title: Proposed systematic nomenclature for orbitides.
abstract: Orbitides are short (5-11 amino acid residue), ribosomally synthesized homodetic plant cyclic peptides characterized by N-to-C amide bonds rather than disulfide bonds. Orbitides can be discovered using mass spectrometry of plant extracts or by identifying DNA sequences coding for the precursor protein. The number of orbitides that have been characterized to date, by a number of different research groups, is modest. The nomenclatural system currently used for the Type VI cyclic peptides has been developed in an ad hoc fashion and is somewhat arbitrary. We propose a systematic naming system specifically for the Type VI cyclic peptides that reflects the taxonomic name of the species producing the orbitides and a numbering system that enables systematic representation of amino acid residues and modifications. The proposed naming system emulates the IUPAC Nomenclature for Natural Products and UniProt, both of which use abbreviations of taxonomic names for the compounds in question. Nomenclature for post-translational modifications also follows the IUPAC precedent, as well as the cyclic peptide literature. Furthermore, the proposed system aims to maintain agreement with the precedents set by the pre-existing literature. An example of the proposed nomenclature is provided using the methionine-containing homodetic peptides of Linum usitatissimum (flaxseed).
authors.affiliation: †Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan S7N 5A8, Canada.|‡Prairie Tide Chemicals Inc., 102 Melville Street, Saskatoon, Saskatchewan S7J 0R1, Canada.
authors.forename: Youn Young
authors.initials: YY
authors.lastname: Shim
authors.affiliation: †Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan S7N 5A8, Canada.
authors.forename: Lester W
authors.initials: LW
authors.lastname: Young
authors.affiliation: §Botanical Alternatives Inc., 176, 8B-3110 Eighth Street E, Saskatoon, Saskatchewan S7H 0W2, Canada.
authors.forename: Paul G
authors.initials: PG
authors.lastname: Arnison
authors.affiliation: ⊥Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
authors.forename: Edward
authors.initials: E
authors.lastname: Gilding
authors.affiliation: †Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan S7N 5A8, Canada.|‡Prairie Tide Chemicals Inc., 102 Melville Street, Saskatoon, Saskatchewan S7J 0R1, Canada.
authors.forename: Martin J T
authors.initials: MJ
authors.lastname: Reaney
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D019597:Flax / Q000737:chemistry; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular; D009842:Oligopeptides / Q000737:chemistry / Q000145:classification*; D010456:Peptides, Cyclic / Q000737:chemistry / Q000145:classification*
chemical_list: D009842:Oligopeptides; D010456:Peptides, Cyclic