2X3T

Glutaraldehyde-crosslinked wheat germ agglutinin isolectin 1 crystal soaked with a synthetic glycopeptide

Summary for 2X3T

• Entry DOI: 10.2210/pdb2x3t/pdb
• Related: 1WGC 2CWG 2UVO 2UWG 2X52 7WGA
• Descriptor: AGGLUTININ ISOLECTIN 1, GLYCOPEPTIDE, 2-acetamido-1-O-carbamoyl-2-deoxy-alpha-D-glucopyranose, ... (6 entities in total)
• Functional Keywords: sugar binding protein-peptide complex, chitin-binding, sugar binding protein/peptide
• Biological source: TRITICUM AESTIVUM (WHEAT); More
• Total number of polymer chains: 6
• Total formula weight: 74173.14

Authors

Schwefel, D.,Maierhofer, C.,Wittmann, V.,Diederichs, K.,Welte, W. (deposition date: 2010-01-26, release date: 2010-06-30, Last modification date: 2024-05-01)

Primary citation

Schwefel, D.,Maierhofer, C.,Beck, J.G.,Seeberger, S.,Diederichs, K.,Moller, H.M.,Welte, W.,Wittmann, V.
Structural Basis of Multivalent Binding to Wheat Germ Agglutinin.
J.Am.Chem.Soc., 132:8704-, 2010

PubMed Abstract: The inhibition of carbohydrate-protein interactions by tailored multivalent ligands is a powerful strategy for the treatment of many human diseases. Crucial for the success of this approach is an understanding of the molecular mechanisms as to how a binding enhancement of a multivalent ligand is achieved. We have synthesized a series of multivalent N-acetylglucosamine (GlcNAc) derivatives and studied their interaction with the plant lectin wheat germ agglutinin (WGA) by an enzyme-linked lectin assay (ELLA) and X-ray crystallography. The solution conformation of one ligand was determined by NMR spectroscopy. Employing a GlcNAc carbamate motif with alpha-configuration and by systematic variation of the spacer length, we were able to identify divalent ligands with unprecedented high WGA binding potency. The best divalent ligand has an IC(50) value of 9.8 microM (ELLA) corresponding to a relative potency of 2350 (1170 on a valency-corrected basis, i.e., per mol sugar contained) compared to free GlcNAc. X-ray crystallography of the complex of WGA and the second best, closely related divalent ligand explains this activity. Four divalent molecules simultaneously bind to WGA with each ligand bridging adjacent binding sites. This shows for the first time that all eight sugar binding sites of the WGA dimer are simultaneously functional. We also report a tetravalent neoglycopeptide with an IC(50) value of 0.9 microM being 25,500 times higher than that of GlcNAc (6400 times per contained sugar) and the X-ray structure analysis of its complex with glutaraldehyde-cross-linked WGA. Comparison of the crystal structure and the solution NMR structure of the neoglycopeptide as well as results from the ELLA suggest that the conformation of the glycopeptide in solution is already preorganized in a way supporting multivalent binding to the protein. Our findings show that bridging adjacent protein binding sites by multivalent ligands is a valid strategy to find high-affinity protein ligands and that even subtle changes of the linker structure can have a significant impact on the binding affinity.

PubMed: 20527753
DOI: 10.1021/JA101646K

Experimental method

X-RAY DIFFRACTION (2.749 Å)