메뉴 건너뛰기




Volumn 2, Issue JUN, 2011, Pages

A computational approach for exploring carbohydrate recognition by lectins in innate immunity

Author keywords

Carbohydrates; Lectins; Molecular docking; Molecular modeling

Indexed keywords


EID: 84859956034     PISSN: None     EISSN: 16643224     Source Type: Journal    
DOI: 10.3389/fimmu.2011.00023     Document Type: Article
Times cited : (17)

References (48)
  • 1
    • 57549092709 scopus 로고    scopus 로고
    • In silico mutagenesis and docking studies of Pseudomonas aeruginosa PA-IIL lectin - predicting binding modes and energies
    • Adam, J., Kfiz, Z., Prokop, M., Wim-merová, M., and Koca, J. (2008). In silico mutagenesis and docking studies of Pseudomonas aeruginosa PA-IIL lectin - predicting binding modes and energies. J. Chem. Inf. Model. 48, 2234-2242.
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 2234-2242
    • Adam, J.1    Kfiz, Z.2    Prokop, M.3    Wim-merová, M.4    Koca, J.5
  • 2
    • 73349128445 scopus 로고    scopus 로고
    • Molecular docking of carbohydrate ligands to antibodies: structural validation against crystal structures
    • Agostino, M., Jene, C., Boyle, T., Ram-sland, P. A., and Yuriev, E. (2009a). Molecular docking of carbohydrate ligands to antibodies: structural validation against crystal structures. J. Chem. Inf. Model. 49, 2749-2760.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 2749-2760
    • Agostino, M.1    Jene, C.2    Boyle, T.3    Ram-sland, P.A.4    Yuriev, E.5
  • 3
    • 70450242830 scopus 로고    scopus 로고
    • In silico analysis of antibody-carbohydrate interactions and its application to xenore-active antibodies
    • Agostino, M., Sandrin, M. S., Thompson, P. E., Yuriev, E., and Rams-land, P. A. (2009b). In silico analysis of antibody-carbohydrate interactions and its application to xenore-active antibodies. Mol. Immunol. 47, 233-246.
    • (2009) Mol. Immunol. , vol.47 , pp. 233-246
    • Agostino, M.1    Sandrin, M.S.2    Thompson, P.E.3    Yuriev, E.4    Rams-land, P.A.5
  • 4
    • 79960669494 scopus 로고    scopus 로고
    • Peptide inhibitors of xenoreactive antibodies mimic the interaction profile of the native carbohydrate antigens
    • Agostino, M., Sandrin, M. S., Thompson, P. E., Ramsland, P. A., and Yuriev, E. (2011). Peptide inhibitors of xenoreactive antibodies mimic the interaction profile of the native carbohydrate antigens. Biopolymers 96,193-206.
    • (2011) Biopolymers , vol.96 , pp. 193-206
    • Agostino, M.1    Sandrin, M.S.2    Thompson, P.E.3    Ramsland, P.A.4    Yuriev, E.5
  • 5
    • 77952842605 scopus 로고    scopus 로고
    • Identification of preferred carbohydrate binding modes in xenoreactive antibodies by combining conformational filters and binding site maps
    • Agostino, M., Sandrin, M. S., Thompson, P. E., Yuriev, E., and Ramsland, P. A. (2010). Identification of preferred carbohydrate binding modes in xenoreactive antibodies by combining conformational filters and binding site maps. Glycobiology 20, 724-735.
    • (2010) Glycobiology , vol.20 , pp. 724-735
    • Agostino, M.1    Sandrin, M.S.2    Thompson, P.E.3    Yuriev, E.4    Ramsland, P.A.5
  • 7
    • 78650486115 scopus 로고    scopus 로고
    • Comparing experimental and computational alanine scanning techniques for probing a prototypical protein-protein interaction
    • Bradshaw, R. T., Patel, B. H., Tate, E. W., Leatherbarrow, R. J., and Gould, I.R. (2011). Comparing experimental and computational alanine scanning techniques for probing a prototypical protein-protein interaction. Protein Eng. Des. Sel. 24, 197-207.
    • (2011) Protein Eng. Des. Sel. , vol.24 , pp. 197-207
    • Bradshaw, R.T.1    Patel, B.H.2    Tate, E.W.3    Leatherbarrow, R.J.4    Gould, I.R.5
  • 8
    • 33947602811 scopus 로고    scopus 로고
    • Siglecs and their role in the immune system
    • Crocker, P. R., Paulson, J. C., and Varki, A. (2007). Siglecs and their role in the immune system. Nat. Rev. Immunol. 7, 255-266.
