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Volumn 117, Issue 28, 2013, Pages 8322-8329

Quantum and all-atom molecular dynamics simulations of protonation and divalent ion binding to phosphatidylinositol 4,5-bisphosphate (PIP2)

Author keywords

[No Author keywords available]

Indexed keywords

CELL MEMBRANES; MAGNESIUM; MOLECULAR DYNAMICS; MOLECULAR MODELING; PHASE SEPARATION; PHOSPHOLIPIDS; PROTONATION;

EID: 84880546495     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp401414y     Document Type: Article
Times cited : (41)

References (48)
  • 1
    • 0035190026 scopus 로고    scopus 로고
    • Cellular Function of Phosphoinositide 3-Kinases: Implications for Development, Homeostasis, and Cancer
    • Katso, R.; Okkenhaug, K.; Ahmadi, K.; White, S.; Timms, J.; Waterfield, M. D. Cellular Function of Phosphoinositide 3-Kinases: Implications for Development, Homeostasis, and Cancer Annu. Rev. Cell Dev. Biol. 2001, 17, 615-675
    • (2001) Annu. Rev. Cell Dev. Biol. , vol.17 , pp. 615-675
    • Katso, R.1    Okkenhaug, K.2    Ahmadi, K.3    White, S.4    Timms, J.5    Waterfield, M.D.6
  • 2
    • 77954650869 scopus 로고    scopus 로고
    • Phosphatidylinositol 4,5-Bisphosphate and PIP5-Kinase Iα Are Required for Invadopodia Formation in Human Breast Cancer Cells
    • Yamaguchi, H.; Yoshida, S.; Muroi, E.; Kawamura, M.; Kouchi, Z.; Nakamura, Y.; Sakai, R.; Fukami, K. Phosphatidylinositol 4,5-Bisphosphate and PIP5-Kinase Iα Are Required for Invadopodia Formation in Human Breast Cancer Cells Cancer Sci. 2010, 101, 1632-1638
    • (2010) Cancer Sci. , vol.101 , pp. 1632-1638
    • Yamaguchi, H.1    Yoshida, S.2    Muroi, E.3    Kawamura, M.4    Kouchi, Z.5    Nakamura, Y.6    Sakai, R.7    Fukami, K.8
  • 3
    • 81555220913 scopus 로고    scopus 로고
    • The Role of PTEN in Tumor Angiogenesis
    • Rodriguez, S.; Huynh-Do, U. The Role of PTEN in Tumor Angiogenesis J. Oncol. 2012, 2012, 141236
    • (2012) J. Oncol. , vol.2012 , pp. 141236
    • Rodriguez, S.1    Huynh-Do, U.2
  • 4
    • 0025214940 scopus 로고
    • Polyphosphoinositide Synthesis in Platelets Stimulated with Low Concentrations of Thrombin Is Enhanced before the Activation of Phospholipase C
    • Lassing, I.; Lindberg, U. Polyphosphoinositide Synthesis in Platelets Stimulated with Low Concentrations of Thrombin Is Enhanced Before the Activation of Phospholipase C FEBS Lett. 1990, 262, 231-233
    • (1990) FEBS Lett. , vol.262 , pp. 231-233
    • Lassing, I.1    Lindberg, U.2
  • 5
    • 47349130804 scopus 로고    scopus 로고
    • Combined Electrostatics and Hydrogen Bonding Determine Intermolecular Interactions between Polyphosphoinositides
    • Levental, I.; CeÌbers, A.; Janmey, P. A. Combined Electrostatics and Hydrogen Bonding Determine Intermolecular Interactions Between Polyphosphoinositides J. Am. Chem. Soc. 2008, 130, 9025-9030
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 9025-9030
    • Levental, I.1    Ceìbers, A.2    Janmey, P.A.3
  • 6
    • 51249114388 scopus 로고    scopus 로고
    • Electrostatic Contribution to the Surface Pressure of Charged Monolayers Containing Polyphosphoinositides
    • Levental, I.; Janmey, P. A.; CeÌbers, A. Electrostatic Contribution to the Surface Pressure of Charged Monolayers Containing Polyphosphoinositides Biophys. J. 2008, 95, 1199-1205
