Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes.
Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes.
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DOI：
10.1371/journal.pbio.1002452
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发表时间：
2016-05
期刊：
影响因子：
9.8
通讯作者：
Wilke CO
中科院分区：
文献类型：
--
作者：
Jack BR;Meyer AG;Echave J;Wilke CO
蛋白质中的功能性残基在进化过程中往往高度保守。然而，功能性位点在多大程度上对附近甚至更远的残基施加进化限制尚不清楚。在此，我们在一个包含524种不同酶的数据集里报告了朝向催化残基的普遍保守梯度：进化保守性随着与蛋白质结构中最近的催化残基距离的增加大致呈线性下降。这种趋势平均涵盖了任何一种酶中80%的残基，并且它与蛋白质进化中已知的结构限制（如残基堆积或溶剂可及性）无关。此外，这种趋势在单体酶和多聚体酶中都存在，且与酶的大小以及活性位点在酶结构中的位置无关。相比之下，蛋白质 - 蛋白质界面处的位点与催化残基不同，它们的保守性较弱，且仅诱导较小的速率梯度。总体而言，这些观察结果表明，功能性位点，特别是催化残基，在酶中诱导了远距离的进化限制。
酶中的催化位点高度保守，但它们是否会影响邻近位点的进化保守性呢？这项研究表明，与随机位点相比，催化残基的不仅是邻近位点，而且第二、第三、第四甚至第五邻近位点都经历了进化限制。
生命的基本生化功能是由被称为酶的大分子来执行的。酶由折叠成三维结构的氨基酸长链组成。在该结构内，一组特定的氨基酸，即活性位点，执行生化功能。在活性位点中将一个氨基酸替换为另一个通常会导致有缺陷的、无功能的酶，因此酶活性位点处或其附近的突变往往是致命的。此外，甚至远离活性位点的突变也被发现会破坏功能。尽管如此，随着生物的进化，酶会积累随机突变。在酶的结构中，这些突变在哪些位置积累而不会造成危害呢？在此，我们在一组超过500种酶的综合数据集中观察到了活性位点与酶结构的远距区域之间存在广泛相互作用的证据。我们表明活性位点严格控制着酶所能容忍的替换。这种控制远远超出了紧邻活性位点的酶区域，涵盖了典型酶结构的80%以上。我们的发现对分子进化、酶工程以及新型酶中活性位点位置的计算预测都具有广泛的影响。
Functional residues in proteins tend to be highly conserved over evolutionary time. However, to what extent functional sites impose evolutionary constraints on nearby or even more distant residues is not known. Here, we report pervasive conservation gradients toward catalytic residues in a dataset of 524 distinct enzymes: evolutionary conservation decreases approximately linearly with increasing distance to the nearest catalytic residue in the protein structure. This trend encompasses, on average, 80% of the residues in any enzyme, and it is independent of known structural constraints on protein evolution such as residue packing or solvent accessibility. Further, the trend exists in both monomeric and multimeric enzymes and irrespective of enzyme size and/or location of the active site in the enzyme structure. By contrast, sites in protein–protein interfaces, unlike catalytic residues, are only weakly conserved and induce only minor rate gradients. In aggregate, these observations show that functional sites, and in particular catalytic residues, induce long-range evolutionary constraints in enzymes. Catalytic sites in enzymes are highly conserved, but do they affect the evolutionary conservation of neighboring sites? This study shows that not just nearby neighbors but also second, third, fourth, and even fifth neighbors of a catalytic residue experience evolutionary constraint compared to a random site. The basic biochemical functions of life are carried out by large molecules called enzymes. Enzymes consist of long chains of amino acids folded into a three-dimensional structure. Within that structure, a specific cluster of amino acids, known as the active site, performs the biochemical function. Substituting one amino acid for another in the active site typically results in a defective, non-functional enzyme, and therefore mutations at or near enzyme active sites are often lethal. Moreover, even mutations far from the active site have been found to disrupt function. Nonetheless, as organisms evolve, enzymes accumulate random mutations. Where in enzymes’ structures do these mutations accumulate without causing harm? Here, we observe evidence for extensive interactions between active sites and distant regions of the enzyme structure, in a comprehensive set of over 500 enzymes. We show that active sites tightly control the substitutions that an enzyme can tolerate. This control extends far beyond regions of the enzyme immediately adjacent to the active site, covering over 80% of a typical enzyme structure. Our findings have broad implications for molecular evolution, for enzyme engineering, and for the computational prediction of active-site locations in novel enzymes.