Comparative molecular dynamics simulations provided insights into the mechanisms of cold-adaption of alginate lyases from the PL7 family

文献类型： 外文期刊

第一作者： Bian, Fei

作者： Bian, Fei;Liang, Xiao-Yue;Wang, Meng;Sun, Zhong-Zhi;Xie, Bin-Bin;Liang, Xiao-Yue;Wang, Meng;Sun, Zhong-Zhi;Xie, Bin-Bin

作者机构：

关键词： Cold adaptation; Alginate lyases; Polysaccharide lyases; Molecular dynamics (MD) simulations; Temperature optimum of activity (T-opt)

期刊名称：EXTREMOPHILES （ 影响因子：2.9； 五年影响因子：2.6 ）

ISSN： 1431-0651

年卷期： 2024 年 28 卷 2 期

页码：

收录情况： SCI

摘要： Alginate is an important polysaccharide that is abundant in the marine environments, including the Polar Regions, and bacterial alginate lyases play key roles in its degradation. Many reported alginate lyases show characteristics of cold-adapted enzymes, including relatively low temperature optimum of activities (T-opt) and low thermal stabilities. However, the cold-adaption mechanisms of alginate lyases remain unclear. Here, we studied the cold-adaptation mechanisms of alginate lyases by comparing four members of the PL7 family from different environments: AlyC3 from the Arctic ocean (Psychromonas sp. C-3), AlyA1 from the temperate ocean (Zobellia galactanivorans), PA1167 from the human pathogen (Pseudomonas aeruginosa PAO1), and AlyQ from the tropic ocean (Persicobacter sp. CCB-QB2). Sequence comparison and comparative molecular dynamics (MD) simulations revealed two main strategies of cold adaptation. First, the Arctic AlyC3 and temperate AlyA1 increased the flexibility of the loops close to the catalytic center by introducing insertions at these loops. Second, the Arctic AlyC3 increased the electrostatic attractions with the negatively charged substrate by introducing a high portion of positively charged lysine at three of the insertions mentioned above. Furthermore, our study also revealed that the root mean square fluctuation (RMSF) increased greatly when the temperature was increased to T-opt or higher, suggesting the RMSF increase temperature as a potential indicator of the cold adaptation level of the PL7 family. This study provided new insights into the cold-adaptation mechanisms of bacterial alginate lyases and the marine carbon cycling at low temperatures.

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