    • (2008) Biophys. J. , vol.95 , pp. 1199-1205
    • Levental, I.1    Janmey, P.A.2    Ceìbers, A.3
  • 7
    • 69249120489 scopus 로고    scopus 로고
    • Calcium-Dependent Lateral Organization in Phosphatidylinositol 4,5-Bisphosphate (PIP2)- and Cholesterol-Containing Monolayers
    • Levental, I.; Christian, D. A.; Wang, Y.-H.; Madara, J. J.; Discher, D. E.; Janmey, P. A. Calcium-Dependent Lateral Organization in Phosphatidylinositol 4,5-Bisphosphate (PIP2)- and Cholesterol-Containing Monolayers Biochemistry 2009, 48, 8241-8248
    • (2009) Biochemistry , vol.48 , pp. 8241-8248
    • Levental, I.1    Christian, D.A.2    Wang, Y.-H.3    Madara, J.J.4    Discher, D.E.5    Janmey, P.A.6
  • 9
    • 79952947758 scopus 로고
    • Calorimetric Investigations of Phosphatidic Acid Bilayers
    • Blume, A. Calorimetric Investigations of Phosphatidic Acid Bilayers Ber. Bunsenges. Phys. Chem. 1978, 82, 917-917
    • (1978) Ber. Bunsenges. Phys. Chem. , vol.82 , pp. 917-917
    • Blume, A.1
  • 10
    • 79960505654 scopus 로고    scopus 로고
    • A Requirement for the P85 PI3K Adapter Protein BCAP in the Protection of Macrophages from Apoptosis Induced by Endoplasmic Reticulum Stress
    • Song, S.; Chew, C.; Dale, B. M.; Traum, D.; Peacock, J.; Yamazaki, T.; Clynes, R.; Kurosaki, T.; Greenberg, S. A Requirement for the P85 PI3K Adapter Protein BCAP in the Protection of Macrophages From Apoptosis Induced by Endoplasmic Reticulum Stress J. Immunol. 2011, 187, 619-625
    • (2011) J. Immunol. , vol.187 , pp. 619-625
    • Song, S.1    Chew, C.2    Dale, B.M.3    Traum, D.4    Peacock, J.5    Yamazaki, T.6    Clynes, R.7    Kurosaki, T.8    Greenberg, S.9
  • 12
    • 0037799198 scopus 로고    scopus 로고
    • A Modular PIP2 Binding Site as a Determinant of Capsaicin Receptor Sensitivity
    • Prescott, E. D.; Julius, D. A Modular PIP2 Binding Site as a Determinant of Capsaicin Receptor Sensitivity Science 2003, 300, 1284-1288
    • (2003) Science , vol.300 , pp. 1284-1288
    • Prescott, E.D.1    Julius, D.2
  • 13
    • 27744586089 scopus 로고    scopus 로고
    • Direct Modulation of Kir Channel Gating by Membrane Phosphatidylinositol 4,5-Bisphosphate
    • Enkvetchakul, D.; Jeliazkova, I.; Nichols, C. G. Direct Modulation of Kir Channel Gating by Membrane Phosphatidylinositol 4,5-Bisphosphate J. Biol. Chem. 2005, 280, 35785-35788
    • (2005) J. Biol. Chem. , vol.280 , pp. 35785-35788
    • Enkvetchakul, D.1    Jeliazkova, I.2    Nichols, C.G.3
  • 14
    • 80053131218 scopus 로고    scopus 로고
    • Structural Basis of PIP2 Activation of the Classical Inward Rectifier K+ Channel Kir2.2
    • Hansen, S. B.; Tao, X.; Mackinnon, R. Structural Basis of PIP2 Activation of the Classical Inward Rectifier K+ Channel Kir2.2 Nature 2011, 477, 495-498
    • (2011) Nature , vol.477 , pp. 495-498
    • Hansen, S.B.1    Tao, X.2    Mackinnon, R.3
  • 15
    • 0037071897 scopus 로고    scopus 로고
    • Alterations in Conserved Kir Channel-PIP2 Interactions Underlie Channelopathies
    • Lopes, C. M. B.; Zhang, H.; Rohacs, T.; Jin, T.; Yang, J.; Logothetis, D. E. Alterations in Conserved Kir Channel-PIP2 Interactions Underlie Channelopathies Neuron 2002, 34, 933-944
    • (2002) Neuron , vol.34 , pp. 933-944
    • Lopes, C.M.B.1    Zhang, H.2    Rohacs, T.3    Jin, T.4    Yang, J.5    Logothetis, D.E.6
