College of Environmental Science and Engineering, Hunan University, Changsha, China.
PLoS One. 2011;6(9):e25647. doi: 10.1371/journal.pone.0025647. Epub 2011 Sep 29.
Previous works have demonstrated that ligninolytic enzymes mediated effective degradation of lignin wastes. The degrading ability greatly relied on the interactions of ligninolytic enzymes with lignin. Ligninolytic enzymes mainly contain laccase (Lac), lignin peroxidase (LiP) and manganese peroxidase (MnP). In the present study, the binding modes of lignin to Lac, LiP and MnP were systematically determined, respectively. Robustness of these modes was further verified by molecular dynamics (MD) simulations. Residues GLU460, PRO346 and SER113 in Lac, residues ARG43, ALA180 and ASP183 in LiP and residues ARG42, HIS173 and ARG177 in MnP were most crucial in binding of lignin, respectively. Interactional analyses showed hydrophobic contacts were most abundant, playing an important role in the determination of substrate specificity. This information is an important contribution to the details of enzyme-catalyzed reactions in the process of lignin biodegradation, which can be used as references for designing enzyme mutants with a better lignin-degrading activity.
先前的研究工作已经证实，木质素降解酶能够有效降解木质素废物。这些酶的降解能力在很大程度上依赖于木质素降解酶与木质素的相互作用。木质素降解酶主要包括漆酶（Lac）、木质素过氧化物酶（LiP）和锰过氧化物酶（MnP）。在本研究中，分别系统地确定了木质素与 Lac、LiP 和 MnP 的结合模式。通过分子动力学（MD）模拟进一步验证了这些模式的稳健性。在 Lac 中，残基 GLU460、PRO346 和 SER113，在 LiP 中，残基 ARG43、ALA180 和 ASP183，以及在 MnP 中，残基 ARG42、HIS173 和 ARG177 分别对木质素的结合最为关键。相互作用分析表明，疏水性接触最为丰富，在确定底物特异性方面起着重要作用。这些信息是木质素生物降解过程中酶催化反应细节的重要贡献，可以作为设计具有更好木质素降解活性的酶突变体的参考。
