Insights on the oxidative half reaction of NCR ERED with citral as

Different computational methods were applied throughout the herein described thesis to complement or explain the experimental results regarding the engineering of NCR ERED. In a collaboration with Dr. Wolfgang Brandt from the Leibniz Institute of Plant Biochemistry in Halle (Saale), Germany, it was also envisioned to correlate calculated activation barriers of the reduction of citral by NCR variants with altered enantioselectivity. To achieve this, semi-empiric quantum mechanics calculations based on the method PM7 have been performed. Surprisingly, however, this initial motivation couldn’t be realized because the mechanism described in literature⁷⁷ (here it is called the

‘classical mechanism’) of the oxidative half reaction of EREDs failed to result in an exergonic reaction, which is a thermodynamic requirement for the reaction to take place by itself.¹⁷³ In consequence, alternative reaction paths were sampled computationally. It should be highlighted that because of the simplifications of the applied method, the following results require additional computational and experimental confirmations.

Nevertheless, these calculations are insofar significant that they point out several

aspects of the oxidative half reaction in EREDs that we might not have fully understood yet.

The endergonic result of the initial calculation according to the ‘classical mechanism’

(Figure 13; chapter 1.3.2) is probably caused by a resulting charge separation that results if the hydrogenation of the C=C double bond happens by hydride transfer of the FMNH2 species and a hydrogen transfer from a catalytically active tyrosine (Y177 in NCR). A beforehand neutral constellation is changed to a charge-separated state involving a negatively charged tyrosine and a positively charged flavin. By structural consideration of the NCR enzyme, it was found that an arginine in position 224 could serve as a base that would justify the often assumed FMNH^-1 species that partially compensates the above-mentioned charge-separation issue and therefore facilitates the hydride transfer (Figure 59). This acid base reaction causes itself a charge separation.

However, the reaction will most likely form equilibrium. Moreover, the flavin becomes neutral by the subsequent hydride transfer. And indeed, calculations confirmed that this transformation is likely to happen. To the best of knowledge, this is the first calculation result that confirms such a catalytically relevant function for this arginine. So far, the arginine was reported to be mainly relevant for stabilizing the phosphate moiety of the flavin in the protein structure.⁶⁵ However, in the discussion of the crystal structure of the OYE plant homologue OPR1 from Solanum lycopersicum such a role of this highly conserved arginine has been hypothesized.¹⁷⁴

Figure 59: Generation of FMNH^-1 species due to prior deprotonation of FMNH₂ by R224 in NCR ERED. The generated negative charge facilitates a subsequent hydride transfer of the flavin as indicated by dashed arrows.

Furthermore, a potentially alternate reaction path (Figure 28, chapter 3.1.1) was calculated to be energetically feasible within the scope of the applied method. As in the

‘classical mechanism’ it involves the hydride transfer from the N5 position of the above

justified FMNH^-1 species, but the initial proton is transferred from a hydrogenated histidine species to form an enol intermediate. It rearranges in the active site and is then transformed by an enzyme-catalyzed keto-enol tautomerization, which involves the tyrosine that is typically described to be catalytically relevant (Y177 in NCR), but also an additional water molecule. In sum, this reaction therefore proceeds non-concerted with respect to hydride and proton addition to the activated C=C double bond. In the following, features of the mechanism and its relevance in comparison to experimental results are discussed.

For the hydride transfer 30.1 kcal/mol was calculated as activation barrier. This high activation barrier is theoretically reasonable in light of the significant hydrogen tunneling contribution that was found experimentally for both, the reductive and the oxidative half reaction in the MR ERED-homologue from Pseudomonas putida M10.^82,83

The assumption of a protonated histidine (H172 in NCR) that results the enol intermediate needs further affirmation. Referring to the histidine side chain pKa value of about 6, this possibility can be theoretically considered.¹⁷⁵ Moreover, it should be taken into account that the surrounding protein environment influences the actually present pKa value of the amino acid residue. In contrast, based on an OYE1 crystal structure, it has though been argued as well that the present hydrogen bond network might render the histidine not to function as an acid as described here.⁶⁵ Furthermore, NCR variant H172A was shown in this work to possess residual activity in the reduction of citral.

However, it should be mentioned that the herein described enol species might in theory also be formed by means of a different hydrogenation pathway.

Especially in light of the found rearrangement and H shift leading to a keto-enol tautomerism, it is interesting to discuss two experimental results, which are not in accordance with the so far described mechanism. For example, several studies have been published reporting on variants of the conserved tyrosine residue (in NCR Y177) that are still fairly active including findings that have been made in this work (chapter 4.1.2).^76,80,81 This is in contrast to initial findings of an inactive OYE1 ERED Y196F variant from Saccharomyces pastorianus that substantiated the definition of the role of this tyrosine initially. It appears that this behavior varies among different EREDs. It is relevant that the herein described mechanism also involves this tyrosine and thus confirms a catalytically important function. However, water is also involved in

the hydrogen shift reaction. It has been hypothesized previously in the above-mentioned knock-out studies that water could substitute the role of the tyrosine. The herein described calculations can be understood as a confirmation of such hypothesis. It should be highlighted that a more complex water network, that has not yet been considered, might be involved in the overall reaction. The second experimental finding refers to a study of Brenna et al. investigating the ERED-mediated hydrogenation of tetra-substituted alkenes. In their study they also found evidence for syn-addition products for some substrates instead of the generally described trans-addition.¹⁷⁶ According to the classically described direct protonation from tyrosine only trans-addition products should be formed. In contrast, the herein described rearrangement of the enol intermediate theoretically also allows for the formation of syn-addition products.

Despite of the fact that these experiments support the calculated finding that the protonation mechanism in the oxidative half reaction might be more complex, these calculation results stand in contrast to recent QM/MM calculations that studied the oxidative half reaction in the thermophilic ERED YqjM from Bacillus subtilis using cyclohexanone as the oxidant. In their study they concluded a confirmation of the proton-donating role of the catalytic tyrosine in the enzyme although they found a non-concerted reaction involving an enolate intermediate.¹⁷⁷ It should be mentioned that this does not affect the findings regarding the potential role of R224 because in their study, an FMNH^-1 species was assumed in the QM calculation part. As in contrast to semi-empiric calculations, QM/MM calculations consider the protein backbone in the MM part of the calculation, they usually result in more accurate results.¹¹² Nevertheless, the different experimental outcomes of the reduction of various substrates by different ERED members also underpin the possibility that also mechanistic details differ in different family members. It might be that the calculation results are restricted to the chosen example of citral reduction in NCR. In summary, the herein presented mechanistic results need further investigation, which involves additional experiments and complementary calculative confirmations. For example, variations at position R224 could further elucidate the role of this amino acid for the NCR ERED mechanism.