Department of Biochemistry and Molecular Biology, Georgia Cancer Center, Augusta University, Augusta, GA, USA
| | - Yuxin Yin
- Department of Pathology, Institute of Systems Biomedicine, School of Basic Medicine, Peking University Health Science Center, Beijing, China
| | - Jun Li
- Department of Biochemistry, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou, China
| | - Mengfeng Li
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou, China.
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China.
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22
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Liu C, Deb S, Ferreira VS, Xu E, Baumgart T. Kinetics of PTEN-mediated PI(3,4,5)P3 hydrolysis on solid supported membranes. PLoS One 2018; 13:e0192667. [PMID: 29447222 PMCID: PMC5813967 DOI: 10.1371/journal.pone.0192667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/26/2018] [Indexed: 11/18/2022] Open
Abstract
Phosphatidylinositides play important roles in cellular signaling and migration. Phosphatidylinositol-3,4,5-trisphosphate (PI(3,4,5)P3) is an important phosphatidylinositide because it acts as a secondary messenger to trigger cell movement and proliferation. A high level of PI(3,4,5)P3 at the plasma membrane is known to contribute to tumorigenesis. One key enzyme that regulates PI(3,4,5)P3 levels at the plasma membrane is phosphatase and tensin homologue deleted on chromosome 10 (PTEN), which dephosphorylates PI(3,4,5)P3 through hydrolysis to form phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2). It has been reported that PI(4,5)P2 is involved in positive feedback in the PI(3,4,5)P3 hydrolysis by PTEN. However, how PI(3,4,5)P3 dephosphorylation by PTEN is regulated, is still under debate. How other PI(3,4,5)P3-binding proteins affect the dephosphorylation kinetics catalyzed by PTEN also remains unclear. Here, we develop a fluorescent-protein biosensor approach to study how PI(3,4,5)P3 dephosphorylation is regulated by PTEN as well as its membrane-mediated feedback mechanisms. Our observation of sigmoidal kinetics of the PI(3,4,5)P3 hydrolysis reaction supports the notion of autocatalysis in PTEN function. We developed a kinetic model to describe the observed reaction kinetics, which allowed us to i) distinguish between membrane-recruitment and allosteric activation of PTEN by PI(4,5)P2, ii) account for the influence of the biosensor on the observed reaction kinetics, and iii) demonstrate that all of these mechanisms contribute to the kinetics of PTEN-mediated catalysis.
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Affiliation(s)
- Chun Liu
- Department of Chemistry, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sanghamitra Deb
- Department of Chemistry, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Vinicius S Ferreira
- Department of Chemistry, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Eric Xu
- Department of Chemistry, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tobias Baumgart
- Department of Chemistry, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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23
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Tietjen GT, Baylon JL, Kerr D, Gong Z, Henderson JM, Heffern CTR, Meron M, Lin B, Schlossman ML, Adams EJ, Tajkhorshid E, Lee KYC. Coupling X-Ray Reflectivity and In Silico Binding to Yield Dynamics of Membrane Recognition by Tim1. Biophys J 2017; 113:1505-1519. [PMID: 28978444 DOI: 10.1016/j.bpj.2017.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 07/28/2017] [Accepted: 08/02/2017] [Indexed: 12/16/2022] Open
Abstract
The dynamic nature of lipid membranes presents significant challenges with respect to understanding the molecular basis of protein/membrane interactions. Consequently, there is relatively little known about the structural mechanisms by which membrane-binding proteins might distinguish subtle variations in lipid membrane composition and/or structure. We have previously developed a multidisciplinary approach that combines molecular dynamics simulation with interfacial x-ray scattering experiments to produce an atomistic model for phosphatidylserine recognition by the immune receptor Tim4. However, this approach requires a previously determined protein crystal structure in a membrane-bound conformation. Tim1, a Tim4 homolog with distinct differences in both immunological function and sensitivity to membrane composition, was crystalized in a closed-loop conformation that is unlikely to support membrane binding. Here we have used a previously described highly mobile membrane mimetic membrane in combination with a conventional lipid bilayer model to generate a membrane-bound configuration of Tim1 in silico. This refined structure provided a significantly improved fit of experimental x-ray reflectivity data. Moreover, the coupling of the x-ray reflectivity analysis with both highly mobile membrane mimetic membranes and conventional lipid bilayer molecular dynamics simulations yielded a dynamic model of phosphatidylserine membrane recognition by Tim1 with atomic-level detail. In addition to providing, to our knowledge, new insights into the molecular mechanisms that distinguish the various Tim receptors, these results demonstrate that in silico membrane-binding simulations can remove the requirement that the existing crystal structure be in the membrane-bound conformation for effective x-ray reflectivity analysis. Consequently, this refined methodology has the potential for much broader applicability with respect to defining the atomistic details of membrane-binding proteins.
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Affiliation(s)
- Gregory T Tietjen
- Program in Biophysical Sciences, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Javier L Baylon
- Center for Biophysics and Quantitative Biology and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois
| | - Daniel Kerr
- Program in Biophysical Sciences, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Zhiliang Gong
- Department of Chemistry, The University of Chicago, Chicago, Illinois
| | | | | | - Mati Meron
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois
| | - Binhua Lin
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois; James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Mark L Schlossman
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois
| | - Erin J Adams
- Program in Biophysical Sciences, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois; Department of Biochemistry and Molecular Biology and Committee on Immunology, The University of Chicago, Chicago, Illinois
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois; College of Medicine and Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois.
| | - Ka Yee C Lee
- Program in Biophysical Sciences, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois; Department of Chemistry, The University of Chicago, Chicago, Illinois; James Franck Institute, The University of Chicago, Chicago, Illinois.
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24
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Hoogerheide DP, Noskov SY, Jacobs D, Bergdoll L, Silin V, Worcester DL, Abramson J, Nanda H, Rostovtseva TK, Bezrukov SM. Structural features and lipid binding domain of tubulin on biomimetic mitochondrial membranes. Proc Natl Acad Sci U S A 2017; 114:E3622-E3631. [PMID: 28420794 PMCID: PMC5422764 DOI: 10.1073/pnas.1619806114] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Dimeric tubulin, an abundant water-soluble cytosolic protein known primarily for its role in the cytoskeleton, is routinely found to be associated with mitochondrial outer membranes, although the structure and physiological role of mitochondria-bound tubulin are still unknown. There is also no consensus on whether tubulin is a peripheral membrane protein or is integrated into the outer mitochondrial membrane. Here the results of five independent techniques-surface plasmon resonance, electrochemical impedance spectroscopy, bilayer overtone analysis, neutron reflectometry, and molecular dynamics simulations-suggest that α-tubulin's amphipathic helix H10 is responsible for peripheral binding of dimeric tubulin to biomimetic "mitochondrial" membranes in a manner that differentiates between the two primary lipid headgroups found in mitochondrial membranes, phosphatidylethanolamine and phosphatidylcholine. The identification of the tubulin dimer orientation and membrane-binding domain represents an essential step toward our understanding of the complex mechanisms by which tubulin interacts with integral proteins of the mitochondrial outer membrane and is important for the structure-inspired design of tubulin-targeting agents.
