Packing is a key selection factor in the evolution of protein hydrophobic cores
Packing is a key selection factor in the evolution of protein hydrophobic cores
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DOI：
10.1021/bi011776v
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发表时间：
2001-12-18
期刊：
影响因子：
2.9
通讯作者：
Stites, WE
中科院分区：
文献类型：
--
作者：
Chen, JM;Stites, WE
在紧密排列折叠的蛋白质中，从优化的范德华相互作用中获得的能量被认为与稳定天然状态的疏水性具有相似的能量量级。如果包装在能量上如此重要，它应该影响蛋白质核心序列的进化。为了验证这一假设，我们测定了葡萄球菌核酸酶主要疏水核心和42种同源蛋白中各种氨基酸侧链的出现情况。在这个蛋白质家族中，大多数这样的位置通常是异亮氨酸、亮氨酸或缬氨酸。在此之前，我们已经构建并测量了12个单突变体、44个双突变体、64个三突变体和32个四突变体的稳定性，这些突变体代表了这三个侧链在葡萄球菌核酸酶核心的两个重叠的四个位置上的所有可能的排列。将这些突变体的稳定性和相互作用能与所有其他突变体的稳定性进行比较，这些突变体具有最常见或一致序列的各种组合。具有一致侧链组合的突变体不一定是最稳定的，但通常具有最佳的相互作用能。换句话说，这些蛋白质比简单地将观察到的单个组分突变的能量效应相加所预测的要稳定得多，显然反映了最常见侧链可能出现的特别有利的包装相互作用。另外构建了12个突变体来测试可能的结果解释。这些突变体的稳定性和相互作用能也支持了包装是指导蛋白质核心序列进化的关键决定因素的结论。
The energy derived from optimized van der Waals interactions in closely packed, folded proteins has been proposed to be of similar energetic magnitude to hydrophobicity in stabilizing the native state. If packing is this energetically important, it should influence the evolution of protein core sequences. To test this hypothesis, the occurrence of various amino acid side chains in the major hydrophobic core of staphylococcal nuclease and 42 homologous proteins was determined. Most such positions in this protein family are usually isoleucine, leucine, or valine. Previously we have constructed and measured the stabilities of 12 single, 44 double, 64 triple, and 32 quadruple mutants, representing all possible permutations of these three side chains at two overlapping sets of four positions to the core of staphylococcal nuclease. The stabilities and interaction energies of those mutants with various combinations of the most common, or consensus, sequence were compared to the stabilities of all other mutants. Mutants which had the consensus side-chain combinations were not necessarily the most stable, but usually were found to have the best interaction energies. In other words, these proteins were far more stable than would be predicted from simply summing the observed energetic effects of the component single mutations, apparently reflecting particularly favorable packing interactions that are possible for the most common side chains. An additional 12 mutants which tested possible alternate explanations of the results were constructed. The stabilities and interaction energies of these mutants also support the conclusion that packing is a crucial determinant guiding the sequence evolution of protein cores.