Pathway success rates.

<p>Convergence of the successful formation of contiguous pathways was determined for each model system. The x-axis indicates the number of selections of random residues. The rate at which any pathway connecting the active and allosteric site, subject to the 6Å distance constraint, is shown on the y-axis. The horizontal line indicates the converged value. (A) PDZ (number of trials = 10 at each selection level), (B) p53 (number of trials = 3 at each selection level), (C) MutS (number of trials = 3 at each selection level).</p

Dependence of prevalence of contiguous pathways in proteins on structural complexity

<div><p>Allostery is a regulatory mechanism in proteins where an effector molecule binds distal from an active site to modulate its activity. Allosteric signaling may occur via a continuous path of residues linking the active and allosteric sites, which has been suggested by large conformational changes evident in crystal structures. An alternate possibility is that the signal occurs in the realm of ensemble dynamics via an energy landscape change. While the latter was first proposed on theoretical grounds, increasing evidence suggests that such a control mechanism is plausible. A major difficulty for testing the two methods is the ability to definitively determine that a residue is directly involved in allosteric signal transduction. Statistical Coupling Analysis (SCA) is a method that has been successful at predicting pathways, and experimental tests involving mutagenesis or domain substitution provide the best available evidence of signaling pathways. However, ascertaining energetic pathways which need not be contiguous is far more difficult. To date, simple estimates of the statistical significance of a pathway in a protein remain to be established. The focus of this work is to estimate such benchmarks for the statistical significance of contiguous pathways for the null model of selecting residues at random. We found that when 20% of residues in proteins are randomly selected, contiguous pathways at the 6 Å cutoff level were found with success rates of 51% in PDZ, 30% in p53, and 3% in MutS. The results suggest that the significance of pathways may have system specific factors involved. Furthermore, the possible existence of false positives for contiguous pathways implies that signaling could be occurring via alternate routes including those consistent with the energetic landscape model.</p></div

PDZ contiguous pathway examples.

<p>The PDZ protein backbone is shown in a cyan tube (PDB ID 1BE9). The allosteric signal travels between the allosteric effector binding site to the peptide ligand binding site (residues Arg 313 (top) and Ala 376 (bottom) highlighted in red ball and stick representation). The 20% of residues randomly selected for the trial appear in dark blue ball and stick. In panels (A-D), lime green balls highlight residues forming a successful contiguous pathway at the 6Å cutoff level. A short, direct path of 4 (A) and 5 (B) residues connects the sites. Longer meandering paths were also discovered: 8 residues (C) and 14 residues (D). In panels (E) and (F), examples of failed pathways are shown. A red surface shows where the pathway failed to connect.</p

Success of pathways as a function of neighbor distance cutoff.

<p>The distance requirement for the contiguous pathway was varied (number of selections = 1000, number of trials = 3) for the three model systems, and was fit with a logistic curve. The best fit equations by system are given by system. PDZ: y = 100.663 + (5.015053–100.663)/(1 + (x/150.7424)^5.362259)^24925470 p53: y = 96.11989 + (0.4398672–96.11989)/(1 + (x/33.24754)^10.47436)^21720600 MutS: y = 100.1441 + (2.080954–100.1441)/(1 + (x/8.69924)^15.53203)^0.3183134.</p