title: Mechanistic insights into the catalytic reaction of plant allene oxide synthase (pAOS) via QM and QM/MM calculations.
abstract: QM cluster and QM/MM protein models have been employed to understand aspects of the reaction mechanism of plant allene oxide synthase (pAOS). In this study we have investigated two reaction mechanisms for pAOS. The standard pAOS mechanism was contrasted with an alternative involving an additional active site molecule which has been shown to facilitate proton coupled electron transfer (PCET) in related systems. Firstly, we found that the results from QM/MM protein model are comparable with those from the QM cluster model, presumably due to the large active site used. Furthermore, the results from the QM cluster model show that the Fe(III) and Fe(IV) pathways for the standard mechanism have similar energetic and structural properties, indicating that the reaction mechanism may well proceed via both pathways. However, while the PCET process is facilitated by an additional active site bound water in other related families, in pAOS it is not, suggesting this type of process is not general to all closely related family members.
authors.affiliation: Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.
authors.forename: Tuanjai
authors.initials: T
authors.lastname: Somboon
authors.affiliation: Faculty of Science, Ibaraki University, Ibaraki 310-8512, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Ochiai
authors.affiliation: Institute of Food Research and Product Development, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.
authors.forename: Witcha
authors.initials: W
authors.lastname: Treesuwan
authors.affiliation: Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.
authors.forename: M Paul
authors.initials: MP
authors.lastname: Gleeson
authors.affiliation: Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Center of Nanotechnology KU, Kasetsart University, Chatuchak, Bangkok 10900 Thailand. Electronic address: fscisph@ku.ac.th.
authors.forename: Supa
authors.initials: S
authors.lastname: Hannongbua
authors.affiliation: Faculty of Science, Ibaraki University, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Ibaraki 319-1106, Japan. Electronic address: smori@mx.ibaraki.ac.jp.
authors.forename: Seiji
authors.initials: S
authors.lastname: Mori
mesh_terms: D055162:Biocatalysis; D019746:Intramolecular Oxidoreductases / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D010940:Plant Proteins / Q000737:chemistry* / Q000378:metabolism; D010944:Plants / Q000201:enzymology*; D011522:Protons; D011789:Quantum Theory; D014867:Water / Q000737:chemistry
chemical_list: D010940:Plant Proteins; D011522:Protons; D014867:Water; D019746:Intramolecular Oxidoreductases; C021377:hydroperoxide isomerase
keywords: AOS; Allene oxide synthase; Cytochrome P450; DFT calculations; QM cluster calculation; QM/MM calculations