Evidence for the adaptation of protein pH-dependence to subcellular pH.
Evidence for the adaptation of protein pH-dependence to subcellular pH.
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DOI：
10.1186/1741-7007-7-69
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发表时间：
2009-10-22
期刊：
影响因子：
5.4
通讯作者：
Warwicker J
中科院分区：
文献类型：
--
作者：
Chan P;Warwicker J
基因组序列和推断的蛋白质编码基因的可用性，导致了几个蛋白质组范围内的等电点研究。通常，等电点分布在源于主要的酸和碱氨基酸侧链PKas的生物模式主题上的变化之后。在这样的分布中的峰的相对群体可能与环境相关，无论是对于整个生物体还是对于亚细胞区室。在亚细胞位置上平均的等电点也有与局部pH不一致的趋势，这可能与溶解度有关。我们现在计算的相关性的其他pH值依赖的属性，计算从三维结构，与亚细胞pH值。对于已知的结构和亚细胞注释的蛋白质，预测的pH值，在蛋白质是最稳定的，平均在一个位置，给出了一个显着更好的相关性与亚细胞pH值比等电点。这一观察结果与蛋白质的累积性质有关，因为单个蛋白质的最大稳定性遵循双峰等电点分布。组氨酸残基的位置是相关性的基础，这是一个结论，测试对背景的蛋白质随机相对于这个功能，并为观察到的相关性大幅下降。存在对蛋白质pH依赖性的约束，与局部pH有关，这表现在组氨酸亚蛋白质组的pKa分布中。这是讨论蛋白质的稳定性，pH值的稳态，质子浓度的波动。
The availability of genome sequences, and inferred protein coding genes, has led to several proteome-wide studies of isoelectric points. Generally, isoelectric points are distributed following variations on a biomodal theme that originates from the predominant acid and base amino acid sidechain pKas. The relative populations of the peaks in such distributions may correlate with environment, either for a whole organism or for subcellular compartments. There is also a tendency for isoelectric points averaged over a subcellular location to not coincide with the local pH, which could be related to solubility. We now calculate the correlation of other pH-dependent properties, calculated from 3D structure, with subcellular pH. For proteins with known structure and subcellular annotation, the predicted pH at which a protein is most stable, averaged over a location, gives a significantly better correlation with subcellular pH than does isoelectric point. This observation relates to the cumulative properties of proteins, since maximal stability for individual proteins follows the bimodal isoelectric point distribution. Histidine residue location underlies the correlation, a conclusion that is tested against a background of proteins randomised with respect to this feature, and for which the observed correlation drops substantially. There exists a constraint on protein pH-dependence, in relation to the local pH, that is manifested in the pKa distribution of histidine sub-proteomes. This is discussed in terms of protein stability, pH homeostasis, and fluctuations in proton concentration.
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