水化层影响酸酐酶内CO2扩散行为的分子动力学模拟

doi:10.11949/j.issn.0438-1157.20150773

化工学报 ›› 2015, Vol. 66 ›› Issue (8): 2903-2910.DOI: 10.11949/j.issn.0438-1157.20150773

水化层影响酸酐酶内CO₂扩散行为的分子动力学模拟

陈功¹, 卢滇楠¹, 吴建中², 刘铮¹

1 工业生物催化教育部重点实验室(筹), 清华大学化工系, 北京 100084;
2 Department of Chemical & Environmental Engineering, University of California, Riverside, CA 92521, USA

收稿日期:2015-06-01 修回日期:2015-06-10 出版日期:2015-08-05 发布日期:2015-08-05
通讯作者: 卢滇楠,刘铮
基金资助:
国家自然科学基金项目(21028006)。

Molecular dynamics simulation for hydration effect on CO₂ diffusion#br# in carbonic anhydrase

CHEN Gong¹, LU Diannan¹, WU Jianzhong², LIU Zheng¹

1 Key Laboratory for Industrial Biocatalysis (Preparing), Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China;
2 Department of Chemical & Environmental Engineering, University of California, Riverside, CA 92521, USA

Received:2015-06-01 Revised:2015-06-10 Online:2015-08-05 Published:2015-08-05
Supported by:
supported by the National Natural Science Foundation of China (21028006).

摘要/Abstract

摘要：

气相中酶分子表面的水化层对其催化行为具有显著的影响。本文采用全原子分子动力学模拟方法考察了气相体系碳酸酐酶表面的水化层对酶结构以及CO₂在酶分子中扩散行为的影响。首先展现了水分子在酶分子及其活性中心周围的分布,研究了水化层厚度对于酶结构以及CO₂扩散速率的影响;发现最有利于CO₂扩散进入酶分子的水化层厚度为0.7 nm。确认了碳酸酐酶内CO₂的吸附位点,通过对其开合状态统计,显示出碳酸酐酶中CO₂扩散通道中的瓶颈位置。上述结果对设计和优化碳酸酐酶催化气相体系中CO₂的吸附和转化提供了依据和启示。

关键词: 碳酸酐酶, CO₂, 扩散, 水化层, 吸附位点

Abstract:

The hydration layer of the enzyme in the bulk gas phase has great effects on its catalytic performance. Molecular dynamics (MD) simulations at all-atom level was applied to investigate the effects of the hydration layer thickness on the diffusion of carbon dioxide molecules into the active site of a carbonic anhydrase enzyme from a bulk gas phase. Based on the distribution of water molecules surrounding the carbonic anhydrase enzyme, the effects of the hydration layer thickness on the protein structure and CO₂ transport from the bulk gas phase to the protein active site was studied. The simulation results suggested an optimal hydration layer thickness of 0.7 nm for CO₂ diffusion. The CO₂ adsorption sites were identified, which compose of the diffusion channel inside the carbonic anhydrase. The MD simulation revealed the open states of these adsorption sites, which may be useful to identify the bottleneck position of the diffusion channel. The molecular insight is helpful for design and optimization of carbonic anhydrase, enabling more efficient CO₂ adsorption and conversion.

Key words: carbonic anhydrase, carbon dioxide, diffusion, hydration layer, adsorption sites

中图分类号:

TQ021.4

陈功, 卢滇楠, 吴建中, 刘铮. 水化层影响酸酐酶内CO₂扩散行为的分子动力学模拟[J]. 化工学报, 2015, 66(8): 2903-2910.

CHEN Gong, LU Diannan, WU Jianzhong, LIU Zheng. Molecular dynamics simulation for hydration effect on CO₂ diffusion#br# in carbonic anhydrase[J]. CIESC Journal, 2015, 66(8): 2903-2910.

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水化层影响酸酐酶内CO₂扩散行为的分子动力学模拟

Molecular dynamics simulation for hydration effect on CO₂ diffusion#br# in carbonic anhydrase

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