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. 1996 Aug;5(8):1466–1476. doi: 10.1002/pro.5560050803

Differences in hydropathic properties of ligand binding at four independent sites in wheat germ agglutinin-oligosaccharide crystal complexes.

C S Wright 1, G E Kellogg 1
PMCID: PMC2143479  PMID: 8844838

Abstract

The binding interactions of N-acetyl-D-neuraminic acid and N,N' diacetyl-chitobiose (GlcNAc-beta-1,4-GlcNAc), observed in crystal complexes of wheat germ agglutinin (WGA) at four independent sites/monomer, were analyzed and compared with the modeling program HINT (Hydropathic INTeractions). This empirical method allows assessment of relative ligand binding strength and is particularly applicable to cases of weak binding where experimental data is absent. Although the four WGA binding sites are interrelated by a fourfold sequence repeat (eight sites/dimer), similarity extends only to the presence of an aromatic amino acid-rich pocket and a conserved serine. Strong binding requires additional interactions from a contacting domain in the second subunit. Ligand positions were either derived from crystal structures and further optimized by modeling and molecular mechanics, or from comparative modeling. Analysis of the overall HINT binding scores for the two types of ligands are consistent with the presence of two high-affinity and two low-affinity sites per monomer. Identity of these sites correlates well with crystal structure occupancies. The high-affinity sites are roughly equivalent, as predicted from solution binding studies. Binding scores for the low-affinity sites are weaker by at least a factor of two. Quantitative estimates for polar, nonpolar, and ionic interactions revealed that H-bonding makes the largest contribution to complex stabilization in the seven bound configurations, consistent with published thermodynamic data. Although the observed nonpolar interactions are small, they may play a critical role in orienting the ligand optimally.

