Size scaling behaviour in protein domains belonging to the all-α, all-β, α / β, and α + β folding classes

Abstract

We studied the size scaling behaviour in an ensemble of 8,614 non-redundant protein domains belonging to the all-α, all-β, α / β, and α + β folding classes. We find that the most compact structural domains can be characterized by an effective exponent ν _eff  = 0.39 ± 0.01, which is larger than the value for “collapsed-polymers,” i.e., ν = 1/3. We also show that the global ν _eff -exponent is an average of the scaling regimes for short and long compact chains, where the values change from ν _eff ≈ 0.37 to ν _eff ≈ 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-β) and (α / β) families appear to be more compact structures than the smallest (all-α)- and (α + β)-domains.