Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea.
Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung-si, Gangwon-do, 25457, Republic of Korea.
Sci Rep. 2021 Jan 28;11(1):2538. doi: 10.1038/s41598-021-82078-7.
Two putative methylglyoxal synthases, which catalyze the conversion of dihydroxyacetone phosphate to methylglyoxal, from Oceanithermus profundus DSM 14,977 and Clostridium difficile 630 have been characterized for activity and thermal stability. The enzyme from O. profundus was found to be hyperthermophilic, with the optimum activity at 80 °C and the residual activity up to 59% after incubation of 15 min at 95 °C, whereas the enzyme from C. difficile was mesophilic with the optimum activity at 40 °C and the residual activity less than 50% after the incubation at 55 °C or higher temperatures for 15 min. The structural analysis of the enzymes with molecular dynamics simulation indicated that the hyperthermophilic methylglyoxal synthase has a rigid protein structure with a lower overall root-mean-square-deviation value compared with the mesophilic or thermophilic counterparts. In addition, the simulation results identified distinct regions with high fluctuations throughout those of the mesophilic or thermophilic counterparts via root-mean-square-fluctuation analysis. Specific molecular interactions focusing on the hydrogen bonds and salt bridges in the distinct regions were analyzed in terms of interatomic distances and positions of the individual residues with respect to the secondary structures of the enzyme. Key interactions including specific salt bridges and hydrogen bonds between a rigid beta-sheet core and surrounding alpha helices were found to contribute to the stabilisation of the hyperthermophilic enzyme by reducing the regional fluctuations in the protein structure. The structural information and analysis approach in this study can be further exploited for the engineering and industrial application of the enzyme.
已对来自深海热泉古菌 Oceanithermus profundus DSM 14,977 和艰难梭菌 Clostridium difficile 630 的两种假定的甲基乙二醛合酶（催化二羟丙酮磷酸转化为甲基乙二醛）进行了活性和热稳定性的特性分析。发现深海热泉古菌的酶是超嗜热的，最适活性在 80°C，在 95°C 孵育 15 分钟后残余活性高达 59%，而艰难梭菌的酶是中温的，最适活性在 40°C，在 55°C 或更高温度下孵育 15 分钟后残余活性低于 50%。通过分子动力学模拟对酶的结构分析表明，超嗜热甲基乙二醛合酶具有刚性的蛋白质结构，与中温或嗜热对应物相比，整体均方根偏差值较低。此外，通过均方根波动分析，模拟结果确定了与中温或嗜热对应物不同的具有高波动的区域。根据原子间距离和单个残基相对于酶的二级结构的位置，分析了特定分子相互作用，重点是不同区域的氢键和盐桥。研究发现，包括刚性β-折叠核心与周围α螺旋之间的特定盐桥和氢键在内的关键相互作用，通过减少蛋白质结构的区域波动，有助于超嗜热酶的稳定。本研究中的结构信息和分析方法可进一步用于该酶的工程和工业应用。