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Selected References

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  1. AUB J. C., TIESLAU C., LANKESTER A. REACTIONS OF NORMAL AND TUMOR CELL SURFACES TO ENZYMES. I. WHEAT-GERM LIPASE AND ASSOCIATED MUCOPOLYSACCHARIDES. Proc Natl Acad Sci U S A. 1963 Oct;50:613–619. doi: 10.1073/pnas.50.4.613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Abraham D. J., Kellogg G. E. The effect of physical organic properties on hydrophobic fields. J Comput Aided Mol Des. 1994 Feb;8(1):41–49. doi: 10.1007/BF00124348. [DOI] [PubMed] [Google Scholar]
  3. Abraham D. J., Leo A. J. Extension of the fragment method to calculate amino acid zwitterion and side chain partition coefficients. Proteins. 1987;2(2):130–152. doi: 10.1002/prot.340020207. [DOI] [PubMed] [Google Scholar]
  4. Bains G., Lee R. T., Lee Y. C., Freire E. Microcalorimetric study of wheat germ agglutinin binding to N-acetylglucosamine and its oligomers. Biochemistry. 1992 Dec 22;31(50):12624–12628. doi: 10.1021/bi00165a012. [DOI] [PubMed] [Google Scholar]
  5. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  6. Bourne Y., Bolgiano B., Liao D. I., Strecker G., Cantau P., Herzberg O., Feizi T., Cambillau C. Crosslinking of mammalian lectin (galectin-1) by complex biantennary saccharides. Nat Struct Biol. 1994 Dec;1(12):863–870. doi: 10.1038/nsb1294-863. [DOI] [PubMed] [Google Scholar]
  7. Burger M. M. A difference in the architecture of the surface membrane of normal and virally transformed cells. Proc Natl Acad Sci U S A. 1969 Mar;62(3):994–1001. doi: 10.1073/pnas.62.3.994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dessen A., Gupta D., Sabesan S., Brewer C. F., Sacchettini J. C. X-ray crystal structure of the soybean agglutinin cross-linked with a biantennary analog of the blood group I carbohydrate antigen. Biochemistry. 1995 Apr 18;34(15):4933–4942. doi: 10.1021/bi00015a004. [DOI] [PubMed] [Google Scholar]
  9. Gussio R., Pattabiraman N., Zaharevitz D. W., Kellogg G. E., Topol I. A., Rice W. G., Schaeffer C. A., Erickson J. W., Burt S. K. All-atom models for the non-nucleoside binding site of HIV-1 reverse transcriptase complexed with inhibitors: a 3D QSAR approach. J Med Chem. 1996 Apr 12;39(8):1645–1650. doi: 10.1021/jm9508088. [DOI] [PubMed] [Google Scholar]
  10. Hester G., Kaku H., Goldstein I. J., Wright C. S. Structure of mannose-specific snowdrop (Galanthus nivalis) lectin is representative of a new plant lectin family. Nat Struct Biol. 1995 Jun;2(6):472–479. doi: 10.1038/nsb0695-472. [DOI] [PubMed] [Google Scholar]
  11. Kronis K. A., Carver J. P. Specificity of isolectins of wheat germ agglutinin for sialyloligosaccharides: a 360-MHz proton nuclear magnetic resonance binding study. Biochemistry. 1982 Jun 22;21(13):3050–3057. doi: 10.1021/bi00256a003. [DOI] [PubMed] [Google Scholar]
  12. Kronis K. A., Carver J. P. Thermodynamics of wheat germ agglutinin-sialyloligosaccharide interactions by proton nuclear magnetic resonance. Biochemistry. 1985 Feb 12;24(4):834–840. doi: 10.1021/bi00325a004. [DOI] [PubMed] [Google Scholar]
  13. Kronis K. A., Carver J. P. Wheat germ agglutinin dimers bind sialyloligosaccharides at four sites in solution: proton nuclear magnetic resonance temperature studies at 360 MHz. Biochemistry. 1985 Feb 12;24(4):826–833. doi: 10.1021/bi00325a003. [DOI] [PubMed] [Google Scholar]
  14. Levitt M. Molecular dynamics of native protein. I. Computer simulation of trajectories. J Mol Biol. 1983 Aug 15;168(3):595–617. doi: 10.1016/s0022-2836(83)80304-0. [DOI] [PubMed] [Google Scholar]
  15. Levitt M., Perutz M. F. Aromatic rings act as hydrogen bond acceptors. J Mol Biol. 1988 Jun 20;201(4):751–754. doi: 10.1016/0022-2836(88)90471-8. [DOI] [PubMed] [Google Scholar]
  16. Lotan R., Sharon N. The fluorescence of wheat germ agglutinin and of its complexes with saccharides. Biochem Biophys Res Commun. 1973 Dec 19;55(4):1340–1346. doi: 10.1016/s0006-291x(73)80041-5. [DOI] [PubMed] [Google Scholar]
  17. Nagata Y., Burger M. M. Wheat germ agglutinin. Molecular characteristics and specificity for sugar binding. J Biol Chem. 1974 May 25;249(10):3116–3122. [PubMed] [Google Scholar]
  18. Privat J. P., Delmotte F., Mialonier G., Bouchard P., Monsigny M. Fluorescence studies of saccharide binding to wheat-germ agglutinin (lectin). Eur J Biochem. 1974 Aug 15;47(1):5–14. doi: 10.1111/j.1432-1033.1974.tb03661.x. [DOI] [PubMed] [Google Scholar]
  19. Privat J. P., Delmotte F., Monsigny M. Protein-sugar interactions. Association of beta-(1 leads to 4) linked N-acetyl-D-glucosamine oligomer derivatives with wheat germ agglutinin (lectin). FEBS Lett. 1974 Sep 15;46(1):224–228. doi: 10.1016/0014-5793(74)80373-x. [DOI] [PubMed] [Google Scholar]
  20. Raikhel N. V., Wilkins T. A. Isolation and characterization of a cDNA clone encoding wheat germ agglutinin. Proc Natl Acad Sci U S A. 1987 Oct;84(19):6745–6749. doi: 10.1073/pnas.84.19.6745. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Sharon N. Lectin-carbohydrate complexes of plants and animals: an atomic view. Trends Biochem Sci. 1993 Jun;18(6):221–226. doi: 10.1016/0968-0004(93)90193-q. [DOI] [PubMed] [Google Scholar]
  22. Weis W. I., Drickamer K., Hendrickson W. A. Structure of a C-type mannose-binding protein complexed with an oligosaccharide. Nature. 1992 Nov 12;360(6400):127–134. doi: 10.1038/360127a0. [DOI] [PubMed] [Google Scholar]
  23. Wireko F. C., Kellogg G. E., Abraham D. J. Allosteric modifiers of hemoglobin. 2. Crystallographically determined binding sites and hydrophobic binding/interaction analysis of novel hemoglobin oxygen effectors. J Med Chem. 1991 Feb;34(2):758–767. doi: 10.1021/jm00106a042. [DOI] [PubMed] [Google Scholar]
  24. Wright C. S. Crystal structure of a wheat germ agglutinin/glycophorin-sialoglycopeptide receptor complex. Structural basis for cooperative lectin-cell binding. J Biol Chem. 1992 Jul 15;267(20):14345–14352. [PubMed] [Google Scholar]
  25. Wright C. S. Crystallographic elucidation of the saccharide binding mode in wheat germ agglutinin and its biological significance. J Mol Biol. 1980 Aug 15;141(3):267–291. doi: 10.1016/0022-2836(80)90181-3. [DOI] [PubMed] [Google Scholar]
  26. Wright C. S., Jaeger J. Crystallographic refinement and structure analysis of the complex of wheat germ agglutinin with a bivalent sialoglycopeptide from glycophorin A. J Mol Biol. 1993 Jul 20;232(2):620–638. doi: 10.1006/jmbi.1993.1415. [DOI] [PubMed] [Google Scholar]
  27. Wright C. S. Refinement of the crystal structure of wheat germ agglutinin isolectin 2 at 1.8 A resolution. J Mol Biol. 1987 Apr 5;194(3):501–529. doi: 10.1016/0022-2836(87)90678-4. [DOI] [PubMed] [Google Scholar]
  28. Wright C. S. Structural comparison of the two distinct sugar binding sites in wheat germ agglutinin isolectin II. J Mol Biol. 1984 Sep 5;178(1):91–104. doi: 10.1016/0022-2836(84)90232-8. [DOI] [PubMed] [Google Scholar]

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