Distance mapping of protein-binding sites using spin-labeled oligosaccharide ligands

Research output: Contribution to journalArticle


The binding of a nitroxide spin-labeled analog of N-acetyllactosamine to galectin-3, a mammalian lectin of 26 kD size, is studied to map the binding sites of this small oligosaccharide on the protein surface. Perturbation of intensities of cross-peaks in the (15)N heteronuclear single quantum coherence (HSQC) spectrum of full-length galectin-3 owing to the bound spin label is used qualitatively to identify protein residues proximate to the binding site for N-acetyllactosamine. A protocol for converting intensity measurements to a more quantitative determination of distances between discrete protein amide protons and the bound spin label is then described. This protocol is discussed as part of a drug design strategy in which subsequent perturbation of chemical shifts of distance mapped amide cross-peaks can be used effectively to screen a library of compounds for other ligands that bind to the target protein at distances suitable for chemical linkage to the primary ligand. This approach is novel in that it bypasses the need for structure determination and resonance assignment of the target protein.


  • Nitin U. Jain
  • Andre Venot
  • Kimiko Umemoto
  • Hakon Leffler
  • James H. Prestegard
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Microbiology in the medical area
  • Immunology in the medical area


  • Nitroxide spin label, galectin-3, drug design, drug screening, distance mapping
Original languageEnglish
Pages (from-to)2393-2400
JournalProtein Science
Issue number11
Publication statusPublished - 2001
Publication categoryResearch