Fedor N. Novikov, Oleg V. Stroganov, Ilyas G. Khaliullin, Nikolay V. Panin, Irina V. Shapovalova, Ghermes G. Chilov and Vytas K. Švedas Molecular modeling of different substrate-binding modes and their role in penicillin acylase catalysis The FEBS Journal 280
Productive, non-productive, and pre-productive binding modes were located by molecular modeling of penicillin acylase interactions with negatively charged substrates. In non- and pre-productive complexes the acyl group occupied a patch on the protein interface spanning from βR263 to αR145. Free energies of substrate binding and near-attack conformation frequencies estimated by molecular modeling corresponded well to experimental KM and kcat values.
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