Cited by 67

The DOI matches its Crossref record.

Molecular Basis for Cooperative Binding of Anionic Phospholipids to the PH Domain of the Arf GAP ASAP1

Jian, Xiaoying, Tang, Wai-Kwan, Zhai, Peng, Roy, Neeladri Sekhar, Luo, Ruibai, Gruschus, James M., Yohe, Marielle E., Chen, Pei-Wen, Li, Yifei, Byrd, R. Andrew, Xia, Di, Randazzo, Paul A.·2015·Structure

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.str.2015.08.008

Cites

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The PH domain of Arf GAP ASAP1 possesses two synergistic lipid-binding sites and binds most efficiently to PI(4,5)P2-containing membranes in the presence of other anionic lipids, such as PS.

    “For example, the PH domain of Arf GAP ASAP1 possesses two synergistic lipid‐binding sites and binds most efficiently to PI(4,5)P2‐containing membranes in the presence of other anionic lipids, such as PS (Jian et al, 2015).”

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

No references could be resolved yet.

Research works printed but not linked: 60

  1. Ainslie, 1972, Transients and cooperativity—slow transition model for relating transients and cooperative kinetics of enzymes, J. Biol. Chem., 247, 7088, 10.1016/S0021-9258(19)44697-8 · DOI
  2. Alessi, 1997, Characterization of a 3-phosphoinositide-dependent protein kinase which phosphorylates and activates protein kinase B alpha, Curr. Biol., 7, 261, 10.1016/S0960-9822(06)00122-9 · DOI
  3. Anand, 2012, Structural analyses of the Slm1-PH domain demonstrate ligand binding in the non-canonical site, PLoS One, 7, e36526, 10.1371/journal.pone.0036526 · DOI
  4. Balla, 2005, Inositol-lipid binding motifs: signal integrators through protein-lipid and protein-protein interactions, J. Cell Sci., 118, 2093, 10.1242/jcs.02387 · DOI
  5. Bellacosa, 1998, Akt activation by growth factors is a multiple-step process: the role of the PH domain, Oncogene, 17, 313, 10.1038/sj.onc.1201947 · DOI
  6. Brown, 1998, ASAP1, a phospholipid-dependent Arf GTPase-activating protein that associates with and is phosphorylated by Src, Mol. Cell. Biol., 18, 7038, 10.1128/MCB.18.12.7038 · DOI
  7. CCP4, 1994, The CCP4 suit: programs for protein crystallography, Acta Crystallogr. D Biol. Crystallogr., 50, 760, 10.1107/S0907444994003112 · DOI
  8. Ceccarelli, 2007, Non-canonical interaction of phosphoinositides with pleckstrin homology domains of Tiam1 and ArhGAP9, J. Biol. Chem., 282, 13864, 10.1074/jbc.M700505200 · DOI
  9. Cha, 1968, A simple method for derivation of rate equations for enzyme-catalyzed reactions under rapid equilibrium assumption or combined assumptions of equilibrium and steady state, J. Biol. Chem., 243, 820, 10.1016/S0021-9258(19)81739-8 · DOI
  10. Chan, 1999, AKT/PKB and other D3 phosphoinositide-regulated kinases: kinase activation by phosphoinositide-dependent phosphorylation, Annu. Rev. Biochem., 68, 965, 10.1146/annurev.biochem.68.1.965 · DOI · Paper page
  11. Che, 2005, Regulation of ASAP1 by phospholipids is dependent on the interface between the PH and Arf GAP domains, Cell. Signal., 17, 1276, 10.1016/j.cellsig.2005.01.007 · DOI
  12. Chen, 2012, Approaches to studying Arf GAPs in cells: in vitro assay with isolated focal adhesions, Curr. Protoc. Cell Biol., 10.1002/0471143030.cb1713s55 · DOI
  13. DiNitto, 2006, Membrane and juxtamembrane targeting by PH and PTB domains, Biochim. Biophys. Acta, 1761, 850, 10.1016/j.bbalip.2006.04.008 · DOI
  14. DiNitto, 2007, Structural basis and mechanism of autoregulation in 3-phosphoinositide-dependent Grp1 family Arf GTPase exchange factors, Mol. Cell, 28, 569, 10.1016/j.molcel.2007.09.017 · DOI
  15. Donaldson, 2003, Multiple roles for Arf6: sorting, structuring, and signaling at the plasma membrane, J. Biol. Chem., 278, 41573, 10.1074/jbc.R300026200 · DOI
  16. Donaldson, 2005, Multiple activities for Arf1 at the Golgi complex, Biochim. Biophys. Acta, 1744, 364, 10.1016/j.bbamcr.2005.03.001 · DOI
