School of Physical and Mathematical SciencesDivision 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

ConclusionFrom 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.

AcknowledgementsMany 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.