Corrigendum to "Sphingosine 1-phosphate pKa and binding constants: Intramolecular and intermolecular influences" [J. Mol. Graph. Model. 26 (2009) 519-528] (DOI:10.1016/j.jmgm.2007.03.004);Sphingosine 1-phosphate pKa and binding constants: Intramolecular and intermolecular influences

Journal of Molecular Graphics and Modelling

Volumn 26, Issue 2, 2007, Pages 519-528

  Naor, Mor M ^a   Walker, Michelle D ^b   Van Brocklyn, James R ^c   Tigyi, Gabor ^b   Parrill, Abby L ^a  

^a University of Memphis   (United States)

^b UNIVERSITY OF TENNESSEE CANCER INSTITUTE   (United States)

^c OHIO STATE UNIVERSITY   (United States)

Author keywords

Agonist; GPCR; pKa; S1P1; Sphingosine 1 phosphate

Indexed keywords

BINDING SITES; CARBOXYLATION; DISSOCIATION; MOLECULAR DYNAMICS; MUTAGENESIS;

A +1 CHARGE; COMPUTATIONAL DISSOCIATION; SPHINGOSINE 1-PHOSPHATE;

ENZYMES;

CARBOXYLIC ACID; SPHINGOSINE 1 PHOSPHATE;

AB INITIO CALCULATION; ANIMAL CELL; ARTICLE; BINDING AFFINITY; CHEMICAL REACTION; CHEMICAL STRUCTURE; CONTROLLED STUDY; DISSOCIATION CONSTANT; HUMAN; HUMAN CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; PKA; PRIORITY JOURNAL; RAT; WILD TYPE;

EID: 34548205718     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2009.09.004     Document Type: Erratum

References (76)

