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Volumn 24, Issue 12, 2014, Pages 1323-1333

Toward a robust computational screening strategy for identifying glycosaminoglycan sequences that display high specificity for target proteins

Author keywords

Glycosaminoglycans; Heparin heparan sulfate; Molecular docking; Specificity; Virtual screening

Indexed keywords

ANTITHROMBIN; DISACCHARIDE; GLYCOSAMINOGLYCAN; HEPARIN; THROMBIN; PROTEIN;

EID: 84964698250     PISSN: 09596658     EISSN: 14602423     Source Type: Journal    
DOI: 10.1093/glycob/cwu077     Document Type: Article
Times cited : (38)

References (33)
  • 1
    • 84905496054 scopus 로고    scopus 로고
    • Development and application of site mapping methods for the design of glycosaminoglycans
    • (in press)
    • Agostino M, Gandhi NS, Mancera RL. 2014. Development and application of site mapping methods for the design of glycosaminoglycans. Glycobiology (in press).
    • (2014) Glycobiology
    • Agostino, M.1    Gandhi, N.S.2    Mancera, R.L.3
  • 2
  • 3
    • 0033531628 scopus 로고    scopus 로고
    • Docking of glycosaminoglycans to heparinbinding proteins: Validation for aFGF, bFGF, and antithrombin and application to IL-8
    • Bitomsky W, Wade RC. 1999. Docking of glycosaminoglycans to heparinbinding proteins: Validation for aFGF, bFGF, and antithrombin and application to IL-8. J Am Chem Soc. 121:3004-3013.
    • (1999) J Am Chem Soc. , vol.121 , pp. 3004-3013
    • Bitomsky, W.1    Wade, R.C.2
  • 5
    • 13244270050 scopus 로고    scopus 로고
    • Crystal structure of thrombin bound to heparin
    • Carter WJ, Cama E, Huntington JA. 2005. Crystal structure of thrombin bound to heparin. J Biol Chem. 280:2745-2749.
    • (2005) J Biol Chem. , vol.280 , pp. 2745-2749
    • Carter, W.J.1    Cama, E.2    Huntington, J.A.3
  • 7
    • 1842692143 scopus 로고
    • A general definition of ring puckering
    • Cremer D, Pople JA. 1975. A general definition of ring puckering. J Am Chem Soc. 97:1354-1358.
    • (1975) J Am Chem Soc. , vol.97 , pp. 1354-1358
    • Cremer, D.1    Pople, J.A.2
  • 8
    • 84882540439 scopus 로고    scopus 로고
    • Antithrombin activation and designing novel heparin mimics
    • Garg HG, Linhardt RJ, Hales CA, editors. Amsterdam: Elsevier Science
    • Desai UR. 2005. Antithrombin activation and designing novel heparin mimics. In: Garg HG, Linhardt RJ, Hales CA, editors. Chemistry and Biology of Heparin and Heparan Sulfate. Amsterdam: Elsevier Science. p. 483-512.
    • (2005) Chemistry and Biology of Heparin and Heparan Sulfate , pp. 483-512
    • Desai, U.R.1
  • 9
    • 84881538094 scopus 로고    scopus 로고
    • The promise of sulfated synthetic small molecules as modulators of glycosaminoglycan function
    • Desai UR. 2013. The promise of sulfated synthetic small molecules as modulators of glycosaminoglycan function. Future Med Chem. 5:1363-1366.
    • (2013) Future Med Chem. , vol.5 , pp. 1363-1366
    • Desai, U.R.1
  • 10
    • 0032571333 scopus 로고    scopus 로고
    • Mechanism of heparin activation of antithrombin. Role of individual residues of the pentasaccharide activating sequence in the recognition of native and activated states of antithrombin
    • Desai UR, Petitou M, Bjork I, Olson ST. 1998. Mechanism of heparin activation of antithrombin. Role of individual residues of the pentasaccharide activating sequence in the recognition of native and activated states of antithrombin. J Biol Chem. 273:7478-7487.
    • (1998) J Biol Chem. , vol.273 , pp. 7478-7487
    • Desai, U.R.1    Petitou, M.2    Bjork, I.3    Olson, S.T.4
  • 11
    • 0035997376 scopus 로고    scopus 로고
    • Order out of chaos: Assembly of ligand binding sites in heparan sulfate
    • Esko JD, Selleck SB. 2002. Order out of chaos: Assembly of ligand binding sites in heparan sulfate. Annu Rev Biochem. 71:435-471.
    • (2002) Annu Rev Biochem. , vol.71 , pp. 435-471
    • Esko, J.D.1    Selleck, S.B.2
  • 12
    • 0027578413 scopus 로고
    • Molecular dynamics study of iduronate ring conformations
