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Next: Results and Discussion Up: Understanding Cytochrome P450 - Previous: SubstratesSubstrate Analogues and

Computational Approach

 

The size of a typical P450 enzyme (approximately 3500 atoms) is prohibitively large to be modelled in its entirety using an ab initio approach at present, even with the efficient methods described in Chapter gif running on modern supercomputers. Therefore, attention must be focused on a smaller region of the enzyme around the active site. Indeed, an important aim of this investigation will be to determine if many properties of an enzyme may be modelled by consideration of only a small portion of the entire molecule. It was desirable to limit the computational resources required and to address the properties of P450s in general, therefore none of the contact residues which define the substrate binding pocket were included in the simulations. The model systems contained only the ligand molecule, haem moiety, tex2html_wrap_inline3186 -ligated cysteine residue and tex2html_wrap_inline3186 -ligated water (if present). Examples of substrate-free, substrate-bound, inhibitor-bound, and substrate analogue-bound systems modelled are shown in Figures gif, gif, gif and gif respectively. No questions of substrate specificity were addressed as this is defined by the geometry of the substrate binding pocket. In the future, questions regarding the nature of the tex2html_wrap_inline2954 -bound system and also specific P450 enzyme species may be addressed. This will require the inclusion of additional contact residues.

Due to the limited size of the system modelled and the uncertainty in the structure of the active sites of most P450s, cytochrome tex2html_wrap_inline3174 (CYP101) was chosen as the subject of this investigation because accurate crystal structures of this enzyme have been obtained. These structures include the enzyme complexed with substrates, substrate analogues and inhibitors. The systems included in this study are listed in Table gif. The use of crystal structures allows the determination of the position of the ligand relative to the active site and the changes in the geometry of the active site caused by ligand binding. This restricts one source of uncertainty in the results obtained from the calculations. At this early stage it is important to limit any possible external sources of error so that any deviations from experimental data can be attributed to the computational modeling approach taken in the simulation.

 

Ligand Nature of Ligand PDBreference Reference
Substrate-free N/A 1PHC [93]
Camphor Substrate 4CP4 [100]
Adamantanone Substrate 5CPP [101]
Camphane Substrate analogue 6CPP [100]
Norcamphor Substrate analogue 7CPP [101]
Metyrapone Inhibitor 1PHG [98]
Table: The tex2html_wrap_inline3174 structures used in the ab initio investigation.

 

This investigation addresses two questions. Firstly, it is important to determine if our ab initio methods accurately reproduce the changes in the spin state of the tex2html_wrap_inline3186 observed experimentally. This serves to validate the use of our approach for the study of the P450 system and will enable more speculative questions to be addressed with confidence. In particular, the rôle of the tex2html_wrap_inline3186 -coordinated water molecule, found in the substrate-free and substrate analogue-bound complexes, is explored.

The calculations were performed with a 600eV cut off energy for the plane wave basis set using a spin-dependent GGA [18] to the exchange-correlation potential. The systems were enclosed in a cubic supercell with a side of length 19Å and contained between 90 and 118 atoms. A non-linear core-corrected pseudopotential was used to describe the ionic core of the iron atom. The main spin dependent calculations were performed on 64 processors of the Hitachi SR2201 parallel supercomputer at the Cambridge High Performance Computing Facility (HPCF). Preliminary calculations were performed on 64 nodes of the Hitachi SR2001 supercomputer at the Maidenhead headquarters of Hitachi Europe Ltd and on 16 nodes of the SR2201 at the Cambridge HPCF. These preliminary calculations primarily involved the relaxation of the hydrogen atoms in the systems into their equilibrium positions as their atomic coordinates were not specified in the crystal structure datasets.


next up previous contents
Next: Results and Discussion Up: Understanding Cytochrome P450 - Previous: SubstratesSubstrate Analogues and

Matthew Segall
Wed Sep 24 12:24:18 BST 1997