On identifying collective displacements in apo-proteins that reveal eventual binding pathways - Fig 1

a. Schematic diagram used for defining the NAP, χi for particle i (see text). The neighbourhood Ωi centred around i is shown as a sphere. The reference positions of the neighbours Rj are shown in light grey while the instantaneous positions rj are shown in dark grey. We have subtracted off the displacement of particle i (Ri = ri) for simplicity. b. The distribution of the eigenvalues λμ of PCP for three locations in the protein T4Lys, location I corresponds to a carboxyl C atom in helix 7, II corresponds to a carboxyl O atom in helix 5 and III corresponds to a C − α atom in a relatively inflexible portion of a β sheet. In each of the locations I and II, which are active during ligand binding, the largest eigenvalue is separated from the rest by a large gap Γi. The Γi is markedly smaller in location III which is relatively inert. Here, we consider the mode corresponding to highest eigen value to be the key mode. Here each set of eigenvalues are normalized by the maximum eigen-value to make it 1. That way Γi (the difference between the eigen-values) can be compared across the three different locations of the protein on equal footing.