An analysis of reentrant loops.

Reentrant loops are an important structural motif in alpha-helical transmembrane proteins. A reentrant loop is a structural motif that goes only halfway through the membrane and then turns back to the side from which it originates. The question of what causes the reentrant loops to form such a unique topology is still unanswered. In this study, we try to answer this question by analyzing the hydrophobicity distribution on the amino acid sequences of the reentrant loops. Our results show that reentrant loops have very low hydrophobicity around the deepest point buried in the membrane and relative high hydrophobicity close to the membrane surfaces. We speculate that this hydrophobicity distribution is a major force that stabilizes the unique reentrant loop structure. Our results also show that this hydrophobicity distribution results in special patterns on protein sequences, which can be captured using profile hidden Markov models (HMMs). The resulting profile HMMs can detect reentrant loops on protein sequences with high sensitivity and perfect specificity.