The binding affinity and reactivity between laccase and phenolic substrates were investigated with bioinformatics analysis, molecular dynamics simulation and quantum chemical calculation. Sequence and structure alignments indicate that the substrate-binding pocket of the laccases include certain conserved amino acid(AA) residues, such as Asp/Glu206, Asn/His208, Asn264, Gly392, His458(using the AA sequence number of PDB: 1KYA, a laccase from Trametes versicolor). Accordingly, the binding affinity between the laccase and the modeled 21 phenolic substrates were calculated with the MM-GBSA method. As a result of the molecular modeling, the inter-molecular hydrogen bonding between the hydroxyl group and Asp206/Asn264, and the π-π interaction between the phenyl group and Phe265, are essential for binding phenolic substrates to the laccase. The quantum chemistry calculations indicate that electronic effects of the additional substituent groups on the substrates would affect reductivity significantly, in particular for the collaborative deprotonation. The electron-donating groups, such as —NH2, —OH, —OCH3 and —CH=CHCH3, enhance the substrate reactivity, while the electron-withdrawing groups not, e.g. —C(=O)NH2 and —Cl. Our theoretical studies revealed that the binding affinity and reactivity stem from the different physiochemical nature, casting fundamental insights to future molecular design of laccase-mediator system.