    • (2007) Nat. Rev. Immunol. , vol.7 , pp. 255-266
    • Crocker, P.R.1    Paulson, J.C.2    Varki, A.3
  • 9
    • 65249118801 scopus 로고    scopus 로고
    • Recognition of man-nosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343
    • Crouch, E., Hartshorn, K., Horlacher, T., Mcdonald, B., Smith, K., Cafarella, T., Seaton, B., Seeberger, P. H., and Head, J. (2009). Recognition of man-nosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Biochemistry 48, 3335-3345.
    • (2009) Biochemistry , vol.48 , pp. 3335-3345
    • Crouch, E.1    Hartshorn, K.2    Horlacher, T.3    Mcdonald, B.4    Smith, K.5    Cafarella, T.6    Seaton, B.7    Seeberger, P.H.8    Head, J.9
  • 10
    • 33745820282 scopus 로고    scopus 로고
    • Contributions of pheny-lalanine 335 to ligand recognition by human surfactant protein D: ring interactions with SP-D ligands
    • Crouch, E., Mcdonald, B., Smith, K., Cafarella, T., Seaton, B., and Head, J. (2006). Contributions of pheny-lalanine 335 to ligand recognition by human surfactant protein D: ring interactions with SP-D ligands. J. Biol. Chem. 281, 18008-18014.
    • (2006) J. Biol. Chem. , vol.281 , pp. 18008-18014
    • Crouch, E.1    Mcdonald, B.2    Smith, K.3    Cafarella, T.4    Seaton, B.5    Head, J.6
  • 11
    • 77949890193 scopus 로고    scopus 로고
    • Lectins as pattern recognition molecules: the effects of epitope density in innate immunity
    • Dam, T. K., and Brewer, C. E (2010). Lectins as pattern recognition molecules: the effects of epitope density in innate immunity. Glycobiology 20, 270-279.
    • (2010) Glycobiology , vol.20 , pp. 270-279
    • Dam, T.K.1    Brewer, C.E.2
  • 13
    • 67650077384 scopus 로고    scopus 로고
    • Docking ligands into flexible and solvated macromolecules 4 Are popular scoring functions accurate for this class of pro teins?
    • Englebienne, P., and Moitessier, N. (2009). Docking ligands into flexible and solvated macromolecules. 4 Are popular scoring functions accurate for this class of pro teins? J. Chem. Inf. Model. 49, 1568-1580.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1568-1580
    • Englebienne, P.1    Moitessier, N.2
  • 14
    • 70450187110 scopus 로고    scopus 로고
    • A possible role for metallic ions in the carbohydrate cluster recognition displayed by a Lewis Y specific antibody
    • doi: 10.1371/jour-nal.pone.0007777
    • Farrugia, W., Scott, A. M., and Ramsland, P. A. (2009). A possible role for metallic ions in the carbohydrate cluster recognition displayed by a Lewis Y specific antibody. PLoS ONE 4, e7777. doi: 10.1371/jour-nal.pone.0007777.
    • (2009) PLoS ONE , vol.4
    • Farrugia, W.1    Scott, A.M.2    Ramsland, P.A.3
  • 15
    • 33947493929 scopus 로고    scopus 로고
    • Multiple modes of binding enhance the affinity of DC-SIGN for high mannose N-linked glycans found on viral gly-coproteins
    • Feinberg, H., Castelli, R., Drickamer, K., Seeberger, P. H., and Weis, W. I. (2007). Multiple modes of binding enhance the affinity of DC-SIGN for high mannose N-linked glycans found on viral gly-coproteins. J. Biol. Chem. 282, 4202-4209.
    • (2007) J. Biol. Chem. , vol.282 , pp. 4202-4209
    • Feinberg, H.1    Castelli, R.2    Drickamer, K.3    Seeberger, P.H.4    Weis, W.I.5
  • 16
    • 79251601252 scopus 로고    scopus 로고
    • Structural basis for langerin recognition of diverse pathogen and mammalian glycans through a sin gle binding site
    • Feinberg, H., Taylor, M. E., Razi, H., Mcbride, R., Knirel, Y. A., Graham, S.A., Drickamer, K., and Weis, W. I. (2011). Structural basis for langerin recognition of diverse pathogen and mammalian glycans through a sin gle binding site. J. Mol. Biol. 405, 1027-1039.