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Affiliation(s)
- David P Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899;
| | - Sergei Y Noskov
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4;
| | - Daniel Jacobs
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Lucie Bergdoll
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Vitalii Silin
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - David L Worcester
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Jeff Abramson
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Institute for Stem Cell Biology and Regenerative Medicine, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, Karnataka, India
| | - Hirsh Nanda
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Tatiana K Rostovtseva
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Sergey M Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892;
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25
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Narayanan T, Wacklin H, Konovalov O, Lund R. Recent applications of synchrotron radiation and neutrons in the study of soft matter. CRYSTALLOGR REV 2017. [DOI: 10.1080/0889311x.2016.1277212] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | - Hanna Wacklin
- European Spallation Source ERIC, Lund, Sweden
- Physical Chemistry, Lund University, Lund, Sweden
| | | | - Reidar Lund
- Department of Chemistry, University of Oslo, Blindern, Oslo, Norway
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26
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Biological Structures. NEUTRON SCATTERING - APPLICATIONS IN BIOLOGY, CHEMISTRY, AND MATERIALS SCIENCE 2017. [DOI: 10.1016/b978-0-12-805324-9.00001-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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27
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Membrane Binding of HIV-1 Matrix Protein: Dependence on Bilayer Composition and Protein Lipidation. J Virol 2016; 90:4544-4555. [PMID: 26912608 DOI: 10.1128/jvi.02820-15] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/15/2016] [Indexed: 01/10/2023] Open
Abstract
UNLABELLED By assembling in a protein lattice on the host's plasma membrane, the retroviral Gag polyprotein triggers formation of the viral protein/membrane shell. The MA domain of Gag employs multiple signals--electrostatic, hydrophobic, and lipid-specific-to bring the protein to the plasma membrane, thereby complementing protein-protein interactions, located in full-length Gag, in lattice formation. We report the interaction of myristoylated and unmyristoylated HIV-1 Gag MA domains with bilayers composed of purified lipid components to dissect these complex membrane signals and quantify their contributions to the overall interaction. Surface plasmon resonance on well-defined planar membrane models is used to quantify binding affinities and amounts of protein and yields free binding energy contributions, ΔG, of the various signals. Charge-charge interactions in the absence of the phosphatidylinositide PI(4,5)P2 attract the protein to acidic membrane surfaces, and myristoylation increases the affinity by a factor of 10; thus, our data do not provide evidence for a PI(4,5)P2 trigger of myristate exposure. Lipid-specific interactions with PI(4,5)P2, the major signal lipid in the inner plasma membrane, increase membrane attraction at a level similar to that of protein lipidation. While cholesterol does not directly engage in interactions, it augments protein affinity strongly by facilitating efficient myristate insertion and PI(4,5)P2 binding. We thus observe that the isolated MA protein, in the absence of protein-protein interaction conferred by the full-length Gag, binds the membrane with submicromolar affinities. IMPORTANCE Like other retroviral species, the Gag polyprotein of HIV-1 contains three major domains: the N-terminal, myristoylated MA domain that targets the protein to the plasma membrane of the host; a central capsid-forming domain; and the C-terminal, genome-binding nucleocapsid domain. These domains act in concert to condense Gag into a membrane-bounded protein lattice that recruits genomic RNA into the virus and forms the shell of a budding immature viral capsid. In binding studies of HIV-1 Gag MA to model membranes with well-controlled lipid composition, we dissect the multiple interactions of the MA domain with its target membrane. This results in a detailed understanding of the thermodynamic aspects that determine membrane association, preferential lipid recruitment to the viral shell, and those aspects of Gag assembly into the membrane-bound protein lattice that are determined by MA.
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28
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Shen Y, Barros M, Vennemann T, Gallagher DT, Yin Y, Linden SB, Heselpoth RD, Spencer DJ, Donovan DM, Moult J, Fischetti VA, Heinrich F, Lösche M, Nelson DC. A bacteriophage endolysin that eliminates intracellular streptococci. eLife 2016; 5. [PMID: 26978792 PMCID: PMC4848087 DOI: 10.7554/elife.13152] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/14/2016] [Indexed: 12/25/2022] Open
Abstract
PlyC, a bacteriophage-encoded endolysin, lyses Streptococcus pyogenes (Spy) on contact. Here, we demonstrate that PlyC is a potent agent for controlling intracellular Spy that often underlies refractory infections. We show that the PlyC holoenzyme, mediated by its PlyCB subunit, crosses epithelial cell membranes and clears intracellular Spy in a dose-dependent manner. Quantitative studies using model membranes establish that PlyCB interacts strongly with phosphatidylserine (PS), whereas its interaction with other lipids is weak, suggesting specificity for PS as its cellular receptor. Neutron reflection further substantiates that PlyC penetrates bilayers above a PS threshold concentration. Crystallography and docking studies identify key residues that mediate PlyCB–PS interactions, which are validated by site-directed mutagenesis. This is the first report that a native endolysin can traverse epithelial membranes, thus substantiating the potential of PlyC as an antimicrobial for Spy in the extracellular and intracellular milieu and as a scaffold for engineering other functionalities. DOI:http://dx.doi.org/10.7554/eLife.13152.001 Streptococcus pyogenes is the bacterium that causes throat infections and other serious infections in humans. Antibiotics such as penicillin are used to treat active infections, but so-called “strep throat infections” often return after treatment. This is because S. pyogenes can enter the cells that line the throat and hide from the antibiotics, which cannot enter the throat cells. Endolysins are enzymes produced by viruses that attack bacteria, and these enzymes target and destroy the bacterial cell wall. A previous study revealed that an endolysin known as PlyC could destroy S. pyogenes bacteria on contact. PlyC and other endolysins have the potential to act as alternatives to common antibiotics, but before these enzymes can be developed as therapeutics, it is important to understand how they interact with human host cells. Like antibiotics, the PlyC endolysin was not expected to enter throat cells. However, Shen, Barros et al. have now discovered that not only can PlyC enter throat cells, it can essentially chase down and kill S. pyogenes that are hiding inside. Other similar enzymes could not act in this way, and further studies confirmed that PlyC could move around inside a throat cell without causing it damage. Shen, Barros et al. also determined that PlyC has a pocket on its surface that binds with a specific component of the throat cell membrane, a molecule called phosphatidylserine. This interaction – which is a bit like a lock and key – grants PlyC access into the cell. While it is clear that PlyC eventually kills S. pyogenes hiding inside throat cells, future experiments will aim to determine how PlyC moves around once inside an infected throat cell. Together, an understanding of how an endolysin enters cells and destroys hiding S. pyogenes will contribute to the development of endolysins with broader activity, which can be used as alternatives to common antibiotics. DOI:http://dx.doi.org/10.7554/eLife.13152.002
