The reaction mechanism of allene oxide synthase: Interplay of theoretical QM/MM calculations and experimental investigations.

Archives of Biochemistry and Biophysics
Kyung-Bin ChoSason Shaik

Abstract

A combined theoretical and experimental study highlights the reaction mechanism of allene oxide synthase (AOS) and its possible link to hydroperoxide lyase (HPL) pathway. A previously published study (Lee et al., Nature 455 (2008) 363) has shown that the F137 residue is of central importance in differentiating between the AOS and HPL pathways after initial identical steps. In the experimental part of this study, we show that wild-type AOS from Arabidopsis or rice in fact produces both AOS and HPL products in a ratio of about 80:15, something that was found only in trace amounts before. Theoretical calculations successfully map the whole AOS pathway with 13(S)-hydroperoxy linolenic and linoleic acid as substrates. Subsequent calculations investigated the effects of in silico F137L mutation at the suggested diverging point of the two pathways. The results show that QM/MM calculations can reasonably reproduce three out of four experimentally available cases, and confirm that the pathways are energetically very close to each other, thus making a switch from one path to other plausible under different circumstances.

References

Feb 6, 1995·Biochemical and Biophysical Research Communications·Y ShibataA Hatanaka
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Apr 11, 2000·Accounts of Chemical Research·D SchröderH Schwarz
Nov 4, 2000·The Journal of Biological Chemistry·A Itoh, G A Howe
Jul 18, 2001·Journal of the American Chemical Society·S P de VisserS Shaik
Feb 6, 2002·Chembiochem : a European Journal of Chemical Biology·M A NoordermeerJ F Vliegenthart
May 25, 2002·Nature·Gunnar I BerglundJanos Hajdu
Sep 12, 2002·Annual Review of Plant Biology·Ivo Feussner, Claus Wasternack
Nov 5, 2002·Current Opinion in Chemical Biology·Sason ShaikDetlef Schröder
Nov 16, 2002·Prostaglandins & Other Lipid Mediators·Nathalie Tijet, Alan R Brash
Nov 16, 2002·Prostaglandins & Other Lipid Mediators·Alexander N Grechkin
Jun 9, 2005·Chemical Reviews·Sason ShaikWalter Thiel
Sep 15, 2005·Journal of the American Chemical Society·Hajime HiraoSason Shaik
Sep 30, 2005·Journal of the American Chemical Society·Etienne DeratWalter Thiel
Jul 11, 2006·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Per E M Siegbahn
Aug 31, 2006·Journal of the American Chemical Society·Rachel K BehanMichael T Green
May 10, 2007·Accounts of Chemical Research·Sason ShaikDevesh Kumar
Jan 5, 2008·Proceedings of the National Academy of Sciences of the United States of America·Martin NewcombStephen G Sligar
Sep 13, 2008·Proceedings of the National Academy of Sciences of the United States of America·Lenong LiXiaoqiang Wang
Apr 7, 2009·Current Opinion in Chemical Biology·Michael T Green
May 5, 2009·The Journal of Physical Chemistry. B·Wenzhen LaiSason Shaik
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus

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Citations

Dec 1, 2012·BMC Plant Biology·Julia ScholzIvo Feussner
Jul 2, 2014·Journal of Molecular Graphics & Modelling·Tuanjai SomboonSeiji Mori
Jul 18, 2012·The Journal of Physical Chemistry. B·Rong-Zhen Liao, Walter Thiel
Feb 18, 2011·Archives of Biochemistry and Biophysics·Helmut Sies

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