Elucidating glycosaminoglycan-protein-protein interactions using carbohydrate microarray and computational approaches

Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):9747-52. doi: 10.1073/pnas.1102962108. Epub 2011 May 31.


Glycosaminoglycan polysaccharides play critical roles in many cellular processes, ranging from viral invasion and angiogenesis to spinal cord injury. Their diverse biological activities are derived from an ability to regulate a remarkable number of proteins. However, few methods exist for the rapid identification of glycosaminoglycan-protein interactions and for studying the potential of glycosaminoglycans to assemble multimeric protein complexes. Here, we report a multidisciplinary approach that combines new carbohydrate microarray and computational modeling methodologies to elucidate glycosaminoglycan-protein interactions. The approach was validated through the study of known protein partners for heparan and chondroitin sulfate, including fibroblast growth factor 2 (FGF2) and its receptor FGFR1, the malarial protein VAR2CSA, and tumor necrosis factor-α (TNF-α). We also applied the approach to identify previously undescribed interactions between a specific sulfated epitope on chondroitin sulfate, CS-E, and the neurotrophins, a critical family of growth factors involved in the development, maintenance, and survival of the vertebrate nervous system. Our studies show for the first time that CS is capable of assembling multimeric signaling complexes and modulating neurotrophin signaling pathways. In addition, we identify a contiguous CS-E-binding site by computational modeling that suggests a potential mechanism to explain how CS may promote neurotrophin-tyrosine receptor kinase (Trk) complex formation and neurotrophin signaling. Together, our combined microarray and computational modeling methodologies provide a general, facile means to identify new glycosaminoglycan-protein-protein interactions, as well as a molecular-level understanding of those complexes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Antigens, Protozoan / chemistry
  • Antigens, Protozoan / genetics
  • Antigens, Protozoan / metabolism
  • Binding Sites / genetics
  • Carbohydrate Sequence
  • Carbohydrates / analysis
  • Chondroitin Sulfates / chemistry
  • Chondroitin Sulfates / metabolism
  • Computer Simulation
  • Fibroblast Growth Factor 2 / chemistry
  • Fibroblast Growth Factor 2 / genetics
  • Fibroblast Growth Factor 2 / metabolism
  • Glycosaminoglycans / chemistry*
  • Glycosaminoglycans / metabolism
  • Microarray Analysis / methods*
  • Models, Molecular*
  • Molecular Sequence Data
  • Oligosaccharides / chemistry
  • Oligosaccharides / metabolism
  • PC12 Cells
  • Protein Binding
  • Protein Structure, Tertiary
  • Proteins / chemistry*
  • Proteins / genetics
  • Proteins / metabolism
  • Rats
  • Receptor, Fibroblast Growth Factor, Type 1 / chemistry
  • Receptor, Fibroblast Growth Factor, Type 1 / genetics
  • Receptor, Fibroblast Growth Factor, Type 1 / metabolism
  • Sequence Homology, Amino Acid
  • Tumor Necrosis Factor-alpha / chemistry
  • Tumor Necrosis Factor-alpha / genetics
  • Tumor Necrosis Factor-alpha / metabolism


  • Antigens, Protozoan
  • Carbohydrates
  • Glycosaminoglycans
  • Oligosaccharides
  • Proteins
  • Tumor Necrosis Factor-alpha
  • VAR2CSA protein, Plasmodium falciparum
  • Fibroblast Growth Factor 2
  • Chondroitin Sulfates
  • Receptor, Fibroblast Growth Factor, Type 1