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Affiliation(s)
- Yang Shen
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States
| | - Marilia Barros
- Department of Physics, Carnegie Mellon University, Pittsburgh, United States
| | - Tarek Vennemann
- Department of Physics, Carnegie Mellon University, Pittsburgh, United States
| | - D Travis Gallagher
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States.,National Institute of Standards and Technology, Gaithersburg, United States
| | - Yizhou Yin
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States
| | - Sara B Linden
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States
| | - Ryan D Heselpoth
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States
| | - Dennis J Spencer
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, United States
| | - David M Donovan
- Animal Biosciences and Biotechnology Lab, Agricultural Research Service, USDA, Beltsville, United States
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Rockville, United States
| | - Vincent A Fischetti
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, United States
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, United States.,Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, United States
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, United States.,Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, United States.,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, United States
| | - Daniel C Nelson
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States.,Department of Veterinary Medicine, University of Maryland, College Park, College Park, United States
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29
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Slochower DR, Wang YH, Radhakrishnan R, Janmey PA. Physical chemistry and membrane properties of two phosphatidylinositol bisphosphate isomers. Phys Chem Chem Phys 2016; 17:12608-15. [PMID: 25901568 DOI: 10.1039/c5cp00862j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The most highly charged phospholipids, polyphosphoinositides, are often involved in signaling pathways that originate at cell-cell and cell-matrix contacts, and different isomers of polyphosphoinositides have distinct biological functions that cannot be explained by separate highly specific protein ligand binding sites [Lemmon, Nat. Rev. Mol. Cell Biol., 2008, 9, 99-111]. PtdIns(3,5)P2 is a low abundance phosphoinositide localized to cytoplasmic-facing membrane surfaces, with relatively few known ligands, yet PtdIns(3,5)P2 plays a key role in controlling membrane trafficking events and cellular stress responses that cannot be duplicated by other phosphoinositides [Dove et al., Nature, 1997, 390, 187-192; Michell, FEBS J., 2013, 280, 6281-6294]. Here we show that PtdIns(3,5)P2 is structurally distinct from PtdIns(4,5)P2 and other more common phospholipids, with unique physical chemistry. Using multiscale molecular dynamics techniques on the quantum level, single molecule, and in bilayer settings, we found that the negative charge of PtdIns(3,5)P2 is spread over a larger area, compared to PtdIns(4,5)P2, leading to a decreased ability to bind divalent ions. Additionally, our results match well with experimental data characterizing the cluster forming potential of these isomers in the presence of Ca(2+) [Wang et al., J. Am. Chem. Soc., 2012, 134, 3387-3395; van den Bogaart et al., Nature, 2011, 479, 552-555]. Our results demonstrate that the different cellular roles of PtdIns(4,5)P2 and PtdIns(3,5)P2in vivo are not simply determined by their localization by enzymes that produce or degrade them, but also by their molecular size, ability to chelate ions, and the partial dehydration of those ions, which might affect the ability of PtdIns(3,5)P2 and PtdIns(4,5)P2 to form phosphoinositide-rich clusters in vitro and in vivo.
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Affiliation(s)
- David R Slochower
- Institute for Medicine and Engineering, University of Pennsylvania, 1080 Vagelos Laboratories, 3340 Smith Walk, Philadelphia, PA, USA.
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Masson GR, Burke JE, Williams RL. Methods in the Study of PTEN Structure: X-Ray Crystallography and Hydrogen Deuterium Exchange Mass Spectrometry. Methods Mol Biol 2016; 1388:215-30. [PMID: 27033079 DOI: 10.1007/978-1-4939-3299-3_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Despite its small size and deceptively simple domain organization, PTEN remains a challenging structural target due to its N- and C-terminal intrinsically disordered segments, and the conformational heterogeneity caused by phosphorylation of its C terminus. Using hydrogen/deuterium exchange mass spectrometry (HDX-MS), it is possible to probe the conformational dynamics of the disordered termini, and also to determine how PTEN binds to lipid membranes. Here, we describe how to purify recombinant, homogenously dephosphorylated PTEN from a eukaryotic system for subsequent investigation with HDX-MS or crystallography.
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Affiliation(s)
- Glenn R Masson
- Laboratory of Molecular Biology, Medical Research Council (MRC), Francis Crick Avenue, Cambridge Biomedical campus, Cambridge, CB2 0QH, UK
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Drive, Victoria, BC, Canada, V8P 5C2
| | - Roger L Williams
- Laboratory of Molecular Biology, Medical Research Council (MRC), Francis Crick Avenue, Cambridge Biomedical campus, Cambridge, CB2 0QH, UK.
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31
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Abstract
PTEN subcellular localization is fundamental in the execution of the distinct PTEN biological activities, including not only its PI(3,4,5)P3 phosphatase activity when associated to membranes but also its subcellular compartment-specific interactions with regulatory and effector proteins, including those exerted in the nucleus. As a consequence, PTEN subcellular localization is tightly regulated in vivo by both intrinsic and extrinsic mechanisms. The plasma membrane/nucleus/cytoplasm partitioning of PTEN has been the focus of several studies, both from a mechanistic and from a disease-association point of view. Here, we summarize the current knowledge on PTEN plasma membrane/nucleus/cytoplasm distribution, and present subcellular fractionation, immunofluorescence, and immunohistochemical methods to study the distribution and shuttling of PTEN between these subcellular compartments.
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Affiliation(s)
- Anabel Gil
- Centro de Investigación Príncipe Felipe, Valencia, 46013, Spain
- Department of Hematology and Medical Oncology, Biomedical Research Institute INCLIVA, Valencia, 46010, Spain
| | - José I López
- Department of Pathology, Cruces University Hospital, University of the Basque Country (UPV/EHU), Barakaldo, 48903, Spain
- Biocruces Health Research Institute, Plaza de Cruces s/n, Barakaldo, Bizkaia, 48903, Spain
| | - Rafael Pulido
- Centro de Investigación Príncipe Felipe, Valencia, 46013, Spain.
