酶架构:通过三酸盐异构酶在催化中模拟疏水的操作
Yashraj S Kulkarni1, Qinghua Liao1, Dušan Petrović2
1Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, Uppsala S-751 24, Sweden.
Journal of the American Chemical Society
|July 8, 2017
概括
三酸盐异构酶 (TIM) 使用疏水来增强催化作用. 这种可以最大限度地减少基布斯的自由能量, 这对于酶活性至关重要.
科学领域:
- 生物化学
- 酶催化
- 计算生物学
背景情况:
- 三酸盐异构酶 (TIM) 是糖解中的关键酶,催化DHAP到GAP的异构化.
- 蒂姆的催化机制涉及构造变化,在催化基E165周围形成一种疏水口袋.
- 恐水性残留物I170和L230形成了TIM活动的关键"",但它们在基质脱质化中的确切作用尚不清楚.
研究的目的:
- 通过计算来研究防水 (I170和L230) 在TIM催化DHAP和GAP中所起的作用.
- 通过实证价值键计算量化评估突变 (I170A,L230A) 对TIM的催化机制的影响.
- 阐明酶催化中的基态和过渡状态效应之间的相互作用.
主要方法:
- 对野生型TIM及其I170A,L230A和I170A/L230A突变进行了详细的经验价值键 (EVB) 计算.
- 计算的重点是TIM活性位点内的DHAP和GAP脱质阶段.
- 结果与实验数据进行了定量比较,以验证计算模型.
主要成果:
- 野生型和突变型TIM的EVB计算与实验数据之间达成了异常的定量一致.
- 在激活障碍和吉布斯自由能量之间确定了0.8的斜率的线性自由能量关系 (LFER).
- 据证明,疏水可以最大限度地减少基板脱质的吉布斯自由能量,主要影响过渡状态.
结论:
- 由I170和L230形成的疏水对于最小化TIM中基质脱质的吉布斯自由能量至关重要.
- 通过的催化增强在很大程度上表达在质子转移的过渡状态.
- 本研究详细描述了TIM催化中的疏水功能,并结合了计算和实验结果.
相关概念视频
Catalytically Perfect Enzymes
5.2K
The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
Most enzymes...
Most enzymes...
5.2K
ATP Synthase: Mechanism
17.9K
In animals, the mitochondrial F1F0 ATP synthase is the key protein that synthesizes ATP molecules through a complex catalytic mechanism. While the nuclear genome encodes the majority of ATP synthase subunits, the mitochondrial genome encodes some of the enzyme's most critical components. The formation of this multi-subunit enzyme is a complex multi-step process regulated at the level of transcription, translation, and assembly. Defects in one or more of these steps can result in decreased...
17.9K
ATP Synthase: Structure
16.3K
ATP synthase or ATPase is among the most conserved proteins found in bacteria, mammals, and plants. This enzyme can catalyze a forward reaction in response to the electrochemical gradient, producing ATP from ADP and inorganic phosphate. ATP synthase can also work in a reverse direction by hydrolyzing ATP and generating an electrochemical gradient. Different forms of ATP synthases have evolved special features to meet the specific demands of the cell. Based on their specific feature, ATP...
16.3K
Induced-fit Model
90.2K
Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...
90.2K
Introduction to Mechanisms of Enzyme Catalysis
11.0K
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...
11.0K
Enzymes
95.9K
Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
95.9K


