10342 INSTITUTO PERUANO DEL DEPORTE PLIEGO :
PRODUCTO PROYECTO: 2112952. CONSTRUCCION E IMPLEMENTACION DEL CENTRO DE SIMULACION DE NEGOCIOS Y ASESORIA EMPRESARIAL DE LA ESPECIALIDAD DE CIENCIAS ADMINISTRATIVAS
The work presented in this chapter covers the biochemical and biophysical analysis of HDCYP102A3, a homologue of the well characterised model enzyme BM3 (CYP102A1). A key aim in this work was the structural characterisation of HDCYP102A3 by x-ray crystallography. Though this aim was unsuccessful, due to insufficient diffraction, a large amount of useful characterisation of the HDCYP102A3 protein was carried out.
A homology model of HDCYP102A3, based on its amino acid sequence and its closest structurally characterised homologue BM3, showed a very similar overall structure. It is, however, difficult to be certain of the similarity from this result, as the technique is likely to produce a model similar to the template structure.
EPR and resonance Raman experiments provided some structural information regarding the haem centre of HDCYP102A3. The EPR spectrum recorded displayed the characteristic signal of a low-spin, hexacoordinate, cysteine ligated haem. The g- values of the signals in the EPR spectrum of HDCYP102A3 are almost identical to those for the haem domain of BM3. This confirms a high level of structural similarity between the two. Resonance Raman spectra showed a strong agreement between most signals for HDCYP102A3 and those found in spectra of BM3, presenting a picture of a haem environment very similar to that found in BM3. These two results both support the view that the homology model is a fair representation (at least of the immediate environment of the haem) of the structure of HDCYP102A3.
Resonance Raman spectra were also recorded with and without bound substrate, and these spectra showed the characteristic shift towards a high-spin haem iron upon binding of fatty acid substrates. Binding titrations were carried out to quantify the binding affinities of a selection of substrates and inhibitor molecules. These experiments revealed that the substrate and inhibitor binding affinities of HDCYP102A3 are similar to those recorded previously for the full length fusion enzyme, with some notable differences. A pattern of higher binding affinity for longer substrate chain lengths was shown, that was not present in the values for the full length enzyme. Additionally, the overall preference for branched-chain fatty acid substrates, shown for the full length enzyme[79], was not evident in the results for the isolated haem domain. Though no binding interaction was observed for palmitic
for other branched chain substrates. In the case of 12- and 13-methylmyristic acids,
Kd values were greater than that for myristic acid (the equivalent straight chain
substrate). These results point to a possible influence upon substrate binding of the presence of the reductase domain and the likely dimeric nature of the full length enzyme. Binding of NPG, a derivatised fatty acid shown to bind tightly to BM3, was
confirmed for HDCYP102A3, albeit with ~20 fold lower affinity (based on Kd
values)[148].
The binding of inhibitors was also shown to differ, with twofold tighter binding in HDCYP102A3 (compared to the full length enzyme) in the case of imidazole and 1- phenylimidazole. Conversely, HDCYP102A3 was shown to have a tenfold reduced affinity for 4-phenylimidazole. Additionally, an inhibitor producing no binding interaction with BM3, 2-phenylimidazole, was shown to bind to HDCYP102A3 likely in a similar conformation as it has been found to bind in P450cam. All of these variations suggest that, despite the structural similarities between CYP102A3 and BM3 haem domains, the binding interactions between ligands and amino acid side chains in the substrate binding cavity (possibly including Phe-89 in CYP102A3, Phe- 87 in BM3) are significantly altered.
Redox potentiometry experiments showed an increase in the haem Fe2+/Fe3+
standard potential in the presence of bound substrate. While a positive shift in this redox potential is expected for a substrate-bound P450 and has been demonstrated in many cases, the magnitude of the increase is unprecedented (>200 mV) and warrants some caution. However, structural influences on the haem (e.g. planarity of the macrocycle and hydrogen binding interactions with its substituent groups) could compound the effects mediated by the high-spin transition in the substrate-bound form, and underlie the larger than expected change in potential observed in substrate-bound HDCYP102A3.
Studies of the stability of HDCYP102A3 to denaturing conditions were carried out by DSC and chemical denaturation. The DSC data acquired, while suffering from
background noise, show what appear to be two unfolding events with Tm 45-50 °C
followed by massive aggregation of the HDCYP102A3 protein. These two unfolding events could well correspond to the separate unfolding of the α and β domains of the protein. This experiment also showed that the protein is stable at temperatures well above what the host species (a soil bacterium) would normally experience.
Chemical denaturation with varying concentrations of GdmCl was used to measure loss of haem during unfolding. It was shown that at concentrations of GdmCl that were highly deleterious to the catalytic activity of BM3 (1-2 M) the effect on the bound haem of HDCYP102A3 was low. This result supports the suggestion that the loss of activity at < 1 M GdmCl in BM3 is due mainly to reductase domain unfolding and FMN dissociation. The GdmCl experiment did not show the same protein aggregation as seen in the DSC experiment. This may be due to the solubilising effect of the denaturant or due to retained secondary structure (with the former being more probable). It should also be noted that the isolated haem domain of CYP102A3 may have a lower stability than the full length enzyme, especially if the latter exists as a dimer which may provide further stability. The HDCYP102A3 protein appeared to exist as two distinct species during this experiment: a low-spin, thiolate ligated haem- containing, intact protein and a denatured protein having lost its haem. No intermediate, partially denatured, spectral species were observed from optical studies. Further studies using far UV, CD or aromatic amino acid fluorescence could provide such information, although one might expect the dissociation/loss of ligation of the haem cofactor to occur at a GdmCl concentration lower of similar to those required for gross conformational perturbations of the protein.
To address concerns about aggregation of HDCYP102A3, especially with regard to planned crystallographic experiments, a MALS experiment was carried out to ascertain the monodispersity of the HDCYP102A3 protein in solution. This experiment showed that the protein was indeed highly monodisperse with negligible levels of aggregation. Encouraged by this result, crystallographic trials were carried out, leading to the generation of two crystal isoforms: one with bound substrate (NPG) and one without. Unfortunately neither of these crystal samples produced sufficient diffraction for structural characterisation. After these discouraging results, studies of HDCYP102A3 were concluded and work commenced on the CYP116B1 fusion system (see Chapters 4 & 5) with the aim of generating data on the structural and biochemical characteristics of this novel class of P450-redox partner fusion enzyme.
Going on from the work on HDCYP102A3 presented in this chapter, further efforts towards structural characterisation could be pursued. The best approach would be to attempt to produce a different crystal isoform, by employing a range of ligands
(substrates or inhibitors) likely to produce conformational change in the protein (or to stabilise and alternative P450 conformer or conformers). Based on the structural similarity highlighted in this work and the homology model, mutagenesis experiments could be undertaken in a similar fashion to those carried out on BM3 to probe various aspects of the enzyme. These include analysis of the effects of mutating key residues on the substrate selectivity, regioselectivity of substrate oxidation and the thermal stability of CYP102A3. The insight gained in these experiments could form part of an overall approach aimed at combining desirable features from all of the CYP102A subfamily enzymes to produce a range of novel biocatalysts for specific applications such as those discussed in the literature on the engineering of BM3 (see section 1.1.10).
Characterisation of Novel Cytochrome P450 Fusion Systems