Fu Xinmiao, Chang Zengyi, Shi Xiaodong, Bu Dongbo, Wang Chao
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
Protein Sci. 2014 Feb;23(2):229-37. doi: 10.1002/pro.2404. Epub 2013 Dec 16.
Small heat shock proteins (sHSPs) are ubiquitous molecular chaperones that prevent the aggregation of various non-native proteins and play crucial roles for protein quality control in cells. It is poorly understood what natural substrate proteins, with respect to structural characteristics, are preferentially bound by sHSPs in cells. Here we compared the structural characteristics for the natural substrate proteins of Escherichia coli IbpB and Deinococcus radiodurans Hsp20.2 with the respective bacterial proteome at multiple levels, mainly by using bioinformatics analysis. Data indicate that both IbpB and Hsp20.2 preferentially bind to substrates of high molecular weight or moderate acidity. Surprisingly, their substrates contain abundant charged residues but not abundant hydrophobic residues, thus strongly indicating that ionic interactions other than hydrophobic interactions also play crucial roles for the substrate recognition and binding of sHSPs. Further, secondary structure prediction analysis indicates that the substrates of low percentage of β-sheets or coils but high percentage of α-helices are un-favored by both IbpB and Hsp20.2. In addition, IbpB preferentially interacts with multi-domain proteins but unfavorably with α + β proteins as revealed by SCOP analysis. Together, our data suggest that bacterial sHSPs, though having broad substrate spectrums, selectively bind to substrates of certain structural features. These structural characteristic elements may substantially participate in the sHSP-substrate interaction and/or increase the aggregation tendency of the substrates, thus making the substrates more preferentially bound by sHSPs.
小分子热休克蛋白（sHSPs）是普遍存在的分子伴侣，可防止各种非天然蛋白质聚集，并在细胞的蛋白质质量控制中发挥关键作用。目前对于细胞中sHSPs优先结合的天然底物蛋白的结构特征了解甚少。在此，我们主要通过生物信息学分析，在多个层面比较了大肠杆菌IbpB和耐辐射球菌Hsp20.2的天然底物蛋白与各自细菌蛋白质组的结构特征。数据表明，IbpB和Hsp20.2都优先结合高分子量或中等酸度的底物。令人惊讶的是，它们的底物含有丰富的带电荷残基，但疏水残基并不丰富，因此强烈表明除疏水相互作用外，离子相互作用在sHSPs的底物识别和结合中也起着关键作用。此外，二级结构预测分析表明，β-折叠或卷曲比例低但α-螺旋比例高的底物不受IbpB和Hsp20.2的青睐。另外，SCOP分析显示，IbpB优先与多结构域蛋白相互作用，而不利于与α + β蛋白相互作用。总之，我们的数据表明，细菌sHSPs虽然具有广泛的底物谱，但会选择性地结合某些结构特征的底物。这些结构特征元件可能在很大程度上参与了sHSP-底物相互作用和/或增加了底物的聚集倾向，从而使底物更优先地被sHSPs结合。