    • (2011) J. Mol. Biol. , vol.405 , pp. 1027-1039
    • Feinberg, H.1    Taylor, M.E.2    Razi, H.3    Mcbride, R.4    Knirel, Y.A.5    Graham, S.A.6    Drickamer, K.7    Weis, W.I.8
  • 18
    • 59149102062 scopus 로고    scopus 로고
    • Glycans: bioactive signals decoded by lectins
    • Gabius, H.-J. (2008). Glycans: bioactive signals decoded by lectins. Biochem. Soc. Trans. 36, 1491-1496.
    • (2008) Biochem. Soc. Trans. , vol.36 , pp. 1491-1496
    • Gabius, H.-J.1
  • 20
    • 78349279980 scopus 로고    scopus 로고
    • Inhibition of HIV-1 entry: multiple keys to close the door
    • Hertje, M., Zhou, M., and Dietrich, U. (2010). Inhibition of HIV-1 entry: multiple keys to close the door. ChemMedChem 5,1825-1835.
    • (2010) ChemMedChem , vol.5 , pp. 1825-1835
    • Hertje, M.1    Zhou, M.2    Dietrich, U.3
  • 21
    • 60049091638 scopus 로고    scopus 로고
    • The flexibility of the LeaLex tumor associated antigen central fragment studied by systematic and stochastic searches as well as dynamic simulations
    • Jackson, T. A., Robertson, V., Imberty, A., and Auzanneau, F.-I. (2009). The flexibility of the LeaLex tumor associated antigen central fragment studied by systematic and stochastic searches as well as dynamic simulations. Bioorg. Med. Chem. 17, 1514-1526.
    • (2009) Bioorg. Med. Chem. , vol.17 , pp. 1514-1526
    • Jackson, T.A.1    Robertson, V.2    Imberty, A.3    Auzanneau, F.-I.4
  • 22
    • 65549153845 scopus 로고    scopus 로고
    • C-type lectins and phagocytosis
    • Kerrigan, A. M., and Brown, G. D. (2009). C-type lectins and phagocytosis. Immunobiology 214, 562-575.
    • (2009) Immunobiology , vol.214 , pp. 562-575
    • Kerrigan, A.M.1    Brown, G.D.2
  • 23
    • 3242879771 scopus 로고    scopus 로고
    • Computational alanine scanning of protein-protein interfaces
    • Kortemme, T., Kim, D. E., and Baker, D. (2004). Computational alanine scanning of protein-protein interfaces. Sci. STKE 2004, pl2.
    • (2004) Sci. STKE , vol.2004
    • Kortemme, T.1    Kim, D.E.2    Baker, D.3
  • 25
    • 0003012148 scopus 로고    scopus 로고
    • How water provides the impetus for molecular recognition in aqueous solution
    • Lemieux, R. U. (1996). How water provides the impetus for molecular recognition in aqueous solution. Acc. Chem. Res. 29, 373-380.
    • (1996) Acc. Chem. Res. , vol.29 , pp. 373-380
    • Lemieux, R.U.1
  • 26
  • 28
    • 5144232009 scopus 로고    scopus 로고
    • Growth-regulatory human galectin-1: crystallographic characterisation of the structural changes induced by single-site mutations and their impact on the thermodynamics of ligand binding
    • López-Lucendo, M. F., Solís, D., André, S., Hirabayashi, J., Kasai, K., Kaltner, H., Gabius, H.-J., and Romero, A. (2004). Growth-regulatory human galectin-1: crystallographic characterisation of the structural changes induced by single-site mutations and their impact on the thermodynamics of ligand binding. J. Mol. Biol. 343, 957-970.
    • (2004) J. Mol. Biol. , vol.343 , pp. 957-970
    • López-Lucendo, M.F.1    Solís, D.2    André, S.3    Hirabayashi, J.4    Kasai, K.5    Kaltner, H.6    Gabius, H.-J.7    Romero, A.8
  • 29
    • 0033587105 scopus 로고    scopus 로고
    • The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: heat-labile enterotoxin, a multivalent test case
    • Minke, W. E., Diller, D. J., Hol, W. G. J., and Verlinde, C. L. M. J. (1999). The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: heat-labile enterotoxin, a multivalent test case. J. Med. Chem. 42, 1778-1788.
    • (1999) J. Med. Chem. , vol.42 , pp. 1778-1788
    • Minke, W.E.1    Diller, D.J.2    Hol, W.G.J.3    Verlinde, C.L.M.J.4
  • 30
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris, G. M., Goodsell, D. S., Hal-liday, R. S., Huey, R., Hart, W. E., Belew, R. K., and Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19, 1639-1662.
