Size scaling behaviour in protein domains belonging to the all-alpha, all-beta, alpha/beta, and alpha plus beta folding classes

We studied the size scaling behaviour in an ensemble of 8,614 non-redundant protein domains belonging to the all-alpha, all-beta, alpha / beta, and alpha + beta folding classes. We find that the most compact structural domains can be characterized by an effective exponent nu (eff) = 0.39 +/- 0.01, which is larger than the value for "collapsed-polymers," i.e., nu = 1/3. We also show that the global nu (eff) -exponent is an average of the scaling regimes for short and long compact chains, where the values change from nu (eff) a parts per thousand 0.37 to nu (eff) a parts per thousand 0.45 at chain length of ca. 269. A transition from short-chain to long-chain scaling behaviour is found in all major folding classes, over a window of chain lengths between 216 and 269 residues. In addition, variations in scaling exponent with respect to folding class indicates that the smallest domains in the (all-beta) and (alpha / beta) families appear to be more compact structures than the smallest (all-alpha)- and (alpha + beta)-domains.