Figure 3

Diversity of viable genotypes in the neutral networks. A) The neutral network diameters in the absence (D) and presence (D') of selection for dimerization, shown as a 2D histogram. We consider each 2D protein structure in turn, with its neutral network of sequences. The dimerization condition (when applied) requires that this protein dimerize specifically with another, particular protein (not shown), chosen arbitrarily. The dimer concentration threshold for viability was set to δ = 0.2. The diameter represents the largest "distance" between any two sequences in the neutral network (the number of amino acid mutations that separate them) [23]. The darkest squares are above the diagonal, indicating that among the 1081 structures, most have neutral networks that shrink when the dimerization condition is applied. However the diameters shrink very little: D' is typically only 1–2 units (amino acids) smaller than D. B) The distance between neutral networks in the absence (D) and presence (D') of selection for dimerization, shown as a 2D histogram. The dimerization selection criterion is the same as above. The darkest squares are above the diagonal, indicating for most pairs of structures, under the dimerization selection criterion, the corresponding neutral networks shrink so that their mutual distance increases (D' > D). However, the increase is small, only 1–2 units.