Ziemys A, Kulys J
Department of Biology, Vytautas Magnus University, Vileikos g. 8, LT-44404 Kaunas, Lithuania; Institute of Biochemistry, Mokslininku g. 12, LT-08662 Vilnius, Lithuania.
Comput Biol Chem. 2005 Apr;29(2):83-90. doi: 10.1016/j.compbiolchem.2004.12.007.
Molecular modeling techniques were applied to study oligomeric derivatives of phenols, which are produced during peroxidase-catalyzed oxidation. The interaction of substrates and oligomers with Arthromyces ramosus peroxidase (ARP) was analyzed by docking and molecular dynamics methods. The most possible interaction site of oligomers is the active center of the peroxidase. The affinity of oligomers increases with increasing length of oligomers. However, the complexed oligomers produce non-productive complexes with the peroxidase. Molecular dynamics studies showed that oligomer-peroxidase complexes are stable. It seems likely that strong and stable, but non-productive docking of the oligomers determinates peroxidase inhibition during the reaction by preventing the access of regular substrates to the active center of the enzyme.