1. Lee M.J., Van Brocklyn J.R., Thangada S., Liu C.H., Hand A.R., Menzeleev R., Spiegel S., and Hla T. Sphingosine-1-phosphate as a ligand for the G protein-coupled receptor EDG-1. Science 279 5356 (1998) 1552-1555
2. An S., Bleu T., Huang W., Hallmark O.G., Coughlin S.R., and Goetzl E.J. Identification of cDNAs encoding two G protein-coupled receptors for lysosphingolipids. FEBS Lett. 417 3 (1997) 279-282
3. MacLennan A.J., Browe C.S., Gaskin A.A., Lado D.C., and Shaw G. Cloning and characterization of a putative G-protein coupled receptor potentially involved in development. Mol. Cell. Neurosci. 5 3 (1994) 201-209
4. Van Brocklyn J.R., Gräler M.H., Bernhardt G., Hobson J.P., and Spiegel S. Sphingosine-1-phosphate is a ligand for the G protein-coupled receptor EDG-6. Blood 95 8 (2000) 2624-2629
5. 2+ signaling pathway. Biochem. Biophys. Res. Commun. 268 2 (2000) 583-589
6. Glickman M., Malek R.L., Kwitek-Black A.E., Jacob H.J., and Lee N.H. Molecular cloning, tissue-specific expression, and chromosomal localization of a novel nerve growth factor-regulated G-protein-coupled receptor, nrg-1. Mol. Cell. Neurosci. 14 2 (1999) 141-152
7. Malek R.L., Toman R.E., Edsall L.C., Wong S., Chiu J., Letterle C.A., Van Brocklyn J.R., Milstien S., Spiegel S., and Lee N.H. Nrg-1 belongs to the endothelial differentiation gene family of G protein-coupled sphingosine-1-phosphate receptors. J. Biol. Chem. 276 8 (2001) 5692-5699
8. Parrill A.L., Sardar V.M., and Yuan H. Sphingosine 1-phosphate and lysophosphatidic acid receptors: agonist and antagonist binding and progress toward development of receptor-specific ligands. Semin. Cell. Dev. Biol. 15 5 (2004) 467-476
9. Takuwa Y. Subtype-specific differential regulation of Rho family G proteins and cell migration by the Edg family sphingosine-1-phosphate receptors. Biochim. Biophys. Acta 1582 1-3 (2002) 112-120
10. Yamaguchi H., Kitayama J., Takuwa N., Arikawa K., Inoki I., Takehara K., Nagawa H., and Takuwa Y. Sphingosine-1-phosphate receptor subtype-specific positive and negative regulation of Rac and haematogenous metastasis of melanoma cells. Biochem. J. 374 Pt 3 (2003) 715-722
11. Tigyi G., Fischer D.J., Baker D., Wang D.A., Yue J., Nusser N., Virag T., Zsiros V., Liliom K., Miller D., and Parrill A. Pharmacological characterization of phospholipid growth-factor receptors. Ann. N.Y. Acad. Sci. 905 (2000) 34-53
12. Van Brocklyn J., Letterle C., Snyder P., and Prior T. Sphingosine-1-phosphate stimulates human glioma cell proliferation through Gi-coupled receptors: role of ERK MAP kinase and phosphatidylinositol 3-kinase beta. Cancer Lett. 181 2 (2002) 195-204
13. 2+ control lysophosphatidate signaling through EDG-2 receptors. J. Biol. Chem. 275 36 (2000) 27520-27530
14. Brinkmann V., Cyster J.G., and Hla T. FTY720: sphingosine 1-phosphate receptor-1 in the control of lymphocyte egress and endothelial barrier function. Am. J. Transplant. 4 7 (2004) 1019-1025
15. Li Z., Chen W., Hale J.J., Lynch C.L., Mills S.G., Hajdu R., Keohane C.A., Rosenbach M.J., Milligan J.A., Shei G.J., Chrebet G., Parent S.A., Bergstrom J., Card D., Forrest M., Quackenbush E.J., Wickham L.A., Vargas H., Evans R.M., Rosen H., and Mandala S. Discovery of potent 3,5-diphenyl-1,2,4-oxadiazole sphingosine-1-phosphate-1 (S1P1) receptor agonists with exceptional selectivity against S1P2 and S1P3. J. Med. Chem. 48 20 (2005) 6169-6173
