title: Effect of microsphere binding site density on the apparent affinity of an interaction partner.
abstract: BACKGROUND
  Flow cytometric microsphere-based binding assays can be used to measure molecular interactions with high sensitivity. We have used multiplexed microsphere technology to explore the effect that binding site density has on the apparent affinity of a soluble interaction partner.
  
  
  METHODS
  The interaction of a nuclear receptor, peroxisome proliferator-activated receptor gamma ligand binding domain (PPARgamma LBD), with a synthetic peptide derived from a nuclear receptor coactivator protein, PPARgamma coactivator-1 alpha (PGC-1alpha), is the interacting system being studied. The density of this peptide coupled to fluorescently unique microsphere populations is varied by co-incubating the biotinylated peptide and avidin-coated microsphere populations with increasing the amounts of free D-biotin. The discrete-density peptide-coupled microsphere populations are combined to conduct a multiplexed binding experiment with Alexa 532-labeled PPARgamma LBD, in the absence or presence of a small molecule ligand.
  
  
  RESULTS
  As the immobilized binding site density of PGC-1alpha peptide on fluorescent microspheres is increased the measured apparent affinity for PPARgamma LBD is increased.
  
  
  CONCLUSIONS
  The density of binding sites immobilized to a surface has a pronounced effect on the apparent affinity for soluble binding partners. By controlling and varying the binding site density it is possible to increase the sensitivity of an interaction assay. In multiplexed assay formats it should be possible to normalize intrinsically unequal binding interactions by individually optimizing the binding site density of the immobilized interaction partner. However, to quantitatively measure intrinsic affinities of molecular interactions, low binding site densities are required and multivalent reagents must be avoided.
authors.affiliation: Department of Gene Expression and Protein Biochemistry, GlaxoSmithKline Discovery Research, Research Triangle Park, North Carolina, USA.
authors.forename: Marie A
authors.initials: MA
authors.lastname: Iannone
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Consler
mesh_terms: D020816:Amino Acid Motifs; D001665:Binding Sites; D001681:Biological Assay; D005434:Flow Cytometry / Q000295:instrumentation*; D005456:Fluorescent Dyes / Q000737:chemistry / Q000378:metabolism; D006360:Heat-Shock Proteins / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008024:Ligands; D008863:Microspheres; D008954:Models, Biological; D047495:PPAR gamma / Q000378:metabolism; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D000071248:Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D005456:Fluorescent Dyes; D006360:Heat-Shock Proteins; D008024:Ligands; D047495:PPAR gamma; C486497:PPARGC1A protein, human; D010455:Peptides; D000071248:Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha; D014157:Transcription Factors