  • 16
    • 44949238672 scopus 로고    scopus 로고
    • Diffusion Coefficient of Fluorescent Phosphatidylinositol 4,5-Bisphosphate in the Plasma Membrane of Cells
    • Golebiewska, U.; Nyako, M.; Woturski, W.; Zaitseva, I.; McLaughlin, S. Diffusion Coefficient of Fluorescent Phosphatidylinositol 4,5-Bisphosphate in the Plasma Membrane of Cells Mol. Biol. Cell 2008, 19, 1663-1669
    • (2008) Mol. Biol. Cell , vol.19 , pp. 1663-1669
    • Golebiewska, U.1    Nyako, M.2    Woturski, W.3    Zaitseva, I.4    McLaughlin, S.5
  • 18
    • 84861309310 scopus 로고    scopus 로고
    • A Role for Sphingomyelin-Rich Lipid Domains in the Accumulation of Phosphatidylinositol-4,5-Bisphosphate to the Cleavage Furrow during Cytokinesis
    • Abe, M.; Makino, A.; Hullin-Matsuda, F.; Kamijo, K.; Ohno-Iwashita, Y.; Hanada, K.; Mizuno, H.; Miyawaki, A.; Kobayashi, T. A Role for Sphingomyelin-Rich Lipid Domains in the Accumulation of Phosphatidylinositol-4, 5-Bisphosphate to the Cleavage Furrow During Cytokinesis Mol. Cell. Biol. 2012, 32, 1396-1407
    • (2012) Mol. Cell. Biol. , vol.32 , pp. 1396-1407
    • Abe, M.1    Makino, A.2    Hullin-Matsuda, F.3    Kamijo, K.4    Ohno-Iwashita, Y.5    Hanada, K.6    Mizuno, H.7    Miyawaki, A.8    Kobayashi, T.9
  • 21
    • 79960182810 scopus 로고    scopus 로고
    • Development of the CHARMM Force Field for Lipids
    • Pastor, R. W.; Mackerell, A. D., Jr. Development of the CHARMM Force Field for Lipids J. Phys. Chem. Lett. 2011, 2, 1526-1532
    • (2011) J. Phys. Chem. Lett. , vol.2 , pp. 1526-1532
    • Pastor, R.W.1    Mackerell, Jr.A.D.2
  • 22
    • 4444351490 scopus 로고    scopus 로고
    • Empirical Force Fields for Biological Macromolecules: Overview and Issues
    • Mackerell, A. D., Jr. Empirical Force Fields for Biological Macromolecules: Overview and Issues J. Comput. Chem. 2004, 25, 1584-1604
    • (2004) J. Comput. Chem. , vol.25 , pp. 1584-1604
    • Mackerell, Jr.A.D.1
  • 23
    • 84986513567 scopus 로고
    • Determining Atom-Centered Monopoles from Molecular Electrostatic Potentials. The Need for High Sampling Density in Formamide Conformational Analysis
    • Breneman, C. M.; Wiberg, K. B. Determining Atom-Centered Monopoles From Molecular Electrostatic Potentials. The Need for High Sampling Density in Formamide Conformational Analysis J. Comput. Chem. 1990, 11, 361-373
    • (1990) J. Comput. Chem. , vol.11 , pp. 361-373
    • Breneman, C.M.1    Wiberg, K.B.2
  • 25
    • 0017100947 scopus 로고
    • Theoretical Studies of Enzymic Reactions: Dielectric, Electrostatic and Steric Stabilization of the Carbonium Ion in the Reaction of Lysozyme
    • Warshel, A.; Levitt, M. Theoretical Studies of Enzymic Reactions: Dielectric, Electrostatic and Steric Stabilization of the Carbonium Ion in the Reaction of Lysozyme J. Mol. Biol. 1976, 103, 227-249
    • (1976) J. Mol. Biol. , vol.103 , pp. 227-249
    • Warshel, A.1    Levitt, M.2
  • 26
    • 0037115887 scopus 로고    scopus 로고
    • Optimization of Quantum Mechanical Molecular Mechanical Partitioning Schemes: Gaussian Delocalization of Molecular Mechanical Charges and the Double Link Atom Method