    • Forster MJ, Mulloy B. 1993. Molecular dynamics study of iduronate ring conformations. Biopolymers. 33:575-588.
    • (1993) Biopolymers. , vol.33 , pp. 575-588
    • Forster, M.J.1    Mulloy, B.2
  • 13
    • 56649100319 scopus 로고    scopus 로고
    • The structure of glycosaminoglycans and their interactions with proteins
    • Gandhi NS, Mancera RL. 2008. The structure of glycosaminoglycans and their interactions with proteins. Chem Biol Drug Des. 72:455-482.
    • (2008) Chem Biol Drug Des. , vol.72 , pp. 455-482
    • Gandhi, N.S.1    Mancera, R.L.2
  • 14
    • 0025764198 scopus 로고
    • Constructing a molecular model of the interaction between antithrombin III and a potent heparin analogue
    • Grootenhuis PDJ, van Boeckel CAA. 1991. Constructing a molecular model of the interaction between antithrombin III and a potent heparin analogue. J Am Chem Soc. 113:2743-2747.
    • (1991) J Am Chem Soc. , vol.113 , pp. 2743-2747
    • Grootenhuis, P.D.J.1    Van-Boeckel, C.A.A.2
  • 15
    • 84871422681 scopus 로고    scopus 로고
    • An unusual antithrombin-binding heparin octasaccharide with an additional 3-O-sulfated glucosamine in the active pentasaccharide sequence
    • Guerrini M, Elli S, Mourier P, Rudd TR, Gaudesi D, Casu B, Boudier C, Torri G, Viskov C. 2013. An unusual antithrombin-binding heparin octasaccharide with an additional 3-O-sulfated glucosamine in the active pentasaccharide sequence. Biochem J. 449:343-351.
    • (2013) Biochem J. , vol.449 , pp. 343-351
    • Guerrini, M.1    Elli, S.2    Mourier, P.3    Rudd, T.R.4    Gaudesi, D.5    Casu, B.6    Boudier, C.7    Torri, G.8    Viskov, C.9
  • 17
    • 33646581724 scopus 로고    scopus 로고
    • Antithrombin-S195A factor Xa-heparin structure reveals the allosteric mechanism of antithrombin activation
    • Johnson DJ, Li W, Adams TE, Huntington JA. 2006. Antithrombin-S195A factor Xa-heparin structure reveals the allosteric mechanism of antithrombin activation. EMBO J. 25:2029-2037.
    • (2006) EMBO J. , vol.25 , pp. 2029-2037
    • Johnson, D.J.1    Li, W.2    Adams, T.E.3    Huntington, J.A.4
  • 18
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones G, Willett P, Glen RC, Leach AR, Taylor R. 1997. Development and validation of a genetic algorithm for flexible docking. J Mol Biol. 267:727-748.
    • (1997) J Mol Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 20
    • 8844263008 scopus 로고    scopus 로고
    • Docking and scoring in virtual screening for drug discovery: Methods and applications
    • Kitchen DB, Decornez H, Furr JR, Bajorath J. 2004. Docking and scoring in virtual screening for drug discovery: Methods and applications. Nat Rev Drug Disc. 3:935-949.
    • (2004) Nat Rev Drug Disc. , vol.3 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Furr, J.R.3    Bajorath, J.4
  • 21
    • 4344590703 scopus 로고    scopus 로고
    • Structure of the antithrombin-thrombin-heparin ternary complex reveals the antithrombotic mechanism of heparin
    • Li W, Johnson DJ, Esmon CT, Huntington JA. 2004. Structure of the antithrombin-thrombin-heparin ternary complex reveals the antithrombotic mechanism of heparin. Nat Struct Mol Biol. 11:857-862.
    • (2004) Nat Struct Mol Biol. , vol.11 , pp. 857-862
    • Li, W.1    Johnson, D.J.2    Esmon, C.T.3    Huntington, J.A.4
  • 22
    • 0025059489 scopus 로고
    • Structure of a dermatan sulfate hexasaccharide that binds to heparin cofactor II with high affinity
    • Maimone MM, Tollefsen DM. 1990. Structure of a dermatan sulfate hexasaccharide that binds to heparin cofactor II with high affinity. J Biol Chem. 265:18263-18271.
    • (1990) J Biol Chem. , vol.265 , pp. 18263-18271
    • Maimone, M.M.1    Tollefsen, D.M.2
  • 23
    • 0037459052 scopus 로고    scopus 로고
    • Structure of beta-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity
    • McCoy AJ, Pei XY, Skinner R, Abrahams JP, Carrell RW. 2003. Structure of beta-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity. J Mol Biol. 326:823-833.
    • (2003) J Mol Biol. , vol.326 , pp. 823-833
    • McCoy, A.J.1    Pei, X.Y.2    Skinner, R.3    Abrahams, J.P.4    Carrell, R.W.5