  17. D'Souza-Schorey, 2006, ARF proteins: roles in membrane traffic and beyond, Nat. Rev. Mol. Cell Biol., 7, 347, 10.1038/nrm1910 · DOI
  18. Emsley, 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr. D Biol. Crystallogr., 60, 2126, 10.1107/S0907444904019158 · DOI · Paper page
  19. Frieden, 1970, Kinetic aspects of regulation of metabolic processes—hysteretic enzyme concept, J. Biol. Chem., 245, 5788, 10.1016/S0021-9258(18)62721-8 · DOI
  20. Gallego, 2010, A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae, Mol. Sys. Biol., 6, 430, 10.1038/msb.2010.87 · DOI
  21. Gillingham, 2007, The small G proteins of the Arf family and their regulators, Annu. Rev. Cell Dev. Biol., 23, 579, 10.1146/annurev.cellbio.23.090506.123209 · DOI
  22. Godi, 2004, FAPPs control Golgi-to-cell-surface membrane traffic by binding to ARF and PtdIns(4)P, Nat. Cell Biol., 6, 393, 10.1038/ncb1119 · DOI
  23. Guerrero-Valero, 2009, Structural and mechanistic insights into the association of PKC alpha-C2 domain to PtdIns(4,5)P-2, Proc. Natl. Acad. Sci. USA, 106, 6603, 10.1073/pnas.0813099106 · DOI · Paper page
  24. He, 2011, Molecular basis of phosphatidylinositol 4-phosphate and ARF1 GTPase recognition by the FAPP1 pleckstrin homology (PH) domain, J. Biol. Chem., 286, 18650, 10.1074/jbc.M111.233015 · DOI
  25. He, 2013, Structural basis for autoinhibition of the guanine nucleotide exchange factor FARP2, Structure, 21, 355, 10.1016/j.str.2013.01.001 · DOI
  26. Huang, 2011, Phosphatidylserine is a critical modulator for Akt activation, J. Cell Biol., 192, 979, 10.1083/jcb.201005100 · DOI
  27. Hyvonen, 1995, Structure of the binding-site for inositol phosphates in a PH domain, EMBO J., 14, 4676, 10.1002/j.1460-2075.1995.tb00149.x · DOI
  28. Jian, 2009, Autoinhibition of Arf GTPase-activating protein activity by the BAR domain in ASAP1, J. Biol. Chem., 284, 1652, 10.1074/jbc.M804218200 · DOI
  29. Kahn, 2006, Nomenclature for the human Arf family of GTP-binding proteins: ARF, ARL, and SAR proteins, J. Cell Biol., 172, 645, 10.1083/jcb.200512057 · DOI
  30. Kahn, 2008, Consensus nomenclature for the human ArfGAP domain-containing proteins, J. Cell Biol., 182, 1039, 10.1083/jcb.200806041 · DOI
  31. Kam, 2000, Phosphoinositide-dependent activation of the ADP-ribosylation factor GTPase-activating protein ASAP1—evidence for the pleckstrin homology domain functioning as an allosteric site, J. Biol. Chem., 275, 9653, 10.1074/jbc.275.13.9653 · DOI
  32. Karathanassis, 2002, Binding of the PX domain of p47(phox) to phosphatidylinositol 3,4-bisphosphate and phosphatidic acid is masked by an intramolecular interaction, EMBO J., 21, 5057, 10.1093/emboj/cdf519 · DOI · Paper page
  33. Koshland, 2002, Proteomics and models for enzyme cooperativity, J. Biol. Chem., 277, 46841, 10.1074/jbc.R200014200 · DOI
  34. Lemmon, 2008, Membrane recognition by phospholipid-binding domains, Nat. Rev. Mol. Cell Biol., 9, 99, 10.1038/nrm2328 · DOI · Paper page
  35. Lemmon, 1995, Specific and high-affinity binding of inositol phosphates to an isolated pleckstrin homology domain, Proc. Natl. Acad. Sci. USA, 92, 10472, 10.1073/pnas.92.23.10472 · DOI · Paper page
  36. Lemmon, 1996, PH domains: diverse sequences with a common fold recruit signaling molecules to the cell surface, Cell, 85, 621, 10.1016/S0092-8674(00)81022-3 · DOI
  37. Liu, 2002, The association of ASAP1, an ADP ribosylation factor-GTPase activating protein, with focal adhesion kinase contributes to the process of focal adhesion assembly, Mol. Biol. Cell, 13, 2147, 10.1091/mbc.e02-01-0018 · DOI
  38. Liu, 2014, Interaction of Fapp1 with Arf1 and PI4P at a membrane surface: an example of coincidence detection, Structure, 22, 421, 10.1016/j.str.2013.12.011 · DOI
  39. Luo, 2007, Kinetic analysis of GTP hydrolysis catalysed by the Arf1-GTP-ASAP1 complex, Biochem. J., 402, 439, 10.1042/BJ20061217 · DOI
  40. Luo, 2008, Dynamic interaction between Arf GAP and PH domains of ASAP1 in the regulation of GAP activity, Cell. Signal., 20, 1968, 10.1016/j.cellsig.2008.07.007 · DOI
