Functional and computational studies of the ligand-associated metal binding site of beta3 integrins

Proteins. 2008 Jun;71(4):1779-91. doi: 10.1002/prot.21859.


A combination of experimental and computational approaches was used to provide a structural context for the role of the beta3 integrin subunit ligand-associated metal binding site (LIMBS) in the binding of physiological ligands to beta3 integrins. Specifically, we have carried out (1) adhesion assays on cells expressing normal alphaIIbeta3, normal alphaVbeta3, or the corresponding beta3 D217A LIMBS mutants; and (2) equilibrium and nonequilibrium (steered) molecular dynamics (MD) simulations of eptifibatide in complex with either a fully hydrated normal alphaIIbeta3 integrin fragment (alphaIIb beta-propeller and the beta3 betaA (I-like), hybrid, and PSI domains) or the equivalent beta3 D217A mutant. Normal alphaIIbeta3 expressing cells adhered to immobilized fibrinogen and echistatin, whereas cells expressing the alphaIIbeta3 D217A LIMBS mutant failed to adhere to either ligand. Similarly, the equivalent alphaVbeta3 mutant was unable to support adhesion to vitronectin or fibrinogen. The alphaIIbeta3 D217A mutation increased the binding of mAb AP5, which recognizes a ligand-induced binding site (LIBS) in the beta3 PSI domain, indicating that this mutation induced allosteric changes in the protein. Steered MD simulating the unbinding of eptifibatide from either normal alphaIIbeta3 or the equivalent beta3 D217A mutant suggested that the reduction in ligand binding caused by the LIMBS mutant required the loss of both the LIMBS and the metal ion-dependent adhesion site (MIDAS) metal ions. Our computational results indicate that the LIMBS plays a crucial role in ligand binding to alphaIIbeta3 by virtue of its effects on the coordination of the MIDAS.

Publication types

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

MeSH terms

  • Antibodies, Monoclonal / metabolism
  • Binding Sites
  • Cell Adhesion
  • Cell Line
  • Computational Biology / methods*
  • Computer Simulation
  • Eptifibatide
  • Fibrinogen / metabolism
  • Humans
  • Integrin beta3 / chemistry*
  • Integrin beta3 / genetics
  • Integrin beta3 / metabolism*
  • Integrin beta3 / physiology
  • Intercellular Signaling Peptides and Proteins
  • Kidney / cytology
  • Ligands
  • Metals / chemistry
  • Models, Molecular
  • Mutation
  • Peptides / metabolism
  • Platelet Aggregation Inhibitors / metabolism
  • Platelet Glycoprotein GPIIb-IIIa Complex / antagonists & inhibitors
  • Protein Binding
  • Protein Structure, Tertiary
  • Transfection


  • Antibodies, Monoclonal
  • Integrin beta3
  • Intercellular Signaling Peptides and Proteins
  • Ligands
  • Metals
  • Peptides
  • Platelet Aggregation Inhibitors
  • Platelet Glycoprotein GPIIb-IIIa Complex
  • echistatin
  • Fibrinogen
  • Eptifibatide