    • Das, D.; Eurenius, K. P.; Billings, E. M.; Sherwood, P.; Chatfield, D. C.; Hodošček, M.; Brooks, B. R. Optimization of Quantum Mechanical Molecular Mechanical Partitioning Schemes: Gaussian Delocalization of Molecular Mechanical Charges and the Double Link Atom Method J. Chem. Phys. 2002, 117, 10534
    • (2002) J. Chem. Phys. , vol.117 , pp. 10534
    • Das, D.1    Eurenius, K.P.2    Billings, E.M.3    Sherwood, P.4    Chatfield, D.C.5    Hodošček, M.6    Brooks, B.R.7
  • 27
    • 34848854765 scopus 로고    scopus 로고
    • Coupling of Fast and Slow Modes in the Reaction Pathway of the Minimal Hammerhead Ribozyme Cleavage
    • Radhakrishnan, R. Coupling of Fast and Slow Modes in the Reaction Pathway of the Minimal Hammerhead Ribozyme Cleavage Biophys. J. 2007, 93, 2391-2399
    • (2007) Biophys. J. , vol.93 , pp. 2391-2399
    • Radhakrishnan, R.1
  • 28
    • 77950258668 scopus 로고    scopus 로고
    • Computational Delineation of the Catalytic Step of a High-Fidelity DNA Polymerase
    • Venkatramani, R.; Radhakrishnan, R. Computational Delineation of the Catalytic Step of a High-Fidelity DNA Polymerase Protein Sci. 2010, 19, 815-825
    • (2010) Protein Sci. , vol.19 , pp. 815-825
    • Venkatramani, R.1    Radhakrishnan, R.2
  • 29
    • 77952338791 scopus 로고    scopus 로고
    • ErbB3/HER3 Intracellular Domain Is Competent to Bind ATP and Catalyze Autophosphorylation
    • Shi, F.; Telesco, S. E.; Liu, Y.; Radhakrishnan, R.; Lemmon, M. A. ErbB3/HER3 Intracellular Domain Is Competent to Bind ATP and Catalyze Autophosphorylation Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 7692-7697
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 7692-7697
    • Shi, F.1    Telesco, S.E.2    Liu, Y.3    Radhakrishnan, R.4    Lemmon, M.A.5
  • 35
    • 84864933800 scopus 로고    scopus 로고
    • Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains
    • Klauda, J. B.; Monje, V.; Kim, T.; Im, W. Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains J. Phys. Chem. B 2012, 116, 9424-9431
    • (2012) J. Phys. Chem. B , vol.116 , pp. 9424-9431
    • Klauda, J.B.1    Monje, V.2    Kim, T.3    Im, W.4
  • 36
    • 66749083288 scopus 로고    scopus 로고
    • CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates, and Inositol
    • Hatcher, E. R.; Guvench, O.; Mackerell, A. D., Jr. CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates, and Inositol J. Chem. Theory Comput. 2009, 5, 1315-1327
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 1315-1327
    • Hatcher, E.R.1    Guvench, O.2    Mackerell, Jr.A.D.3
  • 37
    • 84857082110 scopus 로고    scopus 로고
    • CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates
    • Mallajosyula, S. S.; Guvench, O.; Hatcher, E.; Mackerell, A. D., Jr. CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates J. Chem. Theo. Comput. 2012, 8, 759-776
    • (2012) J. Chem. Theo. Comput. , vol.8 , pp. 759-776
    • Mallajosyula, S.S.1    Guvench, O.2    Hatcher, E.3    Mackerell, Jr.A.D.4
  • 38
    • 68949110664 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations of PIP2 and PIP3 in Lipid Bilayers: Determination of Ring Orientation, and the Effects of Surface Roughness on a Poisson-Boltzmann Description
    • Li, Z.; Venable, R. M.; Rogers, L. A.; Murray, D.; Pastor, R. W. Molecular Dynamics Simulations of PIP2 and PIP3 in Lipid Bilayers: Determination of Ring Orientation, and the Effects of Surface Roughness on a Poisson-Boltzmann Description Biophys. J. 2009, 97, 155-163
