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Issue 15, 2012
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Combining weak affinity chromatography, NMR spectroscopy and molecular simulations in carbohydrate–lysozyme interaction studies

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Abstract

By examining the interactions between the protein hen egg-white lysozyme (HEWL) and commercially available and chemically synthesized carbohydrate ligands using a combination of weak affinity chromatography (WAC), NMR spectroscopy and molecular simulations, we report on new affinity data as well as a detailed binding model for the HEWL protein. The equilibrium dissociation constants of the ligands were obtained by WAC but also by NMR spectroscopy, which agreed well. The structures of two HEWL–disaccharide complexes in solution were deduced by NMR spectroscopy using 1H saturation transfer difference (STD) effects and transferred 1H,1H-NOESY experiments, relaxation-matrix calculations, molecular docking and molecular dynamics simulations. In solution the two disaccharides β-D-Galp-(1→4)-β-D-GlcpNAc-OMe and β-D-GlcpNAc-(1→4)-β-D-GlcpNAc-OMe bind to the B and C sites of HEWL in a syn-conformation at the glycosidic linkage between the two sugar residues. Intermolecular hydrogen bonding and CH/π-interactions form the basis of the protein–ligand complexes in a way characteristic of carbohydrate–protein interactions. Molecular dynamics simulations with explicit water molecules of both the apo-form of the protein and a ligand–protein complex showed structural change compared to a crystal structure of the protein. The flexibility of HEWL as indicated by a residue-based root-mean-square deviation analysis indicated similarities overall, with some residue specific differences, inter alia, for Arg61 that is situated prior to a flexible loop. The Arg61 flexibility was notably larger in the ligand-complexed form of HEWL. N,N′-Diacetylchitobiose has previously been observed to bind to HEWL at the B and C sites in water solution based on 1H NMR chemical shift changes in the protein whereas the disaccharide binds at either the B and C sites or the C and D sites in different crystal complexes. The present study thus highlights that protein–ligand complexes may vary notably between the solution and solid states, underscoring the importance of targeting the pertinent binding site(s) for inhibition of protein activity and the advantages of combining different techniques in a screening process.

Graphical abstract: Combining weak affinity chromatography, NMR spectroscopy and molecular simulations in carbohydrate–lysozyme interaction studies

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Publication details

The article was received on 09 Dec 2011, accepted on 01 Feb 2012 and first published on 06 Mar 2012


Article type: Paper
DOI: 10.1039/C2OB07066A
Org. Biomol. Chem., 2012,10, 3019-3032

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    Combining weak affinity chromatography, NMR spectroscopy and molecular simulations in carbohydrate–lysozyme interaction studies

    J. Landström, M. Bergström, C. Hamark, S. Ohlson and G. Widmalm, Org. Biomol. Chem., 2012, 10, 3019
    DOI: 10.1039/C2OB07066A

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