Kinetic Capacity of a Protein

Abstract

The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum basin of attraction, as parametrised in our model, depends on the number of amino acid species as ln A, independent of protein length. We argue that the extent to which the protein energy landscape can be manipulated is fixed, effecting a trade-off between well breadth, well depth and well number. This clarifies the scope and limits of protein and heteropolymer function.