    • (1998) J. Comput. Chem. , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Hal-liday, R.S.3    Huey, R.4    Hart, W.E.5    Belew, R.K.6    Olson, A.J.7
  • 32
    • 46049089604 scopus 로고    scopus 로고
    • Comparison of docking methods for carbohydrate binding in calcium-dependent lectins and prediction of the carbohydrate binding mode to sea cucumber lectin CEL-III
    • Nurisso, A., Kozmon, S., and Imberty, A. (2008). Comparison of docking methods for carbohydrate binding in calcium-dependent lectins and prediction of the carbohydrate binding mode to sea cucumber lectin CEL-III. Mol. Simul. 34, 469-479.
    • (2008) Mol. Simul. , vol.34 , pp. 469-479
    • Nurisso, A.1    Kozmon, S.2    Imberty, A.3
  • 33
    • 67349258025 scopus 로고    scopus 로고
    • Turning sweet on immunity: galectin-glycan interactions in immune tolerance and inflammation
    • Rabinovich, G. A., and Toscano, M. A. (2009). Turning sweet on immunity: galectin-glycan interactions in immune tolerance and inflammation. Nat. Rev. Immunol. 9, 338-352.
    • (2009) Nat. Rev. Immunol. , vol.9 , pp. 338-352
    • Rabinovich, G.A.1    Toscano, M.A.2
  • 34
    • 3042561937 scopus 로고    scopus 로고
    • Structural convergence of antibody binding of carbohydrate determinants in Lewis Y tumor antigens
    • Ramsland, P. A., Farrugia, W., Bradford, T. M., Hogarth, P. M., and Scott, A. M. (2004). Structural convergence of antibody binding of carbohydrate determinants in Lewis Y tumor antigens. J. Mol. Biol. 340, 809-818.
    • (2004) J. Mol. Biol. , vol.340 , pp. 809-818
    • Ramsland, P.A.1    Farrugia, W.2    Bradford, T.M.3    Hogarth, P.M.4    Scott, A.M.5
  • 35
    • 0034257149 scopus 로고    scopus 로고
    • Automated docking of alpha-(1 -> 4)- and alpha-(1 ->6)-linked glucosyl trisaccha-rides and maltopentaose into the soybean beta-amylase active site
    • Rockey, W. M., Laederach, A., and Reilly, P. J. (2000). Automated docking of alpha-(1 -> 4)- and alpha-(1 ->6)-linked glucosyl trisaccha-rides and maltopentaose into the soybean beta-amylase active site. Proteins 40,299-309.
    • (2000) Proteins , vol.40 , pp. 299-309
    • Rockey, W.M.1    Laederach, A.2    Reilly, P.J.3
  • 36
    • 67649774331 scopus 로고    scopus 로고
    • Galectins in innate immunity: dual functions of host soluble β-galactoside-binding lectins as damage-associated molecular patterns (DAMPs) and as receptors for pathogen-associated molecular patterns (PAMPs)
    • Sato, S., St-Pierre, C., Bhaumik, P., and Nieminen, J. (2009). Galectins in innate immunity: dual functions of host soluble β-galactoside-binding lectins as damage-associated molecular patterns (DAMPs) and as receptors for pathogen-associated molecular patterns (PAMPs). Immunol. Rev. 230, 172-187.
    • (2009) Immunol. Rev. , vol.230 , pp. 172-187
    • Sato, S.1    St-Pierre, C.2    Bhaumik, P.3    Nieminen, J.4
  • 37
    • 0042349565 scopus 로고    scopus 로고
    • High-resolution structural insights into ligand binding and immune cell recognition by human lung surfactant protein D
    • Shrive, A. K., Tharia, H. A., Strong, P., Kishore, U., Burns, I., Rizkallah, P. J., Reid, K. B. M., and Green-hough, T. J. (2003). High-resolution structural insights into ligand binding and immune cell recognition by human lung surfactant protein D. J. Mol. Biol. 331, 509-523.
