Thermodynamics of Residue Networks in Folded Proteins

Abstract: We have recently shown that residues in folded proteins are distributed according to a small-world network topology, which lies between the two extremes of regularity and randomness [Biophys. J., Vol. 86, 2004, pp.85-91]. Here we show that the shortest path lengths between pairs of residues are highly correlated with residue cross-correlations. To find the link between the two quantities, we attempt a thermodynamical formulation of networks. Using a Gibbsian formulation, we first show that random networks with a Poisson distribution of contacts are “ideal” and using a simple model for residue networks we argue that small-world networks display deviations from ideality