Abstract

Carbonic anhydrases catalyze the reversible hydration of carbon dioxide to form bicarbonate, a reaction required for many functions such as carbon assimilation, pH acid–base homeostasis, respiration and photosynthesis via a zinc-hydroxide mechanism for carbon dioxide hydration. In earlier studies, it was revealed that Carbonic anhydrases are inactive at pH 7.5 and active at pH 8.4. This steep pH dependence for its activity led us to design this work to understand its mode of action at atomic level detail. In our microsecond simulation based analysis, it was revealed that the interaction between Glu106 and Thr199 plays a critically important role in its activity. Thr199 co-ordinated loop movement was observed to be acting as a lid, with ‘open’ and ‘close’ mechanism for substrate entry to the core of the catalytic site, where Zn-ion resides and executes its carbon dioxide hydration mechanism. On the other hand, decline in the total secondary structural elements percentage in the protein was observed in correspondence to the pH condition change. The α-helices between Thr125-Gly145 and Val150-Lys170 residues were especially noticed to be losing their structural integrity responsible for formation of dimer and tetramers. In conclusion, our analysis showed that the interaction between Glu106 and Thr199 is crucial for maintaining the structural integrity of the Thr199 coordinated loop, responsible for allowing substrate towards the catalytic site.

Communicated by Ramaswamy H. Sarma

摘要

碳酸酐酶催化二氧化碳的可逆水合形成碳酸氢盐，这是许多功能所需的反应，例如碳同化、pH 酸碱平衡、呼吸作用和光合作用，通过二氧化碳水合的氢氧化锌机制。在早期的研究中，发现碳酸酐酶在 pH 7.5 时无活性，而在 pH 8.4 时有活性。其活性对 pH 值的这种陡峭依赖性使我们设计了这项工作，以了解其在原子级细节上的作用方式。在我们基于微秒模拟的分析中，发现 Glu106 和 Thr199 之间的相互作用在其活性中起着至关重要的作用。观察到 Thr199 协调的环运动充当盖子，具有底物进入催化位点核心的“打开”和“关闭”机制，其中锌离子驻留并执行其二氧化碳水合机制。另一方面，观察到蛋白质中总二级结构元素百分比的下降与pH条件变化相对应。特别注意到 Thr125-Gly145 和 Val150-Lys170 残基之间的 α-螺旋失去了导致二聚体和四聚体形成的结构完整性。总之，我们的分析表明 Glu106 和 Thr199 之间的相互作用对于维持 Thr199 协调环的结构完整性至关重要，负责使底物朝向催化位点。特别注意到 Thr125-Gly145 和 Val150-Lys170 残基之间的 α-螺旋失去了导致二聚体和四聚体形成的结构完整性。总之，我们的分析表明 Glu106 和 Thr199 之间的相互作用对于维持 Thr199 协调环的结构完整性至关重要，负责使底物朝向催化位点。特别注意到 Thr125-Gly145 和 Val150-Lys170 残基之间的 α-螺旋失去了导致二聚体和四聚体形成的结构完整性。总之，我们的分析表明 Glu106 和 Thr199 之间的相互作用对于维持 Thr199 协调环的结构完整性至关重要，负责使底物朝向催化位点。

由 Ramaswamy H. Sarma 传达