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首页> 外文期刊>The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory >Parameterization of Unnatural Amino Acids with Azido and Alkynyl R-Groups for Use in Molecular Simulations
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Parameterization of Unnatural Amino Acids with Azido and Alkynyl R-Groups for Use in Molecular Simulations

机译：用氮杂氨基和炔基R组的非天然氨基酸参数化，用于分子模拟

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摘要

Recent new methods to functionalize proteins at specific amino acid locations use unnatural amino acids that contain azido and alkynyl groups. This capability is unprecedented and enables the creation of site-specific protein devices. Because of the high specificity of these devices, many protein configurations are possible and in silico screens have shown promise in predicting optimal attachment site locations. Therefore, there is significant interest in improving current molecular dynamics (MD) models to include the unique chemistries of these linear moieties. This work uses the force field tool kit to obtain the bonded and nonbonded CHARMM parameters for small molecules that contain azido and alkynyl groups. Next, the reliability of these parameters is tested by running simulated MD analysis to prove that the modeled structures match those found in the literature and quantum theory. Finally, the protein MD simulation compares this parameter set with crystallographic data to give a greater understanding of unnatural amino acid influence on the protein structure.
机译：最近在特定氨基酸位置官能化蛋白质的新方法使用含有含有氮杂和炔基的非天然氨基酸。这种能力是前所未有的，并能够创建特定于地的蛋白质设备。由于这些装置的高特异性，许多蛋白质配置是可能的并且在硅屏幕中已经示出了在预测最佳附接部位位置的希望。因此，对改善电流分子动力学（MD）模型具有显着兴趣，包括这些线性部分的独特化学物质。这项工作使用力现场刀具套件来获得含有氮杂多和炔基的小分子的粘合和非粘合的Charmm参数。接下来，通过运行模拟MD分析来证明所建模的结构与文献和量子理论中发现的结构相匹配来测试这些参数的可靠性。最后，蛋白质MD仿真将该参数设定与晶体数据进行比较，以便更加了解对蛋白质结构的非天然氨基酸的影响。

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