1. School of Physical and Mathematical Sciences
Division of Chemistry and Biological Chemistry
Computational Studies on Metalloenzymes:
Mechanism of Nitration of L-Tryptophan With P450 TxtE Enzyme
Abstract
Cytochrome P450 TxtE is a metalloenzyme containing an iron metal
complex that can catalyse the nitration the amino acid L-tryptophan.
Molecular modelling and quantum mechanical calculations were
carried out on the whole P450 enzyme. AMBER parameters for L-
tryptophan and the iron complex were used to define the quantum
mechanical region.
Further quantum mechanical calculations were carried out to
observe how nitration occurs between ferric(iii) superoxide (iron
complex) with nitric oxide and L-tryptophan with nitrogen dioxide
(positive and neutral forms) using geometry optimization and
transition state scanning.
Method
Conclusion
From the quantum mechanical calculations of ferric superoxide with nitric
oxide, it can be determined that nitration of L-tryptophan uses neutral
nitrogen dioxide in the mechanism using P450 TxtE enzyme.
Rashmi Hiranya Seneviratne N1403520J
Charge and spin on ferric (iii)
superoxide, nitric oxide,
nitrogen dioxide (positive and
neutral forms) and L-
tryptophan were determined
from literature
Geometry optimization
calculations on ferric (iii)
superoxide with nitric oxide
and L-tryptophan with
nitrogen dioxide were carried
out using Gaussian09w
Using results of geometry
optimization, scans of ferric
(iii) superoxide with nitric
oxide and L-tryptophan with
nitrogen dioxide were carried
out
AMBER parameters for L-
tryptophan and ferric (iii)
superoxide were generated
using AMBER software
package and figures from
literature[2]
ONIOM calculation was set
up with a series of
optimization calculations on
hydrogen, carbon and
nitrogen atoms
ONIOM calculation run to
give fully optimized structure
of P450 enzyme.
References
[1] image adapted from Cytochrome P450-catalysed L-tryptophan nitration in thaxtomin
phytotoxin biosynthesis. S.M.Barry, J.A.Kers et al. Nature, October 2012, Nature
Chemical Biology , Vol. 8.
[2] Quantum Mechanically Derived AMBER-compatible Heme Parameters for Various
States of the Cytochrome P450 Catalytic Cycle (Supporting Information). K. Shahrock et
al. 2, January 2012, Journal of Computational Chemistry, Vol. 33, pp. 119-133.
Acknowledgements
Many thanks to Assistant Professor Hajime Hirao for giving me the opportunity to do
this project and for his help and advice, and to Kai Xu for all his guidance throughout
the semester.
Figure 1[1] shows mechanism studied using quantum mechanical calculations on ferric
superoxide, L-tryptophan (Trp) and nitric oxide (NO)
Results
Geometry optimization and PES relaxed scanning gives the
following results. Quantitative results from the ONIOM calculation
were unavailable.