    • (2009) Biophys. J. , vol.97 , pp. 155-163
    • Li, Z.1    Venable, R.M.2    Rogers, L.A.3    Murray, D.4    Pastor, R.W.5
  • 39
    • 77049117291 scopus 로고    scopus 로고
    • A Molecular Dynamics Investigation of Lipid Bilayer Perturbation by PIP2
    • Lupyan, D.; Mezei, M.; Logothetis, D. E.; Osman, R. A Molecular Dynamics Investigation of Lipid Bilayer Perturbation by PIP2 Biophys. J. 2010, 98, 240-247
    • (2010) Biophys. J. , vol.98 , pp. 240-247
    • Lupyan, D.1    Mezei, M.2    Logothetis, D.E.3    Osman, R.4
  • 40
    • 0029633155 scopus 로고
    • The Calculation of the Potential of Mean Force Using Computer Simulations
    • Roux, B. The Calculation of the Potential of Mean Force Using Computer Simulations Comput. Phys. Commun. 1995, 91, 275-282
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 275-282
    • Roux, B.1
  • 41
    • 70350061531 scopus 로고    scopus 로고
    • Ionization Properties of Phosphatidylinositol Polyphosphates in Mixed Model Membranes
    • Kooijman, E. E.; King, K. E.; Gangoda, M.; Gericke, A. Ionization Properties of Phosphatidylinositol Polyphosphates in Mixed Model Membranes Biochemistry 2009, 48, 9360-9371
    • (2009) Biochemistry , vol.48 , pp. 9360-9371
    • Kooijman, E.E.1    King, K.E.2    Gangoda, M.3    Gericke, A.4
  • 42
    • 38549092474 scopus 로고    scopus 로고
    • Membrane Recognition by Phospholipid-Binding Domains
    • Lemmon, M. A. Membrane Recognition by Phospholipid-Binding Domains Nat. Rev. Mol. Cell Biol. 2008, 9, 99-111
    • (2008) Nat. Rev. Mol. Cell Biol. , vol.9 , pp. 99-111
    • Lemmon, M.A.1
  • 45
    • 0002036605 scopus 로고
    • Sur la Décomposition de L'eau et des Corps Qu'elle Tient en Dissolution AÌ L'aide de L'électricité Galvanique
    • de Grotthuss, C. Sur La Décomposition De L'eau Et Des Corps Qu'elle Tient en Dissolution AÌ L'aide De L'électricité Galvanique Ann. Chim. (Paris) 1806, 58, 54-73
    • (1806) Ann. Chim. (Paris) , vol.58 , pp. 54-73
    • De Grotthuss, C.1
  • 46
    • 0024293197 scopus 로고
    • Adsorption of Cations to Phosphatidylinositol 4,5-Bisphosphate
    • Toner, M.; Vaio, G.; McLaughlin, A.; McLaughlin, S. Adsorption of Cations to Phosphatidylinositol 4,5-Bisphosphate Biochemistry 1988, 27, 7435-7443
    • (1988) Biochemistry , vol.27 , pp. 7435-7443
    • Toner, M.1    Vaio, G.2    McLaughlin, A.3    McLaughlin, S.4
  • 47
    • 84862679270 scopus 로고    scopus 로고
    • Regulation of the Electric Charge in Phosphatidic Acid Domains
    • Wang, W.; Anderson, N. A.; Travesset, A.; Vaknin, D. Regulation of the Electric Charge in Phosphatidic Acid Domains J. Phys. Chem. B 2012, 116, 7213-7220
    • (2012) J. Phys. Chem. B , vol.116 , pp. 7213-7220
    • Wang, W.1    Anderson, N.A.2    Travesset, A.3    Vaknin, D.4
  • 48
    • 84876411759 scopus 로고    scopus 로고
    • Increased pH-Sensitivity of Protein Binding to Lipid Membranes through the Electrostatic-Hydrogen Bond Switch
    • Loew, S.; Kooijman, E. E.; May, S. Increased pH-Sensitivity of Protein Binding to Lipid Membranes through the Electrostatic-Hydrogen Bond Switch Chem. Phys. Lipids 2013, 169, 9-18
    • (2013) Chem. Phys. Lipids , vol.169 , pp. 9-18
    • Loew, S.1    Kooijman, E.E.2    May, S.3


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