Effect of alphabet size and foldability requirements on protein structure designability

Abstract

A number of investigators have addressed the issue of why certain protein structures are especially common by considering structure designability, defined as the number of sequences that would successfully fold into any particular native structure. One such approach, based on foldability, suggested that structures could be classified according to their maximum possible foldability and that this optimal foldability would be highly correlated with structure designability. Other approaches have focused on computing the designability of lattice proteins written with reduced two-letter amino acid alphabets. These different approaches suggested contrasting characteristics of the most designable structures. This report compares the designability of lattice proteins over a wide range of amino acid alphabets and foldability requirements. While all alphabets have a wide distribution of protein designabilities, the form of the distribution depends on how protein "viability" is defined. Furthermore, under increasing foldability requirements, the change in designabilities for all alphabets are in good agreement with the previous conclusions of the foldability approach. Most importantly, it was noticed that those structures that were highly designable for the two-letter amino acid alphabets are not especially designable with higher-letter alphabets.