Department of Chemical Engineering, Brigham Young University, Provo, Utah 84602, United States.
J Chem Inf Model. 2020 Oct 26;60(10):5117-5125. doi: 10.1021/acs.jcim.0c00725. Epub 2020 Sep 30.
Functionalization is often needed to harness the power of proteins for beneficial use but can cause losses to stability and/or activity. State of the art methods to limit these deleterious effects accomplish this by substituting an amino acid in the wild-type molecule into an unnatural amino acid, such as -azidophenylalanine (pAz), but selecting the residue for substitution a priori remains an elusive goal of protein engineering. The results of this work indicate that all-atom molecular dynamics simulation can be used to determine whether substituting pAz for a natural amino acid will be detrimental to experimentally determined protein stability. These results offer significant hope that local deviations from wild-type structure caused by pAz incorporation observed in simulations can be a predictive metric used to reduce the number of costly experiments that must be done to find active proteins upon substitution with pAz and subsequent functionalization.
功能化通常是为了利用蛋白质的功能而进行的，但这可能导致稳定性和/或活性的损失。为了限制这些有害影响，最先进的方法是将野生型分子中的一个氨基酸替换为非天然氨基酸，如叠氮苯丙氨酸（pAz），但预先选择用于替换的残基仍然是蛋白质工程的一个难以捉摸的目标。这项工作的结果表明，全原子分子动力学模拟可用于确定用 pAz 替换天然氨基酸是否会对实验确定的蛋白质稳定性产生不利影响。这些结果为通过 pAz 掺入观察到的模拟中偏离野生型结构的局部偏差是否可以作为预测指标提供了重要希望，该预测指标可用于减少必须进行的昂贵实验的数量，这些实验必须在使用 pAz 进行取代和随后的功能化后找到具有活性的蛋白质。