  41. Maffucci, 2001, Specificity in pleckstrin homology (PH) domain membrane targeting: a role for a phosphoinositide-protein co-operative mechanism, FEBS Lett., 506, 173, 10.1016/S0014-5793(01)02909-X · DOI
  42. Malaby, 2013, Structural basis for membrane recruitment and allosteric activation of cytohesin family Arf GTPase exchange factors, Proc. Natl. Acad. Sci. USA, 110, 14213, 10.1073/pnas.1301883110 · DOI
  43. Milburn, 2003, Binding of phosphatidylinositol 3,4,5-trisphosphate to the pleckstrin homology domain of protein kinase B induces a conformational change, Biochem. J., 375, 531, 10.1042/bj20031229 · DOI
  44. Moravcevic, 2012, Conditional peripheral membrane proteins: facing up to limited specificity, Structure, 20, 15, 10.1016/j.str.2011.11.012 · DOI
  45. Nie, 2006, A BAR domain in the N terminus of the Arf GAP ASAP1 affects membrane structure and trafficking of epidermal growth factor receptor, Curr. Biol., 16, 130, 10.1016/j.cub.2005.11.069 · DOI
  46. Oda, 2003, CrkL directs ASAP1 to peripheral focal adhesions, J. Biol. Chem., 278, 6456, 10.1074/jbc.M210817200 · DOI
  47. Otwinowski, 1997, Processing of X-ray diffraction data collected in oscillation mode, Method Enzymol., 276, 307, 10.1016/S0076-6879(97)76066-X · DOI · Paper page
  48. Randazzo, 1994, GTP hydrolysis by ADP-ribosylation factor is dependent on both an ADP-ribosylation factor GTPase-activating protein and acid phospholipids, J. Biol. Chem., 269, 10758, 10.1016/S0021-9258(17)34124-8 · DOI
  49. Randazzo, 1995, The myristoylated amino-terminus of ADP-ribosylation factor-1 is a phospholipid-sensitive and GTP-sensitive switch, J. Biol. Chem., 270, 14809, 10.1074/jbc.270.24.14809 · DOI
  50. Randazzo, 2001, Assay and purification of phosphoinositide-dependent ADP-ribosylation factor (ARF) GTPase activating proteins, Method Enzymol., 329, 343, 10.1016/S0076-6879(01)29096-X · DOI
  51. Randazzo, 2013, Quantitative analysis of guanine nucleotide exchange factors (GEFs) as enzymes, Cell. Log, 3, e27609, 10.4161/cl.27609 · DOI
  52. Rossman, 2002, A crystallographic view of interactions between Dbs and Cdc42: PH domain-assisted guanine nucleotide exchange, EMBO J., 21, 1315, 10.1093/emboj/21.6.1315 · DOI · Paper page
  53. Scheffzek, 2012, Pleckstrin homology (PH) like domains—versatile modules in protein-protein interaction platforms, FEBS Lett., 586, 2662, 10.1016/j.febslet.2012.06.006 · DOI
  54. Sprang, 1997, G protein mechanisms: insights from structural analysis, Annu. Rev. Biochem., 66, 639, 10.1146/annurev.biochem.66.1.639 · DOI
  55. Thomas, 2002, High-resolution structure of the pleckstrin homology domain of protein kinase B/Akt bound to phosphatidylinositol (3,4,5)-trisphosphate, Curr. Biol., 12, 1256, 10.1016/S0960-9822(02)00972-7 · DOI
  56. Vagin, 2000, An approach to multi-copy search in molecular replacement, Acta Crystallogr. D Biol. Crystallogr., B56, 1622, 10.1107/S0907444900013780 · DOI
  57. Vetter, 2001, Signal transduction—the guanine nucleotide-binding switch in three dimensions, Science, 294, 1299, 10.1126/science.1062023 · DOI · Paper page
  58. Volpicelli-Daley, 2005, Isoform-selective effects of the depletion of ADP-ribosylation factors 1-5 on membrane traffic, Mol. Biol. Cell, 16, 4495, 10.1091/mbc.e04-12-1042 · DOI
  59. Whitty, 2008, Cooperativity and biological complexity, Nat. Chem. Biol., 4, 435, 10.1038/nchembio0808-435 · DOI
  60. Wittinghofer, 2011, Structure-function relationships of the G domain, a canonical switch motif, Annu. Rev. Biochem., 80, 943, 10.1146/annurev-biochem-062708-134043 · DOI

Cited by

Sorted by citations

Metadata

Authors
Jian, X., Tang, W.-K., Zhai, P., Roy, N. S., Luo, R., Gruschus, J. M., Yohe, M. E., Chen, P.-W., Li, Y., Byrd, R. A., Xia, D., & Randazzo, P. A.
Venue
Structure
Publisher
Elsevier BV
Published
2015-11
Volume
23
Issue
11
Pages
1977-1988
ISSN
0969-2126
Cited by
67
References
0
Language
en

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review