对GH11西兰酶的催化机制的洞察:基于中子结构的基质扭曲的计算分析
Toyokazu Ishida1, Jerry M Parks2, Jeremy C Smith2
1Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan.
Journal of the American Chemical Society
|September 22, 2020
概括
这项研究阐明了GH11西兰酶的生物质分解机制,揭示了具有过渡性离子中间体的保留机制. 计算证实了该酶在没有重组能量损失的情况下加速糖化.
科学领域:
- 生物化学
- 酵素学
- 计算化学
背景情况:
- 由西兰酶分解生物质的反应机制,特别是GH11西兰酶的糖化步骤,是有争议的.
- 了解这种机制对于高效的纤维素半纤维素 (xylan) 水解至关重要.
研究的目的:
- 阐明GH11西兰酶中糖化步骤的详细反应机制.
- 在西兰水解过程中调查有争议的氧碳离子中间体的形成.
主要方法:
- 使用ab initio量子力学/分子力学 (QM/MM) 计算,包括QM/MM-CCSD(T)/6-31(+) G**//MP2/6-31+G**/AMBER.
- 利用最近的中子晶体结构来确定其余的质子化状态.
主要成果:
- 计算支持双位移计划中的基本保留机制.
- 估计自由能量障碍大约为18kcal/mol,其中糖键裂变是决定速度的步骤.
- 氧化碳离子中间体是暂时形成的,但不会积累,估计寿命为几十个皮秒.
结论:
- 酶基质复合物在-1亚位点呈现出扭曲的酸盐残留物几何.
- 蛋白质环境在引导催化残留物进行质子转移方面发挥着关键作用.
- 通过精确调整催化残留物来实现有效的酶催化,避免重组能量损失.
相关概念视频
Catalysis
The presence of a catalyst affects the rate of a chemical reaction. A catalyst is a substance that can increase the reaction rate without being consumed during the process. A basic comprehension of a catalysts’ role during chemical reactions can be understood from the concept of reaction mechanisms and energy diagrams.
Introduction to Mechanisms of Enzyme Catalysis
For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild...
Introduction to Mechanisms of Enzyme Catalysis
For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild...
Heterogeneous Catalysis
Heterogeneous catalysis involves a catalyst in a different phase from the reactants. It is a process where the catalyst and the reactants are in distinct phases, typically solid and gas or liquid.Most heterogeneous catalysts are metals, metal oxides, or acids. The list includes transition metals like iron (Fe), cobalt (Co), nickel (Ni), palladium (Pd), platinum (Pt), chromium (Cr), manganese (Mn), tungsten (W), silver (Ag), and copper (Cu). These metals possess partially vacant d orbitals that...


