Evidence for strained interactions between side-chains and the polypeptide backbone.
Evidence for strained interactions between side-chains and the polypeptide backbone.
复制标题
侧链和多肽主链之间紧张相互作用的证据。
DOI：
10.1016/s0022-2836(05)80008-7
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发表时间：
1994
影响因子：
5.6
通讯作者：
Shortle,D
中科院分区：
文献类型：
--
作者：
Stites,WE;Meeker,AK;Shortle,D
在大多数蛋白质中，一小部分但很重要的残基采用φ、ψ角，从而在侧链原子和肽骨架之间产生不利的空间相互作用。对于小蛋白葡萄球菌核酸酶，X-射线结构显示，133个残基中有18个占据不寻常的，据推测，积极不利的骨架构象。为了量化这些局部相互作用产生的应变能的量，我们分析了用甘氨酸替换野生型侧链所伴随的稳定性变化，甘氨酸是一种可以获得更大的φ，矩形而没有能量损失的残基。为了校正可能伴随该突变的许多其他稳定性损失来源，将甘氨酸突变体与相同位置处的丙氨酸突变体进行比较，然后将所得自由能差ΔΔGG→ A与核酸酶中由相似氨基酸类型占据的所有其他未应变位置处的平均ΔΔGG→ A进行比较。此外，通过用对所有其他残基类型不利的φ，矩形取代野生型中被甘氨酸占据的六个位置中的每一个处的丙氨酸来引入潜在的空间冲突。数据表明，在优选的α-螺旋和β-折叠区域之外具有φ、矩形的残基代表局部应变能的位点，其使天然状态的稳定性降低1至2 kcal/mol，并且在某些情况下，降低多达3至4 kcal/mol。考虑到球状蛋白质中10 ~ 20%的残基在优选的α-螺旋和β-折叠区域之外采用φ，矩形，这意味着在100个残基的蛋白质中存在大约20 kcal/mol的应变能，其可以通过适当的突变来减轻。
In most proteins, a small but significant fraction of residues adoptφ,ψangles that generate unfavorable steric interactions between side-chain atoms and the peptide backbone. For the small protein staphylococcal nuclease, the X-ray structure reveals that 18 of 133 residues occupy unusual and, presumably, energetically unfavorable backbone conformations. To quantify the amount of strain energy generated by these local interactions, we have analyzed the changes in stability that accompany replacement of the wild-type side-chain with glycine, a residue that can access a much larger set ofφ,ψangles without energy penalty. To correct for the many other sources of stability loss that might accompany this mutation, the glycine mutant was compared to an alanine mutant at the same position and the resulting free energy difference ΔΔGG→Awas then compared to the average ΔΔGG→Aat all other, unstrained positions in the nuclease occupied by similar amino acid types. In addition, potential steric clashes were introduced by substituting alanine at each of six positions occupied in the wild-type by glycine withφ,ψangles that are unfavorable for all other residue types. The data suggest that residues withφ,ψangles outside the preferred α-helical andβ-sheet regions represent sites of local strain energy that lower the stability of the native state by 1 to 2 kcal/mol and, in some cases, as much as 3 to 4 kcal/mol. Given that 10 to 20% of residues in globular proteins adoptφ,ψangles outside the preferred α-helical andβ-sheet regions, this implies that there is on the order of 20 kcal/mol of strain energy in a protein of 100 residues that may be relieved by appropriate mutations.