Phylogenetic approaches to the identification and characterization of protein families and superfamilies.
Phylogenetic approaches to the identification and characterization of protein families and superfamilies.
复制标题
蛋白质家族和超家族的鉴定和表征的系统发育方法。
DOI：
10.1089/mcg.1996.1.129
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发表时间：
1996
期刊：
影响因子：
--
通讯作者：
SaierJr,MH
中科院分区：
文献类型：
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作者：
SaierJr,MH
随着大规模基因组测序的出现，对计算分析的需求呈指数级增长。测序错误必须得到纠正，编码的蛋白质必须得到鉴定，功能必须分配给这些蛋白质，和遥远的系统发育关系必须得到承认，以最大限度地提高产量的信息可从基因组测序计划。计算机和人脑都有其局限性，但将它们结合起来使用，生物学家可以极大地扩展他或她的分析能力。计算机技术可以用来估计蛋白质的结构、功能、生物起源和进化。在这篇综述中，几个蛋白质家族，特别是运输，受体和转录调节蛋白质家族，现有的计算机程序的应用说明了我们目前的能力和局限性。虽然一些多结构域蛋白质家族在进化上是同质的，但其他家族具有镶嵌起源。证据的性质和发生频率的结构域改组，剪接，融合，删除和重复特定的蛋白质家族的进化过程中进行评估。它表明，特定的酶，受体，转运蛋白和转录调控蛋白的家庭共享一个共同的进化起源，经常分歧，因为域剪接和连接的功能。一些大家族在进化过程中逐渐出现，而另一些则是突然发展起来的，这是由于在相对较短的时间内发生的基因内或基因间（或两者）复制事件的爆发。有人认为，能量耦合到运输是一个晚发生的，叠加在预先存在的溶质促进机制。它还表明，几个.运输蛋白家族已经相互独立地进化，采用不同的路线，在不同的时间在进化历史中，给拓扑结构相似的跨膜蛋白复合物。
With the advent of megabase genome sequencing, the need for computational analyses increases exponentially. Sequencing errors must be corrected, encoded proteins must be identified, functions must be assigned to these proteins, and distant phylogenetic relationships must be recognized in order to maximize the yield of information obtainable from genome sequencing projects. Both the computer and the human brain have their limitations, but using them in combination, the biologist can vastly extend his or her analytic capabilities. Computer techniques can be used to estimate protein structure, function, biogenesis, and evolution. In this review, the application of available computer programs to several protein families, particularly transport, receptor, and transcriptional regulatory protein families, illustrate our current capabilities and limitations. Although some multidomain protein families are evolutionarily homogeneous, others have mosaic origins. Evidence concerning the nature and frequency of occurrence of domain shuffling, splicing, fusion, deletion, and duplication during evolution of specific protein families is evaluated. It is shown that specific families of enzymes, receptors, transport proteins, and transcriptional regulatory proteins share a common evolutionary origin, frequently diverging in function because of domain splicing and ligation. Some large families arose gradually over evolutionary time, whereas others developed suddenly, due to bursts of intragenic or intergenic (or both) duplication events occurring over relatively short periods of time. It is argued that energy coupling to transport was a late occurrence, superimposed on preexisting mechanisms of solute facilitation. It is also shown that several.transport protein families have evolved independently of each other, employing different routes, at different times in evolutionary history, to give topologically similar transmembrane protein complexes.