Molecular dynamics studies on the mutational structures of a nylon-6 byproduct-degrading enzyme

• Published in: Chemical physics letters 2011-04, Vol.507 (1), p.157-161
• Main Authors: Baba, Takeshi, Kamiya, Katsumasa, Matsui, Toru, Shibata, Naoki, Higuchi, Yoshiki, Kobayashi, Tatsuya, Negoro, Seiji, Shigeta, Yasuteru
• Format: Article
• Language: English
• ISSN: 0009-2614; 1873-4448
• DOI: 10.1016/j.cplett.2011.03.046

[Display omitted] ► Wild-type and mutant structures of nylon-6 byproduct-degrading enzyme are determined. ► We sampled 25 000 data from 10–35 ns simulations to analyze MD trajectories. ► An importance of water exclusion environment around the catalytic site is proposed. ► A possibility that water behave as an inhibitor of the degradation is suggested. In order to understand roles of E168 and Y170 residues in loop-segment (N166–V177) of nylon-6 byproduct-degrading enzymes, we determined substrate-binding structures of E168Q and Y170F mutants using molecular dynamics simulation with in silico mutations. We found that movement of the loop-segment plays key roles not only in allowing the substrate to be bound by induced fit mechanism but also in forming water-exclusive environment. Fluctuations of the loop-segment in the mutant enzymes caused a room near the catalytic site, where water molecules can access. We propose that the water located exclusivity at the catalytic site is a major factor of its activity.