发现一个古老的原则和蛋白质分类问题的优雅解决方案
Detection of an ancient principle and an elegant solution to the protein classification problem
摘要：
这项工作是关于发展一个有充分根据的，理论上合理的，最不复杂的指标与酶的蛋白质分类。催化结构域作为酶家族的特征分子，很容易被识别。鉴于分类问题到目前为止似乎是棘手的，从催化域派生的分类模式将是令人满意的。在这里，我表明，存在一个自然的从头算，如果不明显的基础上理论，酶的催化结构域是唯一的信息，其监管。这说明了它的功能。基于这一假设，描述了一种将钾离子通道正确分类到它们各自的亚家族中的方法。为了使这一原则更加坚实，通过共同进化分析寻求并获得了额外的验证。协同进化分析揭示了钾离子通道蛋白是功能模块化的概念的偏离。这一发现进行了讨论，根据流行的概念域。这些研究表明，基因的催化结构域与其结合结构域的显着共同进化是进化中融合和交换事件之后的一个专门的必要过程。这一发现的许多方面可能在蛋白质科学中普遍存在。
英文摘要：
This work is concerned with the development of a well-founded, theoretically justified, and least complicated metric for the classification of proteins with reference to enzymes. As the signature of an enzyme family, a catalytic domain is easily fingerprinted. Given that the classification problem has so far seemed intractable, a classification schema derived from the catalytic domain would be satisfying. Here I show that there exists a natural ab initio if nonobvious basis to theorize that the catalytic domain of an enzyme is uniquely informative about its regulation. This annotates its function. Based on this hypothesis, a method that correctly classifies potassium ion channels into their respective subfamilies is described. To put the principle on firmer ground, extra validation was sought and obtained through co-evolutionary analyses. The co-evolutionary analyses reveal a departure from the notion that potassium ion channel proteins are functionally modular. This finding is discussed in light of the prevailing notion of domain. These studies establish that significant co-evolution of the catalytic domain of a gene with its conjoint domain is a specialized, necessary process following fusion and swapping events in evolution. Instances of this discovery are likely to be found pervasive in protein science.
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