- Biocruces Health Research Institute, Plaza de Cruces s/n, Barakaldo, Bizkaia, 48903, Spain.
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48013, Spain.
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Membrane Binding of the Rous Sarcoma Virus Gag Protein Is Cooperative and Dependent on the Spacer Peptide Assembly Domain. J Virol 2015; 90:2473-85. [PMID: 26676779 DOI: 10.1128/jvi.02733-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 12/09/2015] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED The principles underlying membrane binding and assembly of retroviral Gag proteins into a lattice are understood. However, little is known about how these processes are related. Using purified Rous sarcoma virus Gag and Gag truncations, we studied the interrelation of Gag-Gag interaction and Gag-membrane interaction. Both by liposome binding and by surface plasmon resonance on a supported bilayer, Gag bound to membranes much more tightly than did matrix (MA), the isolated membrane binding domain. In principle, this difference could be explained either by protein-protein interactions leading to cooperativity in membrane binding or by the simultaneous interaction of the N-terminal MA and the C-terminal nucleocapsid (NC) of Gag with the bilayer, since both are highly basic. However, we found that NC was not required for strong membrane binding. Instead, the spacer peptide assembly domain (SPA), a putative 24-residue helical sequence comprising the 12-residue SP segment of Gag and overlapping the capsid (CA) C terminus and the NC N terminus, was required. SPA is known to be critical for proper assembly of the immature Gag lattice. A single amino acid mutation in SPA that abrogates assembly in vitro dramatically reduced binding of Gag to liposomes. In vivo, plasma membrane localization was dependent on SPA. Disulfide cross-linking based on ectopic Cys residues showed that the contacts between Gag proteins on the membrane are similar to the known contacts in virus-like particles. Taken together, we interpret these results to mean that Gag membrane interaction is cooperative in that it depends on the ability of Gag to multimerize. IMPORTANCE The retroviral structural protein Gag has three major domains. The N-terminal MA domain interacts directly with the plasma membrane (PM) of cells. The central CA domain, together with immediately adjoining sequences, facilitates the assembly of thousands of Gag molecules into a lattice. The C-terminal NC domain interacts with the genome, resulting in packaging of viral RNA. For assembly in vitro with purified Gag, in the absence of membranes, binding of NC to nucleic acid somehow facilitates further Gag-Gag interactions that lead to formation of the Gag lattice. The contributions of MA-mediated membrane binding to virus particle assembly are not well understood. Here, we report that in the absence of nucleic acid, membranes provide a platform that facilitates Gag-Gag interactions. This study demonstrates that the binding of Gag, but not of MA, to membranes is cooperative and identifies SPA as a major factor that controls this cooperativity.
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Heinrich F, Chakravarthy S, Nanda H, Papa A, Pandolfi PP, Ross AH, Harishchandra RK, Gericke A, Lösche M. The PTEN Tumor Suppressor Forms Homodimers in Solution. Structure 2015; 23:1952-1957. [PMID: 26299948 DOI: 10.1016/j.str.2015.07.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/20/2015] [Accepted: 07/25/2015] [Indexed: 12/01/2022]
Abstract
As the phosphoinositol-3-kinase antagonist in the PI3K pathway, the PTEN tumor suppressor exerts phosphatase activity on diacylphosphatidylinositol triphosphate in the plasma membrane. Even partial loss of this activity enhances tumorigenesis, but a mechanistic basis for this aspect of PTEN physiology has not yet been established. It was recently proposed that PTEN mutations have dominant-negative effects in cancer via PTEN dimers. We show that PTEN forms homodimers in vitro, and determine a structural model of the complex from SAXS and Rosetta docking studies. Our findings shed new light on the cellular control mechanism of PTEN activity. Phosphorylation of the unstructured C-terminal tail of PTEN reduces PTEN activity, and this result was interpreted as a blockage of the PTEN membrane binding interface through this tail. The results presented here instead suggest that the C-terminal tail functions in stabilizing the homodimer, and that tail phosphorylation interferes with this stabilization.
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Affiliation(s)
- Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Srinivas Chakravarthy
- BioCAT, Center for Synchrotron Radiation Research and Instrumentation, Argonne National Laboratory, Argonne, IL 60439, USA; Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Hirsh Nanda
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Antonella Papa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC 3800, Australia; Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Alonzo H Ross
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Rakesh K Harishchandra
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Arne Gericke
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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Nguyen HN, Yang JM, Miyamoto T, Itoh K, Rho E, Zhang Q, Inoue T, Devreotes PN, Sesaki H, Iijima M. Opening the conformation is a master switch for the dual localization and phosphatase activity of PTEN. Sci Rep 2015. [PMID: 26216063 PMCID: PMC4517176 DOI: 10.1038/srep12600] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Tumor suppressor PTEN mainly functions at two subcellular locations, the plasma membrane and the nucleus. At the plasma membrane, PTEN dephosphorylates the tumorigenic second messenger PIP3, which drives cell proliferation and migration. In the nucleus, PTEN controls DNA repair and genome stability independently of PIP3. Whereas the concept that a conformational change regulates protein function through post-translational modifications has been well established in biology, it is unknown whether a conformational change simultaneously controls dual subcellular localizations of proteins. Here, we discovered that opening the conformation of PTEN is the crucial upstream event that determines its key dual localizations of this crucial tumor suppressor. We identify a critical conformational switch that regulates PTEN's localization. Most PTEN molecules are held in the cytosol in a closed conformation by intramolecular interactions between the C-terminal tail and core region. Dephosphorylation of the tail opens the conformation and exposes the membrane-binding regulatory interface in the core region, recruiting PTEN to the membrane. Moreover, a lysine at residue 13 is also exposed and when ubiquitinated, transports PTEN to the nucleus. Thus, opening the conformation of PTEN is a key mechanism that enhances its dual localization and enzymatic activity, providing a potential therapeutic strategy in cancer treatments.
