Protein evolution is structure dependent and non-homogeneous across the tree of life
Protein evolution is structure dependent and non-homogeneous across the tree of life
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蛋白质进化是结构依赖的并且在整个生命树中是非同质的
DOI：
10.1145/3388440.3412473
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Braun, Edward L.
中科院分区：
文献类型：
--
作者：
Pandey, Akanksha;Braun, Edward L.
蛋白质序列进化是一个复杂的过程，在整个生命树和蛋白质内部的位点之间变化。比较特定分类群的进化率矩阵（“进化枝特异性模型”）可以揭示这种差异，并提供关于蛋白质进化模式随时间变化的基础信息。然而，进化枝特异性模型只能在分类群之间的差异超过蛋白质之间的差异时才能提供这一信息。我们通过证明进化枝特异性模型拟合可以区分我们所研究的四个分类群（脊椎动物、植物、卵菌和酵母）的蛋白质来证明这一点。在70%的情况下，模型可以正确地根据起源支系对蛋白质进行分类。相对较少的维度可以解释模型之间的差异。如果对所有站点的模型参数取平均值，则模型之间80%的方差反映了进化；对于考虑蛋白质结构的模型，50%的方差反映了相对溶剂可及性，25%反映了进化支。在长期有效种群规模较小的分类群中，宽松的净化选择似乎可以解释大部分的枝间差异。对溶剂暴露位点的宽松选择与取代时氨基酸侧链体积的变化程度相关；模型之间的其他差异更为复杂。除了揭示蛋白质进化的信息外，我们的进化支特异性模型也代表了系统基因组推断的工具。可用性：模型文件可从https://github.com/ebraun68/clade_specific_prot_models获取。
Protein sequence evolution is a complex process that varies across the tree of life and among-sites within proteins. Comparing evolutionary rate matrices for specific taxa ('clade-specific models') can reveal this variation and provide information about the basis for changes in the paterns of protein evolution over time. However, clade-specific models can only provide this information if the variation among taxa exceeds the variation among proteins. We showed this to be the case by demonstrating that clade-specific model fit could distinguish among proteins from the four taxa that we examined (vertebrates, plants, oomycetes, and yeasts). Model fit classified proteins correctly by clade of origin >70% of the time. A relatively small number of dimensions can explain differences among models. If model parameters are averaged across all sites ~80% of the variance among models reflects clade; for models that consider protein structure ~50% of the variance reflected relative solvent accessibility and ~25% reflected clade. Relaxed purifying selection in taxa with smaller long-term effective population sizes appears to explain much of the among clade variance. Relaxed selection on solvent-exposed sites was correlated with the degree of change in amino acid side-chain volume for substitutions; other differences among models were more complex. Beyond the information they reveal about protein evolution, our clade-specific models also represent tools for phylogenomic inference. Availability: model files are available from htps://github.com/ebraun68/clade_specific_prot_models.
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氨基酸取代过程中谱系特异性的差异。
影响因子：
5.6
作者：
Huzurbazar, Snehalata;Kolesov, Grigory;Massey, Steven E.;Harris, Katherine C.;Churbanov, Alexander;Liberles, David A.
通讯作者：
Liberles, David A.
影响因子：
3.3
作者：
N. Goldman;J. Thorne;David C. Jones
通讯作者：
N. Goldman;J. Thorne;David C. Jones
DOI：
10.1093/protein/7.11.1323
发表时间：
1994-11-01
期刊：
PROTEIN ENGINEERING
影响因子：
--
作者：
BENNER, SA;COHEN, MA;GONNET, GH
通讯作者：
GONNET, GH
DOI：
10.1101/378893
发表时间：
2018-08
期刊：
bioRxiv
影响因子：
--
作者：
Claudia C. Weber;S. Whelan
通讯作者：
Claudia C. Weber;S. Whelan
影响因子：
6.5
作者：
Jayaswal, Vivek;Robinson, John;Jermiin, Lars
通讯作者：
Jermiin, Lars