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首页> 外文期刊>BioTechnology: An Indian Journal >Analysis of chloride ion-proline interaction of dehalogenase enzymes bymolecular dynamics simulation
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Analysis of chloride ion-proline interaction of dehalogenase enzymes bymolecular dynamics simulation

机译：分子动力学模拟分析脱卤酶中氯离子-脯氨酸的相互作用

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摘要

This work reports the preference of chloride ion -Proline amino acid interaction among the dehalogenase enzyme. We retrieved 22 dehalogenase and non dehalogenase enzyme available crystallographic structure (from PDB) that contains chloride ion in the structure. Further 3.5 angstrom proximity amino acid residues from the chloride ion was computed for all the selected proteins by an in house built software. The result indicates, in case of the dehalogenase enzymes contains proline residues proximity to chloride ion was uniquely identified. Again a case study was performed to identify the dynamics of the proline residue with respect to the Cl- ion, by considering the protein having PDB ID 1EDB. The dynamics study during 5 nanosecond MD simulation by GROMACS 4.0.5 reveals that both 223 proline and 226 Val interact with the Cl- ion more frequently and PRO CA- CL atomic distance is little fluctuated (fluctuation range within 0.5 angstrom). Then to check the structure, function relationship, 3 different substitution mutations were performed on Proline position according to the comparable molecular weight. Then the mutant structures were subjected to 1 nano second molecular dynamics simulation. The result indicates Proline present proximity to chloride ions is important for the dehalogenase enzyme activity.
机译：这项工作报告了脱卤酶之间氯离子-脯氨酸氨基酸相互作用的偏好。我们检索了22种脱卤酶和非脱卤酶可用的晶体结构（来自PDB），该晶体结构中含有氯离子。通过内部构建的软件，为所有选定的蛋白质计算出氯离子的另外3.5埃邻近氨基酸残基。结果表明，在脱卤素酶中含有脯氨酸残基的情况下，可以唯一地识别出接近氯离子的位置。通过考虑具有PDB ID 1EDB的蛋白质，再次进行了案例研究，以鉴定脯氨酸残基相对于Cl离子的动力学。通过GROMACS 4.0.5在5纳秒的MD模拟过程中进行的动力学研究表明，223脯氨酸和226 Val与Cl-离子的相互作用更频繁，PRO CA- CL原子距离几乎没有波动（波动范围在0.5埃以内）。然后检查结构，功能关系，根据可比较的分子量在脯氨酸位置进行了3个不同的取代突变。然后对突变体结构进行1纳秒分子动力学模拟。结果表明脯氨酸目前与氯离子的接近性对于脱卤酶的活性很重要。

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