title: Characterizing the structural and folding properties of long-sequence hypomurocin B peptides and their analogs.
abstract: We studied the folding processes of long-sequence hypomurocin (HM) peptides and their analogs by means of molecular dynamics methods, focusing on the formation of various helical structures and intramolecular H-bonds. The evolution of different helical conformations, such as the 310 -, α-, and left-handed α-helices, was examined, taking into account the entire sequence and each amino acid of peptides. The results indicated that the HM peptides and their analogs possessed a propensity to adopt helical conformations, and they showed a preference for the 310 -helical structure over the α-helical one. The evolution of a variety of the intramolecular H-bonds, including local and non-local interactions, was also investigated. The results pointed out that on the one hand, the appearance of local, helix-stabilizing H-bonds correlated with the presence of helical conformations, and on the other hand, the non-local H-bonds did not affect significantly the formation of helical structures. Additionally, comparing the structural and folding features of HM peptides and their analogs, our study led to the observation that the L-D isomerism of isovaline amino acid induced effects on the folding processes of these long-sequence peptaibol molecules. Accordingly, the HM peptides and their analogs could be characterized by typical structural and folding properties. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 645-657, 2016.
authors.affiliation: Hungarian Academy of Sciences, Institute of Biophysics, Biological Research Centre, Temesvári Krt. 62, Szeged, H-6726, Hungary.
authors.forename: János
authors.initials: J
authors.lastname: Horváth
authors.affiliation: Hungarian Academy of Sciences, Institute of Biophysics, Biological Research Centre, Temesvári Krt. 62, Szeged, H-6726, Hungary.
authors.forename: Zoltán
authors.initials: Z
authors.lastname: Násztor
authors.affiliation: Faculty of Medicine, Department of Medical Chemistry, University of Szeged, Dóm Tér 8, Szeged, H-6720, Hungary.
authors.forename: Ferenc
authors.initials: F
authors.lastname: Bartha
authors.affiliation: MTA-SZTE Supramolecular and Nanostructured Materials Research Group of Hungarian Academy of Sciences, University of Szeged, Dóm tér 8, H-6720, Szeged, Hungary.
authors.forename: Ferenc
authors.initials: F
authors.lastname: Bogár
authors.affiliation: Hungarian Academy of Sciences, Institute of Biophysics, Biological Research Centre, Temesvári Krt. 62, Szeged, H-6726, Hungary. leitgeb.balazs@brc.mta.hu.|Faculty of Science and Informatics, Department of Microbiology, University of Szeged, Közép Fasor 52, Szeged, H-6726, Hungary. leitgeb.balazs@brc.mta.hu.
authors.forename: Balázs
authors.initials: B
authors.lastname: Leitgeb
mesh_terms: D006860:Hydrogen Bonding; D010455:Peptides / Q000737:chemistry*; D010569:Perylene / Q000031:analogs & derivatives* / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011809:Quinones / Q000737:chemistry*
chemical_list: D010455:Peptides; D011809:Quinones; C437341:hypomycin B; D010569:Perylene
keywords: helical structure; hypomurocin; intramolecular H-bond; molecular dynamics; peptaibol