Robustness of Reconstructed Ancestral Protein Functions to Statistical Uncertainty
Robustness of Reconstructed Ancestral Protein Functions to Statistical Uncertainty
复制标题
DOI：
10.1093/molbev/msw223
复制
发表时间：
2017-02-01
影响因子：
10.7
通讯作者：
Thornton, Joseph W.
中科院分区：
文献类型：
--
作者：
Eick, Geeta N.;Bridgham, Jamie T.;Thornton, Joseph W.
关于古代蛋白质的功能和历史突变对它们的影响的假设经常使用祖先蛋白质重建（APR）进行测试-祖先序列的系统发育推断，然后进行合成和实验表征。通常，一些序列位点被模糊地重建，具有两个或更多个统计上合理的状态。在何种程度上推断的功能和突变的影响是强大的祖先序列的不确定性还没有系统地研究。为了解决这个问题，我们在三个具有不同功能、结构和不确定性程度的结构域家族中重建了祖先蛋白质;然后，我们实验性地表征了当使用几种方法引入不确定性时这些蛋白质的功能鲁棒性，包括从每个位点的后验分布中采样氨基酸状态，并将序列中每个模糊位点的替代氨基酸状态并入一种“最坏的可能情况”蛋白质。在每一种情况下，关于祖先蛋白质功能和关键历史突变影响的定性结论对序列不确定性都是稳健的，即使在掺入大量替代氨基酸时也观察到类似的功能。有一些变化的定量描述符之间的功能合理的序列，这表明，实验表征的鲁棒性是特别重要的，当需要定量估计的古代生化参数。最坏的合理情况下的方法似乎提供了一个有效的策略，用于表征祖先蛋白质的功能鲁棒性，大量的序列不确定性。从后验分布采样有时会产生人为的非功能性蛋白质的序列重建与大量的歧义。
Hypotheses about the functions of ancient proteins and the effects of historical mutations on them are often tested using ancestral protein reconstruction (APR)-phylogenetic inference of ancestral sequences followed by synthesis and experimental characterization. Usually, some sequence sites are ambiguously reconstructed, with two or more statistically plausible states. The extent to which the inferred functions and mutational effects are robust to uncertainty about the ancestral sequence has not been studied systematically. To address this issue, we reconstructed ancestral proteins in three domain families that have different functions, architectures, and degrees of uncertainty; we then experimentally characterized the functional robustness of these proteins when uncertainty was incorporated using several approaches, including sampling amino acid states from the posterior distribution at each site and incorporating the alternative amino acid state at every ambiguous site in the sequence into a single "worst plausible case" protein. In every case, qualitative conclusions about the ancestral proteins' functions and the effects of key historical mutations were robust to sequence uncertainty, with similar functions observed even when scores of alternate amino acids were incorporated. There was some variation in quantitative descriptors of function among plausible sequences, suggesting that experimentally characterizing robustness is particularly important when quantitative estimates of ancient biochemical parameters are desired. The worst plausible case method appears to provide an efficient strategy for characterizing the functional robustness of ancestral proteins to large amounts of sequence uncertainty. Sampling from the posterior distribution sometimes produced artifactually nonfunctional proteins for sequences reconstructed with substantial ambiguity.