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Affiliation(s)
- Hoai-Nghia Nguyen
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jr-Ming Yang
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Takafumi Miyamoto
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Kie Itoh
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Elmer Rho
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Qiang Zhang
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Takanari Inoue
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Peter N Devreotes
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Hiromi Sesaki
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Miho Iijima
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD
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Harishchandra RK, Neumann BM, Gericke A, Ross AH. Biophysical methods for the characterization of PTEN/lipid bilayer interactions. Methods 2015; 77-78:125-35. [PMID: 25697761 PMCID: PMC4388815 DOI: 10.1016/j.ymeth.2015.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 12/22/2022] Open
Abstract
PTEN, a tumor suppressor protein that dephosphorylates phosphoinositides at the 3-position of the inositol ring, is a cytosolic protein that needs to associate with the plasma membrane or other subcellular membranes to exert its lipid phosphatase function. Upon membrane association PTEN interacts with at least three different lipid entities: An anionic lipid that is present in sufficiently high concentration to create a negative potential that allows PTEN to interact electrostatically with the membrane, phosphatidylinositol-4,5-bisphosphate, which interacts with PTEN's N-terminal end and the substrate, usually phosphatidylinositol-3,4,5-trisphosphate. Many parameters influence PTEN's interaction with the lipid bilayer, for example, the lateral organization of the lipids or the presence of other chemical species like cholesterol or other lipids. To investigate systematically the different steps of PTEN's complex binding mechanism and to explore its dynamic behavior in the membrane bound state, in vitro methods need to be employed that allow for a systematic variation of the experimental conditions. In this review we survey a variety of methods that can be used to assess PTEN lipid binding affinity, the dynamics of its membrane association as well as its dynamic behavior in the membrane bound state.
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Affiliation(s)
- Rakesh K Harishchandra
- Worcester Polytechnic Institute, Department of Chemistry and Biochemistry, Worcester, MA 01605, USA
| | - Brittany M Neumann
- Worcester Polytechnic Institute, Department of Chemistry and Biochemistry, Worcester, MA 01605, USA
| | - Arne Gericke
- Worcester Polytechnic Institute, Department of Chemistry and Biochemistry, Worcester, MA 01605, USA
| | - Alonzo H Ross
- University of Massachusetts Medical School, Department of Biochemistry and Molecular Pharmacology, Worcester, MA 01605, USA.
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Castle PM, Zolman KD, Kohout SC. Voltage-sensing phosphatase modulation by a C2 domain. Front Pharmacol 2015; 6:63. [PMID: 25904865 PMCID: PMC4389355 DOI: 10.3389/fphar.2015.00063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/10/2015] [Indexed: 11/13/2022] Open
Abstract
The voltage-sensing phosphatase (VSP) is the first example of an enzyme controlled by changes in membrane potential. VSP has four distinct regions: the transmembrane voltage-sensing domain (VSD), the inter-domain linker, the cytosolic catalytic domain, and the C2 domain. The VSD transmits the changes in membrane potential through the inter-domain linker activating the catalytic domain which then dephosphorylates phosphatidylinositol phosphate (PIP) lipids. The role of the C2, however, has not been established. In this study, we explore two possible roles for the C2: catalysis and membrane-binding. The Ci-VSP crystal structures show that the C2 residue Y522 lines the active site suggesting a contribution to catalysis. When we mutated Y522 to phenylalanine, we found a shift in the voltage dependence of activity. This suggests hydrogen bonding as a mechanism of action. Going one step further, when we deleted the entire C2 domain, we found voltage-dependent enzyme activity was no longer detectable. This result clearly indicates the entire C2 is necessary for catalysis as well as for modulating activity. As C2s are known membrane-binding domains, we tested whether the VSP C2 interacts with the membrane. We probed a cluster of four positively charged residues lining the top of the C2 and suggested by previous studies to interact with phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] (Kalli et al., 2014). Neutralizing those positive charges significantly shifted the voltage dependence of activity to higher voltages. We tested membrane binding by depleting PI(4,5)P2 from the membrane using the 5HT2C receptor and found that the VSD motions as measured by voltage clamp fluorometry (VCF) were not changed. These results suggest that if the C2 domain interacts with the membrane to influence VSP function it may not occur exclusively through PI(4,5)P2. Together, this data advances our understanding of the VSP C2 by demonstrating a necessary and critical role for the C2 domain in VSP function.
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Affiliation(s)
- Paul M Castle
- Department of Cell Biology and Neuroscience, Montana State University Bozeman, MT, USA
| | - Kevin D Zolman
- Department of Cell Biology and Neuroscience, Montana State University Bozeman, MT, USA
| | - Susy C Kohout
- Department of Cell Biology and Neuroscience, Montana State University Bozeman, MT, USA
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38
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Kalinowski A, Yaron PN, Qin Z, Shenoy S, Buehler MJ, Lösche M, Dahl KN. Interfacial binding and aggregation of lamin A tail domains associated with Hutchinson-Gilford progeria syndrome. Biophys Chem 2014; 195:43-8. [PMID: 25194277 PMCID: PMC4212650 DOI: 10.1016/j.bpc.2014.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 07/28/2014] [Accepted: 08/03/2014] [Indexed: 12/16/2022]
Abstract
Hutchinson-Gilford progeria syndrome is a premature aging disorder associated with the expression of ∆50 lamin A (∆50LA), a mutant form of the nuclear structural protein lamin A (LA). ∆50LA is missing 50 amino acids from the tail domain and retains a C-terminal farnesyl group that is cleaved from the wild-type LA. Many of the cellular pathologies of HGPS are thought to be a consequence of protein-membrane association mediated by the retained farnesyl group. To better characterize the protein-membrane interface, we quantified binding of purified recombinant ∆50LA tail domain (∆50LA-TD) to tethered bilayer membranes composed of phosphatidylserine and phosphocholine using surface plasmon resonance. Farnesylated ∆50LA-TD binds to the membrane interface only in the presence of Ca(2+) or Mg(2+) at physiological ionic strength. At extremely low ionic strength, both the farnesylated and non-farnesylated forms of ∆50LA-TD bind to the membrane surface in amounts that exceed those expected for a densely packed protein monolayer. Interestingly, the wild-type LA-TD with no farnesylation also associates with membranes at low ionic strength but forms only a single layer. We suggest that electrostatic interactions are mediated by charge clusters with a net positive charge that we calculate on the surface of the LA-TDs. These studies suggest that the accumulation of ∆50LA at the inner nuclear membrane observed in cells is due to a combination of aggregation and membrane association rather than simple membrane binding; electrostatics plays an important role in mediating this association.
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Affiliation(s)
- Agnieszka Kalinowski
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA 15213, United States
| | - Peter N Yaron
- Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA 15213, United States
| | - Zhao Qin
- Department of Civil and Environmental Engineering, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Siddharth Shenoy
- Department of Physics, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA 15213, United States
| | - Markus J Buehler
- Department of Civil and Environmental Engineering, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Mathias Lösche
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA 15213, United States; Department of Civil and Environmental Engineering, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
| | - Kris Noel Dahl
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA 15213, United States; Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA 15213, United States.