16. Hale J.J., Lynch C.L., Neway W., Mills S.G., Hajdu R., Keohane C.A., Rosenbach M.J., Milligan J.A., Shei G.J., Parent S.A., Chrebet G., Bergstrom J., Card D., Ferrer M., Hodder P., Strulovici B., Rosen H., and Mandala S. A rational utilization of high-throughput screening affords selective, orally bioavailable 1-benzyl-3-carboxyazetidine sphingosine-1-phosphate-1 receptor agonists. J. Med. Chem. 47 27 (2004) 6662-6665
17. Yan L., Hale J.J., Lynch C.L., Budhu R., Gentry A., Mills S.G., Hajdu R., Keohane C.A., Rosenbach M.J., Milligan J.A., Shei G.J., Chrebet G., Bergstrom J., Card D., Rosen H., and Mandala S.M. Design and synthesis of conformationally constrained 3-(N-alkylamino)propylphosphonic acids as potent agonists of sphingosine-1-phosphate (S1P) receptors. Bioorg. Med. Chem. Lett. 14 19 (2004) 4861-4866
18. Hale J.J., Yan L., Neway W.E., Hajdu R., Bergstrom J.D., Milligan J.A., Shei G.J., Chrebet G.L., Thornton R.A., Card D., Rosenbach M., Rosen H., and Mandala S. Synthesis, stereochemical determination and biochemical characterization of the enantiomeric phosphate esters of the novel immunosuppressive agent FTY720. Bioorg. Med. Chem. 12 18 (2004) 4803-4807
19. Hale J.J., Doherty G., Toth L., Mills S.G., Hajdu R., Keohane C.A., Rosenbach M., Milligan J., Shei G.J., Chrebet G., Bergstrom J., Card D., Forrest M., Sun S.Y., West S., Xie H., Nomura N., Rosen H., and Mandala S. Selecting against S1P3 enhances the acute cardiovascular tolerability of 3-(N-benzyl)aminopropylphosphonic acid S1P receptor agonists. Bioorg. Med. Chem. Lett. 14 13 (2004) 3501-3505
20. Hale J.J., Doherty G., Toth L., Li Z., Mills S.G., Hajdu R., Ann Keohane C., Rosenbach M., Milligan J., Shei G.J., Chrebet G., Bergstrom J., Card D., Rosen H., and Mandala S. The discovery of 3-(N-alkyl)aminopropylphosphonic acids as potent S1P receptor agonists. Bioorg. Med. Chem. Lett. 14 13 (2004) 3495-3499
21. Hale J.J., Neway W., Mills S.G., Hajdu R., Ann Keohane C., Rosenbach M., Milligan J., Shei G.J., Chrebet G., Bergstrom J., Card D., Koo G.C., Koprak S.L., Jackson J.J., Rosen H., and Mandala S. Potent S1P receptor agonists replicate the pharmacologic actions of the novel immune modulator FTY720. Bioorg. Med. Chem. Lett. 14 12 (2004) 3351-3355
22. Foss Jr. F.W., Clemens J.J., Davis M.D., Snyder A.H., Zigler M.A., Lynch K.R., and Macdonald T.L. Synthesis, stability, and implications of phosphothioate agonists of sphingosine-1-phosphate receptors. Bioorg. Med. Chem. Lett. 15 20 (2005) 4470-4474
23. Clemens J.J., Davis M.D., Lynch K.R., and Macdonald T.L. Synthesis of 4(5)-phenylimidazole-based analogues of sphingosine-1-phosphate and FTY720: discovery of potent S1P1 receptor agonists. Bioorg. Med. Chem. Lett. 15 15 (2005) 3568-3572
24. Clemens J.J., Davis M.D., Lynch K.R., and Macdonald T.L. Synthesis of para-alkyl aryl amide analogues of sphingosine-1-phosphate: discovery of potent S1P receptor agonists. Bioorg. Med. Chem. Lett. 13 20 (2003) 3401-3404
25. Lefkowitz R.J., Cotecchia S., Samama P., and Costa T. Constitutive activity of receptors coupled to guanine nucleotide regulatory proteins. Trends Pharmacol. Sci. 14 8 (1993) 303-307
26. Samama P., Pei G., Costa T., Cotecchia S., and Lefkowitz R.J. Negative antagonists promote an inactive conformation of the beta 2-adrenergic receptor. Mol. Pharmacol. 45 3 (1994) 390-394
27. Jo E., Sanna M.G., Gonzalez-Cabrera P.J., Thangada S., Tigyi G., Osborne D.A., Hla T., Parrill A.L., and Rosen H. S1P1-selective in vivo-active agonists from high-throughput screening: off-the-shelf chemical probes of receptor interactions, signaling, and fate. Chem. Biol. 12 6 (2005) 703-715