  • 24
    • 84869073602 scopus 로고    scopus 로고
    • On the specificity of heparin/heparan sulfate binding to proteins. Anion-binding sites on antithrombin and thrombin are fundamentally different
    • Mosier PD, Krishnasamy C, Kellogg GE, Desai UR. 2012. On the specificity of heparin/heparan sulfate binding to proteins. Anion-binding sites on antithrombin and thrombin are fundamentally different. PLoS ONE. 7:e48632.
    • (2012) PLoS ONE , vol.7 , pp. e48632
    • Mosier, P.D.1    Krishnasamy, C.2    Kellogg, G.E.3    Desai, U.R.4
  • 25
    • 0033650826 scopus 로고    scopus 로고
    • Conformation and dynamics of heparin and heparan sulfate
    • Mulloy B, Forster MJ. 2000. Conformation and dynamics of heparin and heparan sulfate. Glycobiology. 10:1147-1156.
    • (2000) Glycobiology. , vol.10 , pp. 1147-1156
    • Mulloy, B.1    Forster, M.J.2
  • 26
    • 0025730441 scopus 로고
    • Quantitative characterization of the thrombin-heparin interaction. Discrimination between specific and nonspecific binding models
    • Olson ST, Halvorson HR, Björk I. 1991. Quantitative characterization of the thrombin-heparin interaction. Discrimination between specific and nonspecific binding models. J Biol Chem. 266:6342-6352.
    • (1991) J Biol Chem. , vol.266 , pp. 6342-6352
    • Olson, S.T.1    Halvorson, H.R.2    Björk, I.3
  • 27
    • 0031002162 scopus 로고    scopus 로고
    • A unique trisaccharide sequence in heparin mediates the early step of antithrombin III activation
    • Petitou M, Barzu T, Herault JP, Herbert JM. 1997. A unique trisaccharide sequence in heparin mediates the early step of antithrombin III activation. Glycobiology. 7:323-327.
    • (1997) Glycobiology. , vol.7 , pp. 323-327
    • Petitou, M.1    Barzu, T.2    Herault, J.P.3    Herbert, J.M.4
  • 28
    • 26244432935 scopus 로고    scopus 로고
    • Control of the coagulation system by serpins. Getting by with a little help from glycosaminoglycans
    • Pike RN, Buckle AM, le Bonniec BF, Church FC. 2005. Control of the coagulation system by serpins. Getting by with a little help from glycosaminoglycans. FEBS J. 272:4842-4851.
    • (2005) FEBS J. , vol.272 , pp. 4842-4851
    • Pike, R.N.1    Buckle, A.M.2    Le-Bonniec, B.F.3    Church, F.C.4
  • 29
    • 44249097241 scopus 로고    scopus 로고
    • Depiction of the forces participating in the 2-O-sulfo-alpha-L-iduronic acid conformational preference in heparin sequences in aqueous solutions
    • Pol-Fachin L, Verli H. 2008. Depiction of the forces participating in the 2-O-sulfo-alpha-L-iduronic acid conformational preference in heparin sequences in aqueous solutions. Carbohydr Res. 343:1435-1445.
    • (2008) Carbohydr Res. , vol.343 , pp. 1435-1445
    • Pol-Fachin, L.1    Verli, H.2
  • 30
    • 33745119433 scopus 로고    scopus 로고
    • Finding a needle in a haystack: Development of a combinatorial virtual screening approach for identifying high specificity heparin/heparan sulfate sequence(s)
    • Raghuraman A, Mosier PD, Desai UR. 2006. Finding a needle in a haystack: Development of a combinatorial virtual screening approach for identifying high specificity heparin/heparan sulfate sequence(s). J Med Chem. 49: 3553-3562.
    • (2006) J Med Chem. , vol.49 , pp. 3553-3562
    • Raghuraman, A.1    Mosier, P.D.2    Desai, U.R.3
  • 31
    • 77956521262 scopus 로고    scopus 로고
    • Understanding dermatan sulfateheparin cofactor II interaction through virtual library screening
    • Raghuraman A, Mosier PD, Desai UR. 2010. Understanding dermatan sulfateheparin cofactor II interaction through virtual library screening. ACS Med Chem Lett. 1:281-285.
    • (2010) ACS Med Chem Lett. , vol.1 , pp. 281-285
    • Raghuraman, A.1    Mosier, P.D.2    Desai, U.R.3
  • 33
    • 0028922586 scopus 로고
    • LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
    • Wallace AC, Laskowski RA, Thornton JM. 1995. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8:127-134.
    • (1995) Protein Eng. , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3


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