Antibody accessibility of the gp120 polypeptide surface containing the 2G12 epitopea

Radius of probe (Å)Glycan-protein surface area ratio when radial distance from mannose epitope (Å) is:
  • a Surface accessibility is dependent on the size of the probe, with water, for example, being able to penetrate into small crevices that are not accessible to bulky aromatic side chains. To analyze the degree to which the gp120 polypeptide surface was accessible beneath overlying glycan residues, the 2G12 epitope was analyzed with spherical probes of different radii, ranging from 1.4 Å, the radius of a water molecule, to 10 Å, the radius of an antibody epitope. Because the precise extent of the 2G12 epitope is not known, a range of boundaries extending from the known 2G12 mannose binding site was considered. At each radial boundary distance (columns) and probe radius (rows), the ratio of glycan surface area to polypeptide surface area was calculated for different potential epitopes. The actual 2G12 paratope is likely to be a mixture of different probe radii, with the 2G12 epitope boundary within the range of radial distances presented here.