28. Wang D.A., Lorincz Z., Bautista D.L., Liliom K., Tigyi G., and Parrill A.L. A single amino acid determines lysophospholipid specificity of the S1P1 (EDG1) and LPA1 (EDG2) phospholipid growth factor receptors. J. Biol. Chem. 276 52 (2001) 49213-49220
29. Fujiwara Y., Sardar V., Tokumura A., Baker D., Murakami-Murofushi K., Parrill A., and Tigyi G. Identification of residues responsible for ligand recognition and regioisomeric selectivity of lysophosphatidic acid receptors expressed in mammalian cells. J. Biol. Chem. 280 41 (2005) 35038-35050
30. Inagaki Y., Pham T.T., Fujiwara Y., Kohno T., Osborne D.A., Igarashi Y., Tigyi G., and Parrill A.L. Sphingosine 1-phosphate analogue recognition and selectivity at S1P4 within the endothelial differentiation gene family of receptors. Biochem. J. 389 Pt 1 (2005) 187-195
31. Virag T., Elrod D.B., Liliom K., Sardar V.M., Parrill A.L., Yokoyama K., Durgam G., Deng W., Miller D.D., and Tigyi G. Fatty alcohol phosphates are subtype-selective agonists and antagonists of lysophosphatidic acid receptors. Mol. Pharmacol. 63 5 (2003) 1032-1042
32. Sardar V.M., Bautista D.L., Fischer D.J., Yokoyama K., Nusser N., Virag T., Wang D.A., Baker D.L., Tigyi G., and Parrill A.L. Molecular basis for lysophosphatidic acid receptor antagonist selectivity. Biochim. Biophys. Acta 1582 1-3 (2002) 309-317
33. Parrill A.L., Wang D., Bautista D.L., Van Brocklyn J.R., Lorincz Z., Fischer D.J., Baker D.L., Liliom K., Spiegel S., and Tigyi G. Identification of Edg1 receptor residues that recognize sphingosine 1-phosphate. J. Biol. Chem. 275 50 (2000) 39379-39384
34. Li H., and Jensen J.H. Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: new energy gradients and molecular surface tessellation. J. Comput. Chem. 25 12 (2004) 1449-1462
35. Tanford C., and Kirkwood J.G. Theory of protein titration curves. I. General equations for impenentrable spheres. J. Am. Chem. Soc. 79 20 (1957) 5333-5339
36. Shire S.J., Hanania G.I.H., and Gurd F.R.N. Electrostatic effects in myoglobin. Hydrogen ion equilibria in sperm whale ferrimyoglobin. Biochemistry 13 14 (1974) 2967-2974
37. a, proton transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry 20 11 (1981) 3167-3177
38. a's of ionizable groups in proteins: atomic details from a continuum electrostatic model. Biochemistry 29 44 (1990) 10219-10225
39. Robitaille P.L., Robitaille P.A., Brown G.G.J., and Brown G.G. An analysis of the pH-dependent chemical-shift behavior of phosphorus-contaning metabolites. J. Magn. Reson. 92 (1991) 73-84
40. Barone V., and Cossi M. Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J. Phys. Chem. A 102 11 (1998) 1995-2001
41. Cossi M., Rega N., Scalmani G., and Barone V. Energies, structures, and electronic properties of molecules in solution with the C-PCM. J. Comput. Chem. 24 6 (2003) 669-681
42. Cances E., Mennucci B., and Tomasi J. A new integral equation formalism for the polarizable continuum model: theoretical background and applications to isotropic and anisotropic dielectrics. J. Chem. Phys. 107 8 (1997) 3032-3041
43. Schmidt M.W., Baldridge K.K., Boatz J.A., Elbert S.T., Gordon M.S., Jensen J.H., Koseki S., Matsunaga N., Nguyen K.A., Su S.J., Windus T.L., Dupuis M., and Montgomery J.A. General atomic and molecular electronic-structure system. J. Comput. Chem. 14 11 (1993) 1347-1363