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39
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Yap TL, Jiang Z, Heinrich F, Gruschus JM, Pfefferkorn CM, Barros M, Curtis JE, Sidransky E, Lee JC. Structural features of membrane-bound glucocerebrosidase and α-synuclein probed by neutron reflectometry and fluorescence spectroscopy. J Biol Chem 2014; 290:744-54. [PMID: 25429104 DOI: 10.1074/jbc.m114.610584] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutations in glucocerebrosidase (GCase), the enzyme deficient in Gaucher disease, are a common genetic risk factor for the development of Parkinson disease and related disorders, implicating the role of this lysosomal hydrolase in the disease etiology. A specific physical interaction exists between the Parkinson disease-related protein α-synuclein (α-syn) and GCase both in solution and on the lipid membrane, resulting in efficient enzyme inhibition. Here, neutron reflectometry was employed as a first direct structural characterization of GCase and α-syn·GCase complex on a sparsely-tethered lipid bilayer, revealing the orientation of the membrane-bound GCase. GCase binds to and partially inserts into the bilayer with its active site most likely lying just above the membrane-water interface. The interaction was further characterized by intrinsic Trp fluorescence, circular dichroism, and surface plasmon resonance spectroscopy. Both Trp fluorescence and neutron reflectometry results suggest a rearrangement of loops surrounding the catalytic site, where they extend into the hydrocarbon chain region of the outer leaflet. Taking advantage of contrasting neutron scattering length densities, the use of deuterated α-syn versus protiated GCase showed a large change in the membrane-bound structure of α-syn in the complex. We propose a model of α-syn·GCase on the membrane, providing structural insights into inhibition of GCase by α-syn. The interaction displaces GCase away from the membrane, possibly impeding substrate access and perturbing the active site. GCase greatly alters membrane-bound α-syn, moving helical residues away from the bilayer, which could impact the degradation of α-syn in the lysosome where these two proteins interact.
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Affiliation(s)
| | - Zhiping Jiang
- From the Laboratory of Molecular Biophysics, NHLBI, and
| | - Frank Heinrich
- the Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, and the Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899
| | | | | | - Marilia Barros
- the Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, and
| | - Joseph E Curtis
- the Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899
| | - Ellen Sidransky
- the Medical Genetics Branch, NHGRI, National Institutes of Health, Bethesda, Maryland 20892
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40
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Kim S, Rahman MM, Noh K, Lee JJ, Kim YJ. Investigating the Regulatory Interaction of Linker Region of Ciona intestinalis Voltage-sensitive Phosphatase with Lipid Membrane. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.11.3389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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41
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Nanda H, Heinrich F, Lösche M. Membrane association of the PTEN tumor suppressor: neutron scattering and MD simulations reveal the structure of protein-membrane complexes. Methods 2014; 77-78:136-46. [PMID: 25461777 DOI: 10.1016/j.ymeth.2014.10.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/10/2014] [Accepted: 10/14/2014] [Indexed: 12/31/2022] Open
Abstract
Neutron reflection (NR) from planar interfaces is an emerging technology that provides unique and otherwise inaccessible structural information on disordered molecular systems such as membrane proteins associated with fluid bilayers, thus addressing one of the remaining challenges of structural biology. Although intrinsically a low-resolution technique, using structural information from crystallography or NMR allows the construction of NR models that describe the architecture of protein-membrane complexes at high resolution. In addition, a combination of these methods with molecular dynamics (MD) simulations has the potential to reveal the dynamics of protein interactions with the bilayer in atomistic detail. We review recent advances in this area by discussing the application of these techniques to the complex formed by the PTEN phosphatase with the plasma membrane. These studies provide insights in the cellular regulation of PTEN, its interaction with PI(4,5)P2 in the inner plasma membrane and the pathway by which its substrate, PI(3,4,5)P3, accesses the PTEN catalytic site.
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Affiliation(s)
- Hirsh Nanda
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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42
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Benedetto A, Heinrich F, Gonzalez MA, Fragneto G, Watkins E, Ballone P. Structure and Stability of Phospholipid Bilayers Hydrated by a Room-Temperature Ionic Liquid/Water Solution: A Neutron Reflectometry Study. J Phys Chem B 2014; 118:12192-206. [DOI: 10.1021/jp507631h] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Antonio Benedetto
- School
of Physics, University College Dublin−UCD, Belfield Campus, Dublin 4, Ireland
| | - Frank Heinrich
- Department
of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Center
for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | | | | | - Erik Watkins
- Institute Laue-Langevin, Grenoble, France
- Lujan
Neutron Scattering Center, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Pietro Ballone
- Center
for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia (IIT), 00161 Roma, Italy
- Department
of Physics, Universita’ di Roma “La Sapienza”, 00185 Roma, Italy
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43
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Yasui M, Matsuoka S, Ueda M. PTEN hopping on the cell membrane is regulated via a positively-charged C2 domain. PLoS Comput Biol 2014; 10:e1003817. [PMID: 25211206 PMCID: PMC4161299 DOI: 10.1371/journal.pcbi.1003817] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 07/17/2014] [Indexed: 11/19/2022] Open
Abstract
PTEN, a tumor suppressor that is frequently mutated in a wide spectrum of cancers, exerts PI(3,4,5)P3 phosphatase activities that are regulated by its dynamic shuttling between the membrane and cytoplasm. Direct observation of PTEN in the interfacial environment can offer quantitative information about the shuttling dynamics, but remains elusive. Here we show that positively charged residues located in the cα2 helix of the C2 domain are necessary for the membrane localization of PTEN via stable electrostatic interactions in Dictyostelium discoideum. Single-molecule imaging analyses revealed that PTEN molecules moved distances much larger than expected had they been caused by lateral diffusion, a phenomenon we call “hopping.” Our novel single-particle tracking analysis method found that the cα2 helix aids in regulating the hopping and stable-binding states. The dynamically established membrane localization of PTEN was revealed to be essential for developmental processes and clarified a fundamental regulation mechanism of the protein quantity and activity on the plasma membrane. The plasma membrane is a major chemical reaction field in living cells, and the molecular mechanisms of protein-membrane interactions are important for many cellular functions. In this report, we have discovered that the PTEN protein, which transits between the cytoplasm and membrane, hops along the plasma membrane of living cells. We tracked individual PTEN molecules on the membrane by single molecule imaging and analyzed the hopping behavior by developing a novel analysis method, which measures the rebinding probability of membrane-bound proteins after detaching from the membrane. We found that positively charged amino acids in the C2 domain of PTEN, which were reported to be important for its phosphatase activity on the membrane, are required to suppress excessive hopping and stabilize PTEN membrane binding. The stable electrostatic interactions localize PTEN to the plasma membrane and play an indispensable role in regulating the size of the multicellular structures formed under a starving environment. Our results suggest electrostatic interactions between the protein and membrane regulate protein quantity and activity.
