In Silico Conformational Analysis of the Short-Sequence Hypomurocin A Peptides

Abstract

In this theoretical study, a conformational analysis was performed on short-sequence hypomurocin A peptides, in order to identify their characteristic structural properties. For each hypomurocin A molecule, not only the backbone conformations, but also the side-chain conformations were examined. The results indicated that certain tetrapeptide units could be characterized by types I and III β-turn structures, and considering the helical conformations, it could be concluded that the hypomurocin A peptides showed a preference for the 310-helical structure over the α-helical structure. Beside the backbone conformations, the side-chain conformations were investigated, and the preferred rotamer states of the side-chains of amino acids were determined. Furthermore, the occurrence of i ← i + 3 and i ← i + 4 intramolecular H-bonds was studied, which could play a role in the structural stabilization of β-turns and helical conformations. On the whole, our theoretical study supplied a comprehensive characterization of the three-dimensional structure of short-sequence hypomurocin A peptides.

Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations

“…Regarding short-sequence peptaibols, of which HZ is a representative, not much simulation work seems to have been done. Merely conformational analyses of shortsequence peptaibols in aqueous solution were reported, investigating trichobrachin A and B (53) and hypomurocin A (54). Further, an MD simulation study of the lipopeptaibol trichogin GA IV showed that such a short lipidated molecule interacts better with bilayers that are thinner by themselves, or, alternatively, the binding of the lipopeptaibol may induce local thinning of the membrane (55).…”

Diversity of Linear Non-Ribosomal Peptide in Biocontrol Fungi

“…Hypomurocins have 13 analogs (A and B series) (Table 14) purified from Hypocrea muroiana which is a BF not only inhibiting various plant diseases, but also promoting plant growth [96], excepting hypomurocin B that is found in Trichoderma harzianum [59,97]. Hypomurocin A has mixed helical conformation containing αand 3 10 -helices, as well as types I and III β-turn structures to link the helical [98][99][100]. Hypomurocin B consists of 18 amino acid residues to form the 3 10 -helical structure rather than by α-helical structure [101].…”