Protein–Support Interactions for Rationally Designed Bilirubin Oxidase Based Cathode: A Computational Study

Abstract

An example of biocathode based on bilirubin oxidase (BOx) was used to demonstrate how density functional theory can be combined with docking simulations in order to study the interface interactions between the enzyme and specifically designed electrode surface. The electrode surface was modified through the adsorption of bilirubin, the natural substrate for BOx, and the prepared electrode was electrochemically characterized using potentiostatic measurements. The experimentally determined current densities showed that the presence of bilirubin led to significant improvement of the cathode operation. On the basis of the computationally calculated binding energies of bilirubin to the graphene support and BOx and the analysis of the positioning of bilirubin relative to the support and T1 Cu atom of the enzyme, we hypothesize that the bilirubin serves as a geometric and electronic extension of the support. The computational results further confirm that the modification of the electrode surface with bilirubin provides an optimal orientation of BOx toward the support but also show that bilirubin facilitates the interfacial electron transfer by decreasing the distance between the electrode surface and the T1 Cu atom.

Redox Potential‐Dependent Formation of an Unusual His–Trp Bond in Bilirubin Oxidase

“…Thismay account for why the substrate tends to bind to the outsideo ft he pocket of M467Q BOD in the present docking simulation. The bilirubin molecule of WT/Model 1 is placed close enough to His462-NE2 (4.4 )a nd Trp396-CB (4.6 )( Figure 3a), suggesting that these residues are candidates for the electron transfer pathway.T he binding affinity of the WT/Model 1w as calculated to be À7.2 kcal mol À1 ,c onsistent with that of the reported value (À7.8kcal mol À1 )b ased on the density functional theory (DFT) calculation performed by Matanovic et al [14] The bilirubin-T1Cud istance is 8.1 in our WT/Model 1, similart ot he value (7.5 for the flexible pocket/ flexible bilirubin model)o ft he DFT study.…”

Integration of Platinum Group Metal‐Free Catalysts and Bilirubin Oxidase into a Hybrid Material for Oxygen Reduction: Interplay of Chemistry and Morphology

“…[50,51] Studiesp reviously conducted by our group demonstratedt hat the significant positive effect observed is owed to an enzyme-substrate recognitione vent and subsequent propere nzymeo rientation, [62] not to surface chemistry alone. [50,51] Studiesp reviously conducted by our group demonstratedt hat the significant positive effect observed is owed to an enzyme-substrate recognitione vent and subsequent propere nzymeo rientation, [62] not to surface chemistry alone.…”

“…It is interesting to mention that modification of carbon electrodes with ap yrrole-containing organicc ompound (bilirubin) was found to have ar emarkable positive effect on BOx cathodes. [50,51] Studiesp reviously conducted by our group demonstratedt hat the significant positive effect observed is owed to an enzyme-substrate recognitione vent and subsequent propere nzymeo rientation, [62] not to surface chemistry alone. The modificationp rocedure wasb eneficial for positioning BOx closer relative to the support by providing optimal orientation of the enzyme and facilitating the interfacial electron transfer by decreasing the distance betweent he electrode surface and the T1 Cu.…”

Controlling Redox Enzyme Orientation at Planar Electrodes

“…SAM-functionalized gold surfaces have been modeled in numerous simulation works on enzyme-surface interactions, for example, to probe the enzyme binding orientation as a function of the surface charge [149]. Matanovic et al used a combination of Density Functional Theory (DFT) and docking simulations to study the oriented interaction between bilirubin oxidase and a graphene electrode functionalized with bilirubin [159].…”