Studying the structural and folding features of long-sequence trichobrachin peptides.

In this theoretical study, the folding processes of long-sequence trichobrachin peptides (i.e., TB IIb peptides) were investigated by molecular dynamics methods. The formation of various helical structures (i.e., 310 -, α-, and left-handed α-helices) was studied with regard to the entire sequence of peptides, as well as to each amino acid. The results pointed out that TB IIb molecules showed a propensity to form helical conformations, and they could be characterized by 310 -helical structure rather than by α-helical structure. The formation of local (i.e., i←i+3 and i←i+4) as well as of non-local (i.e., i←i+n, where n>4; and all i→i+n) H-bonds was also examined. The results revealed that the occurrence of local, helix-stabilizing H-bonds was in agreement with the appearance of helical conformations, and the non-local H-bonds did not produce relevant effects on the evolution of helical structures. Based on the data obtained by our structural investigation, differences were observed between the TB IIb peptides, according to the type of amino acid located in the 17th position of their sequences. In summary, the folding processes were explored for TB IIb molecules, and our theoretical study led to the conclusion that these long-sequence peptaibols showed characteristic structural and folding features.