    • (2003) J. Mol. Biol. , vol.331 , pp. 509-523
    • Shrive, A.K.1    Tharia, H.A.2    Strong, P.3    Kishore, U.4    Burns, I.5    Rizkallah, P.J.6    Reid, K.B.M.7    Green-hough, T.J.8
  • 38
    • 13644272606 scopus 로고    scopus 로고
    • Structural and thermodynamic studies on cation- π interactions in lectin-ligand complexes: high-affinity galectin-3 inhibitors through fine-tuning of an arginine-arene interaction
    • Sörme, P., Arnoux, P., Kahl-Knutsson, B., Leffler, H., Rini, J. M., and Nilsson, U. J. (2005). Structural and thermodynamic studies on cation- π interactions in lectin-ligand complexes: high-affinity galectin-3 inhibitors through fine-tuning of an arginine-arene interaction. J. Am. Chem. Soc. 127, 1737-1743.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 1737-1743
    • Sörme, P.1    Arnoux, P.2    Kahl-Knutsson, B.3    Leffler, H.4    Rini, J.M.5    Nilsson, U.J.6
  • 39
    • 77952239985 scopus 로고    scopus 로고
    • Langerin functions as an antiviral receptor on Langer-hans cells
    • Van Der Vlist, M., and Geijtenbeek, T. B. H. (2010). Langerin functions as an antiviral receptor on Langer-hans cells. Immunol. Cell Biol. 88, 410-415.
    • (2010) Immunol. Cell Biol. , vol.88 , pp. 410-415
    • Van Der Vlist, M.1    Geijtenbeek, T.B.H.2
  • 40
    • 33750014560 scopus 로고    scopus 로고
    • Solvated docking: introducing water into the modelling of bio-molecular complexes
    • Van Dijk, A. D. J., and Bonvin, A. M. J. J. (2006). Solvated docking: introducing water into the modelling of bio-molecular complexes. Bioinformatics 22,2340-2347.
    • (2006) Bioinformatics , vol.22 , pp. 2340-2347
    • Van Dijk, A.D.J.1    Bonvin, A.M.J.J.2
  • 43
    • 70350041296 scopus 로고    scopus 로고
    • Paths reunited: initiation of the classical and lectin pathways of complement activation
    • Wallis, R., Mitchell, D. A., Schmid, R., Schwaeble, W. J., and Keeble, A. H. (2010). Paths reunited: initiation of the classical and lectin pathways of complement activation. Immunobi-ology 215, 1-11.
    • (2010) Immunobi-ology , vol.215 , pp. 1-11
    • Wallis, R.1    Mitchell, D.A.2    Schmid, R.3    Schwaeble, W.J.4    Keeble, A.H.5
  • 45
    • 79952181220 scopus 로고    scopus 로고
    • Challenges and advances in computational docking: 2009 in review
    • Yuriev, E., Agostino, M., and Ramsland, P. A. (2011). Challenges and advances in computational docking: 2009 in review. J. Mol. Recognit. 24, 149-164.
    • (2011) J. Mol. Recognit. , vol.24 , pp. 149-164
    • Yuriev, E.1    Agostino, M.2    Ramsland, P.A.3
  • 46
    • 22944433255 scopus 로고    scopus 로고
    • Three-dimensional structures of carbohydrate determinants of Lewis system antigens: implications for effective antibody targeting of cancer
    • Yuriev, E., Farrugia, W., Scott, A. M., and Ramsland, P. A. (2005). Three-dimensional structures of carbohydrate determinants of Lewis system antigens: implications for effective antibody targeting of cancer. Immunol. Cell Biol. 83, 709-717.
    • (2005) Immunol. Cell Biol. , vol.83 , pp. 709-717
    • Yuriev, E.1    Farrugia, W.2    Scott, A.M.3    Ramsland, P.A.4
  • 47
    • 0034958059 scopus 로고    scopus 로고
    • Docking of combinatorial peptide libraries into a broadly cross-reactive human IgM
    • Yuriev, E., Ramsland, P. A., and Edmundson, A. B. (2001). Docking of combinatorial peptide libraries into a broadly cross-reactive human IgM. J. Mol. Recognit. 14,172-184.
    • (2001) J. Mol. Recognit. , vol.14 , pp. 172-184
    • Yuriev, E.1    Ramsland, P.A.2    Edmundson, A.B.3
  • 48
    • 46049119803 scopus 로고    scopus 로고
    • Antibody-ligand docking: insights into peptide-carbohydrate mimicry
    • Yuriev, E., Sandrin, M. S., and Ramsland, P. A. (2008). Antibody-ligand docking: insights into peptide-carbohydrate mimicry. Mol. Simul. 34,461-468.
    • (2008) Mol. Simul. , vol.34 , pp. 461-468
    • Yuriev, E.1    Sandrin, M.S.2    Ramsland, P.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.