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Affiliation(s)
- Masato Yasui
- Laboratories for Nanobiology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- Laboratory for Cell Signaling Dynamics, QBiC (Quantitative Biology Center), RIKEN, Suita, Osaka, Japan
- Laboratory of Single Molecule Biology, Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Satomi Matsuoka
- Laboratory for Cell Signaling Dynamics, QBiC (Quantitative Biology Center), RIKEN, Suita, Osaka, Japan
- * E-mail:
| | - Masahiro Ueda
- Laboratories for Nanobiology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- Laboratory for Cell Signaling Dynamics, QBiC (Quantitative Biology Center), RIKEN, Suita, Osaka, Japan
- Laboratory of Single Molecule Biology, Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
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Heinrich F, Lösche M. Zooming in on disordered systems: neutron reflection studies of proteins associated with fluid membranes. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1838:2341-9. [PMID: 24674984 PMCID: PMC4082750 DOI: 10.1016/j.bbamem.2014.03.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 03/13/2014] [Accepted: 03/17/2014] [Indexed: 11/23/2022]
Abstract
Neutron reflectometry (NR) is an emerging experimental technique for the structural characterization of proteins interacting with fluid bilayer membranes under conditions that mimic closely the cellular environment. Thus, cellular processes can be emulated in artificial systems and their molecular basis studied by adding cellular components one at a time in a well-controlled environment while the resulting structures, or structural changes in response to external cues, are monitored with neutron reflection. In recent years, sample environments, data collection strategies and data analysis were continuously refined. The combination of these improvements increases the information which can be obtained from NR to an extent that enables structural characterization of protein-membrane complexes at a length scale that exceeds the resolution of the measurement by far. Ultimately, the combination of NR with molecular dynamics (MD) simulations can be used to cross-validate the results of the two techniques and provide atomic-scale structural models. This review discusses these developments in detail and demonstrates how they provide new windows into relevant biomedical problems. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.
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Affiliation(s)
- Frank Heinrich
- Physics Department, Carnegie Mellon University, Pittsburgh, PA, U.S.A.; NIST Center for Neutron Research, Gaithersburg, MD, U.S.A
| | - Mathias Lösche
- Physics Department, Carnegie Mellon University, Pittsburgh, PA, U.S.A.; NIST Center for Neutron Research, Gaithersburg, MD, U.S.A..
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Kreis P, Leondaritis G, Lieberam I, Eickholt BJ. Subcellular targeting and dynamic regulation of PTEN: implications for neuronal cells and neurological disorders. Front Mol Neurosci 2014; 7:23. [PMID: 24744697 PMCID: PMC3978343 DOI: 10.3389/fnmol.2014.00023] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/12/2014] [Indexed: 01/13/2023] Open
Abstract
PTEN is a lipid and protein phosphatase that regulates a diverse range of cellular mechanisms. PTEN is mainly present in the cytosol and transiently associates with the plasma membrane to dephosphorylate PI(3,4,5)P3, thereby antagonizing the PI3-Kinase signaling pathway. Recently, PTEN has been shown to associate also with organelles such as the endoplasmic reticulum (ER), the mitochondria, or the nucleus, and to be secreted outside of the cell. In addition, PTEN dynamically localizes to specialized sub-cellular compartments such as the neuronal growth cone or dendritic spines. The diverse localizations of PTEN imply a tight temporal and spatial regulation, orchestrated by mechanisms such as posttranslational modifications, formation of distinct protein–protein interactions, or the activation/recruitment of PTEN downstream of external cues. The regulation of PTEN function is thus not only important at the enzymatic activity level, but is also associated to its spatial distribution. In this review we will summarize (i) recent findings that highlight mechanisms controlling PTEN movement and sub-cellular localization, and (ii) current understanding of how PTEN localization is achieved by mechanisms controlling posttranslational modification, by association with binding partners and by PTEN structural or activity requirements. Finally, we will discuss the possible roles of compartmentalized PTEN in developing and mature neurons in health and disease.
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Affiliation(s)
- Patricia Kreis
- MRC Centre for Developmental Neurobiology, King's College London London, UK
| | - George Leondaritis
- MRC Centre for Developmental Neurobiology, King's College London London, UK ; Institute of Biochemistry, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Ivo Lieberam
- MRC Centre for Developmental Neurobiology, King's College London London, UK
| | - Britta J Eickholt
- MRC Centre for Developmental Neurobiology, King's College London London, UK ; Institute of Biochemistry, Charité - Universitätsmedizin Berlin Berlin, Germany
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Kalli AC, Devaney I, Sansom MSP. Interactions of phosphatase and tensin homologue (PTEN) proteins with phosphatidylinositol phosphates: insights from molecular dynamics simulations of PTEN and voltage sensitive phosphatase. Biochemistry 2014; 53:1724-32. [PMID: 24588644 PMCID: PMC4167384 DOI: 10.1021/bi5000299] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
The
phosphatase and tensin homologue (PTEN) and the Ciona
intestinalis voltage sensitive phosphatase (Ci-VSP) are both
phosphatidylinositol phosphate (PIP) phosphatases that contain a C2
domain. PTEN is a tumor suppressor protein that acts as a phosphatase
on PIP3 in mammalian cell membranes. It contains two principal
domains:
a phosphatase domain (PD) and a C2 domain. Despite detailed structural
and functional characterization, less is known about its mechanism
of interaction with PIP-containing lipid bilayers. Ci-VSP consists
of an N-terminal transmembrane voltage sensor domain and a C-terminal
PTEN domain, which in turn contains a PD and a C2 domain. The nature
of the interaction of the PTEN domain of Ci-VSP with membranes has
not been well established. We have used multiscale molecular dynamics
simulations to define the interaction mechanisms
of PTEN and of the Ci-VSP PTEN domains with PIP-containing lipid bilayers.
Our results suggest a novel mechanism of association of the PTEN with
such bilayers, in which an initial electrostatics-driven encounter
of the protein and bilayer is followed by reorientation of the protein
to optimize its interactions with PIP molecules in the membrane. Although
a PIP3 molecule binds close to the active site of PTEN,
our simulations suggest a further conformational change of the protein
may be required for catalytically productive binding to occur. Ci-VSP
interacted with membranes in an orientation comparable to that of
PTEN but bound directly to PIP-containing membranes without a subsequent
reorientation step. Again, PIP3 bound close to the active
site of the Ci-VSP PD, but not in a catalytically productive manner.
Interactions of Ci-VSP with the bilayer induced clustering of PIP
molecules around the protein.