44. Barone V., Cossi M., and Tomasi J. A new definition of cavities for the computation of solvation free energies by the polarizable continuum model. J. Chem. Phys. 107 8 (1997) 3210-3221
45. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Zakrzewski V.G., Montgomery Jr. J.A., Stratmann R.E., Burant J.C., Dapprich S., Millam J.M., Daniels A.D., Kudin K.N., Strain M.C., Farkas O., Tomasi J., Barone V., Cossi M., Cammi R., Mennucci B., Pomelli C., Adamo C., Clifford S., Ochterski J., Petersson G.A., Ayala P.Y., Cui Q., Morokuma K., Malick D.K., Rabuck A.D., Raghavachari K., Foresman J.B., Cioslowski J., Ortiz J.V., Baboul A.G., Stefanov B.B., Liu G., Liashenko A., Piskorz P., Komaromi I., Gomperts R., Martin R.L., Fox D.J., Keith T., Al-Laham M.A., Peng C.Y., Nanayakkara A., Gonzalez C., Challacombe M., Gill P.M.W., Johnson B.G., Chen W., Wong M.W., Andres J.L., Head-Gordon M., Replogle E.S., and Pople J.A. Gaussian 98 RA (1998), Gaussian I, Pittsburgh, PA
46. Becke A. Density-functional thermochemistry. 3. The role of exact exchange. J. Chem. Phys. 98 7 (1993) 5648-5652
47. Lee C., Yang W., and Parr R.G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B Condens. Matter 37 2 (1988) 785-789
48. Parrill A.L., Wang D.-A., Bautista D.L., Van Brocklyn J.R., Lorincz Z., Fischer D.J., Baker D.L., Liliom K., Spiegel S., and Tigyi G. Identification of Edg1 receptor residues that recognize sphingosine 1-phosphate. J. Biol. Chem. 275 50 (2000) 39379-39384
49. 4 within the endothelial differentiation gene family of receptors. Biochem. J. 389 (2005) 187-195
50. Fujiwara Y., Osborne D.A., Walker M.D., Wang D.A., Bautista D.A., Liliom K., Van Brocklyn J.R., Parrill A.L., and Tigyi G. Identification of the hydrophobic ligand binding pocket of the S1P1 receptor. J. Biol. Chem. 282 4 (2007) 2374-2385
51. Halgren T.A. Merch molecular force field. I. Basis, form, scope, parameterization, and preformance of MMFF94. J. Comput. Chem. 17 5/6 (1996) 490-519
52. a values in creatine kinase and alpha1-antitrypsin. Proteins 57 4 (2004) 799-803
53. McQuarrie D. Statistical Thermodynamics (1973), University Science Books, Mill Valley, CA
54. Tsukahara T., Tsukahara R., Yasuda S., Makarova N., Valentine W.J., Allison P., Yuan H., Baker D.L., Li Z., Bittman R., Parrill A., and Tigyi G. Different residues mediate recognition of 1-O-oleyl-lysophosphatidic acid and rosiglitazone in the ligand binding domain of PPAR1. J. Biol. Chem. (2005)
55. Brinkmann V., Davis M.D., Heise C.E., Albert R., Cottens S., Hof R., Bruns C., Prieschl E., Baumruker T., Hiestand P., Foster C.A., Zollinger M., and Lynch K.R. The immune modulator, FTY720, targets sphingosine 1-phosphate receptors. J. Biol. Chem. 277 24 (2002) 21453-21457
56. Hla T. Signaling and biological actions of sphingosine 1-phosphate. Pharmacol. Res. 47 5 (2003) 401-407
57. Matloubian M., Lo C.G., Cinamon G., Lesneski M.J., Xu Y., Brinkmann V., Allende M.L., Proia R.L., and Cyster J.G. Lymphocyte egress from thymus and peripheral lymphoid organs is dependent on S1P receptor 1. Nature 427 6972 (2004) 355-360
58. English D., Kovala A.T., Welch Z., Harvey K.A., Siddiqui R.A., Brindley D.N., and Garcia J.G.N. Induction of endothelial cell chemotaxis by sphingosine 1-phosphate and stabilization of endothelial monolayer barrier function by lysophosphatidic acid, potential mediators of hematopoietic angiogenesis. J. Hematother. Stem Cell. Res. 8 (1999) 627-634
59. 3 (EDG3). Blood 102 6 (2003) 2099-2107
60. Chae S.S., Paik J.H., Furneaux H., and Hla T. Requirement for sphingosine 1-phosphate receptor-1 in tumor angiogenesis demonstrated by in vivo RNA interference. J. Clin. Invest. 114 8 (2004) 1082-1089
