Classification and prediction of beta-turn types

Abstract

Although a beta-turn consists of only four amino acids, it assumes many different types in proteins. Is this basically dependent on the tetrapeptide sequence alone or is it due to a variety of interactions with the other part of a protein? To answer this question, a residue-coupled model is proposed that can reflect the sequence-coupling effect for a tetrapeptide in not only a beta-turn or non-beta-turn, but also different types of a beta-turn. The predicted results by the model for 6022 tetrapeptides indicate that the rates of correct prediction for beta-turn types I, I', II, II', VI, and VIII and non-beta-turns are 68.54%, 93.60%, 85.19%, 97.75%, 100%, 88.75%, and 61.02%, respectively. Each of these seven rates is significantly higher than 1/7 = 14.29%, the completely randomized rate, implying that the formation of different beta-turn types or non-beta-turns is considerably correlated with the sequences of a tetrapeptide.