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Affiliation(s)
- Antreas C Kalli
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
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Stahelin RV, Scott JL, Frick CT. Cellular and molecular interactions of phosphoinositides and peripheral proteins. Chem Phys Lipids 2014; 182:3-18. [PMID: 24556335 DOI: 10.1016/j.chemphyslip.2014.02.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/05/2014] [Accepted: 02/05/2014] [Indexed: 12/23/2022]
Abstract
Anionic lipids act as signals for the recruitment of proteins containing cationic clusters to biological membranes. A family of anionic lipids known as the phosphoinositides (PIPs) are low in abundance, yet play a critical role in recruitment of peripheral proteins to the membrane interface. PIPs are mono-, bis-, or trisphosphorylated derivatives of phosphatidylinositol (PI) yielding seven species with different structure and anionic charge. The differential spatial distribution and temporal appearance of PIPs is key to their role in communicating information to target proteins. Selective recognition of PIPs came into play with the discovery that the substrate of protein kinase C termed pleckstrin possessed the first PIP binding region termed the pleckstrin homology (PH) domain. Since the discovery of the PH domain, more than ten PIP binding domains have been identified including PH, ENTH, FYVE, PX, and C2 domains. Representative examples of each of these domains have been thoroughly characterized to understand how they coordinate PIP headgroups in membranes, translocate to specific membrane docking sites in the cell, and function to regulate the activity of their full-length proteins. In addition, a number of novel mechanisms of PIP-mediated membrane association have emerged, such as coincidence detection-specificity for two distinct lipid headgroups. Other PIP-binding domains may also harbor selectivity for a membrane physical property such as charge or membrane curvature. This review summarizes the current understanding of the cellular distribution of PIPs and their molecular interaction with peripheral proteins.
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Affiliation(s)
- Robert V Stahelin
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN 46617, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, United States.
| | - Jordan L Scott
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Cary T Frick
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
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Heinrich F, Nanda H, Goh HZ, Bachert C, Lösche M, Linstedt AD. Myristoylation restricts orientation of the GRASP domain on membranes and promotes membrane tethering. J Biol Chem 2014; 289:9683-91. [PMID: 24505136 DOI: 10.1074/jbc.m113.543561] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mammalian Golgi reassembly stacking protein (GRASP) proteins are Golgi-localized homotypic membrane tethers that organize Golgi stacks into a long, contiguous ribbon-like structure. It is unknown how GRASPs undergo trans pairing given that cis interactions between the proteins in the plane of the membrane are intrinsically favored. To test the hypothesis that myristoylation of the self-interacting GRASP domain restricts its orientation on the membrane to favor trans pairing, we established an in vitro assay that recapitulates GRASP-dependent membrane tethering and used neutron reflection under similar conditions to determine the orientation of the GRASP domain. In vivo, the membrane association of GRASP proteins is conferred by the simultaneous insertion of an N-terminal myristic acid and binding to a Golgi-associated binding partner. In our assay, the latter contact was replaced using a C-terminal hexa-His moiety, which bound to Ni(2+)-conjugated lipids incorporated into a substrate-supported bilayer lipid membrane. Nonmyristoylated protein lacked a fixed orientation on the membrane and inefficiently tethered liposomes. In contrast, myristoylated GRASP promoted tethering and exhibited a unique membrane complex. Thus, myristoylation restricts the membrane orientation of the GRASP domain favoring interactions in trans for membrane tethering.
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Kalli AC, Morgan G, Sansom MSP. Interactions of the auxilin-1 PTEN-like domain with model membranes result in nanoclustering of phosphatidyl inositol phosphates. Biophys J 2014; 105:137-45. [PMID: 23823232 DOI: 10.1016/j.bpj.2013.05.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 11/18/2022] Open
Abstract
Auxilin-1 is a neuron-specific membrane-binding protein involved in a late stage of clathrin-mediated endocytosis. It recruits Hsc70, thus initiating uncoating of the clathrin-coated vesicles. Interactions of auxilin-1 with the vesicle membrane are crucial for this function and are mediated via an N-terminal PTEN-like domain. We have used multiscale molecular dynamics simulations to probe the interactions of the auxilin-1 PTEN-like domain with lipid bilayers containing differing phospholipid composition, including bilayers containing phosphatidyl inositol phosphates. Our results suggest a novel, to our knowledge, model for the auxilin/membrane encounter and subsequent interactions. Negatively charged lipids (especially PIP2) enhance binding of auxilin to lipid bilayers and facilitate its correct orientation relative to the membrane. Mutations in three basic residues (R301E/R307E/K311E) of the C2 subdomain of the PTEN-like domain perturbed its interaction with the bilayer, changing its orientation. The interaction of membrane-bound auxilin-1 PTEN-like domain with negatively charged lipid headgroups results in nanoclustering of PIP2 molecules in the adjacent bilayer leaflet.
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Affiliation(s)
- Antreas C Kalli
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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50
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Human junctophilin-2 undergoes a structural rearrangement upon binding PtdIns(3,4,5)P3 and the S101R mutation identified in hypertrophic cardiomyopathy obviates this response. Biochem J 2014; 456:205-17. [PMID: 24001019 PMCID: PMC3898329 DOI: 10.1042/bj20130591] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
JP2 (junctophilin-2) is believed to hold the transverse tubular and jSR (junctional sarcoplasmic reticulum) membranes in a precise geometry that facilitates excitation–contraction coupling in cardiomyocytes. We have expressed and purified human JP2 and shown using electron microscopy that the protein forms elongated structures ~15 nm long and 2 nm wide. Employing lipid-binding assays and quartz crystal microbalance with dissipation we have determined that JP2 is selective for PS (phosphatidylserine), with a Kd value of ~0.5 μM, with the N-terminal domain mediating this interaction. JP2 also binds PtdIns(3,4,5)P3 at a different site than PS, resulting in the protein adopting a more flexible conformation; this interaction is modulated by both Ca2+ and Mg2+ ions. We show that the S101R mutation identified in patients with hypertrophic cardiomyopathy leads to modification of the protein secondary structure, forming a more flexible molecule with an increased affinity for PS, but does not undergo a structural transition in response to binding PtdIns(3,4,5)P3. In conclusion, the present study provides new insights into the structural and lipid-binding properties of JP2 and how the S101R mutation may have an effect upon the stability of the dyad organization with the potential to alter JP2–protein interactions regulating Ca2+ cycling. We have purified human JP2 (junctophilin-2) and the S101R hypertrophic cardiomyopathy mutant. JP2 interacts with phosphatidylserine, Kd ~0.5 μM, and PtdIns(3,4,5)P3 at different sites; divalent cations perturb the association. S101R has a modified structure and phospholipid-binding properties.
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