61. Osborne N., and Stainier D.Y. Lipid receptors in cardiovascular development. Annu. Rev. Physiol. 65 (2003) 23-43
62. Kohno T., Matsuyuki H., Inagaki Y., and Igarashi Y. Sphingosine 1-phosphate promotes cell migration through the activation of Cdc42 in Edg-6/S1P4-expressing cells. Genes Cells 8 (2003) 685-697
63. Graler M.H., Grosse R., Kusch A., Kremmer E., Gudermann T., and Lipp M. The sphingosine 1-phosphate receptor S1P4 regulates cell shape and motility via coupling to Gi and G12/13. J. Cell. Biochem. 89 3 (2003) 507-519
64. Osada M., Yatomi Y., Ohmori T., Ikeda H., and Ozaki Y. Enhancement of sphingosine 1-phosphate-induced migration of vascular endothelial cells and smooth muscle cells by an EDG-5 antagonist. Biochem. Biophys. Res. Commun. 299 3 (2002) 483-487
65. Arikawa K., Takuwa N., Yamaguchi H., Sugimoto N., Kitayama J., Nagawa H., Takehara K., and Takuwa Y. Ligand-dependent inhibition of B16 melanoma cell migration and invasion via endogenous S1P2 G protein-coupled receptor. Requirement of inhibition of cellular RAC activity. J. Biol. Chem. 278 35 (2003) 32841-32851
66. Rosenfeldt H.M., Hobson J.P., Macyka M., Olivera A., Nava V.E., Milstien S., and Spiegel S. EDG-1 links the PDGF receptor to Src and focal adnesion kinase activation leading to lamellipodia formation and cell migration. FASEB J. 15 (2001) 2649-2659
67. Durgam G.G., Tsukahara R., Makarova N., Walker M.D., Fujiwara Y., Pigg K.R., Baker D.L., Sardar V.M., Parrill A.L., Tigyi G., and Miller D.D. Synthesis and pharmacological evaluation of second-generation phosphatidic acid derivatives as lysophosphatidic acid receptor ligands. Bioorg. Med. Chem. Lett. 16 3 (2006) 633-640
68. 1-selective in vivo-active agonists from high throughput screening: off-the-shelf chemical probes of receptor interactions, signaling and fate. Chem. Biol. 12 (2005) 703-715
69. Holdsworth G., Osborne D.A., Pham T.T., Fells J.I., Hutchinson G., Milligan G., and Parrill A.L. A single amino acid determines preference between phospholipids and reveals length restriction for activation of the S1P4 receptor. BMC Biochem. 5 1 (2004) 12
70. Virag T., Elrod D.B., Liliom K., Sardar V.M., Parrill A.L., Yokoyama K., Durgam G., Deng W., Miller D.D., and Tigyi G. Fatty alcohol phosphates are subtype-selective agonists and antagonists of LPA receptors. Mol. Pharmacol. 63 5 (2003) 1032-1042
71. Sardar V.M., Bautista D.L., Fischer D.J., Yokoyama K., Nusser N., Virag T., Wang D., Baker D.L., Tigyi G., and Parrill A.L. Molecular basis for lysophosphatidic acid receptor antagonist selectivity. Biochim. Biophys. Acta 1582 1-3 (2002) 309-317
72. Honig B., and Nicholls A. Classical electrostatics in biology and chemistry. Science 268 5214 (1995) 1144-1149
73. a. J. Am. Chem. Soc. 127 45 (2005) 15848-15861
74. Kooijman E.E., Carter K.M., van Laar E.G., Chupin V., Burger K.N., and de Kruijff B. What makes the bioactive lipids phosphatidic acid and lysophosphatidic acid so special?. Biochemistry 44 51 (2005) 17007-17015
75. Lim H.S., Oh Y.S., Suh P.G., and Chung S.K. Syntheses of sphingosine-1-phosphate stereoisomers and analogues and their interaction with EDG receptors. Bioorg. Med. Chem. Lett. 13 2 (2003) 237-240
76. Lim H.S., Park J.J., Ko K., Lee M.H., and Chung S.K. Syntheses of sphingosine-1-phosphate analogues and their interaction with EDG/S1P receptors. Bioorg. Med. Chem. Lett. 14 10 (2004) 2499-2503