The effect of long-range interactions on the secondary structure formation of proteins
The effect of long-range interactions on the secondary structure formation of proteins
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DOI：
10.1110/ps.051479505
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发表时间：
2005-08-01
期刊：
影响因子：
8
通讯作者：
Kihara, D
中科院分区：
文献类型：
--
作者：
Kihara, D
长程残基相互作用对蛋白质二级结构的影响已经讨论了很长时间，并且经常被引用为当前精确二级结构预测的限制。有几个实验的例子，其中一个局部序列本身是不足以确定其二级结构，但一个大的数据集上的全面调查尚未完成。有趣的是，一些早期的研究否认了长程相互作用对二级结构预测准确性的负面影响。在这里，我们引入了残基接触顺序（RCO），它直接表示在序列中的位置方面的接触残基的分离，并检查RCO和预测精度之间的关系。在我们的分析中使用了2777个非同源蛋白质的大数据集。与以前的研究不同，我们确实发现，预测精度下降，因为残基与更远的残基接触。此外，RCO和预测精度之间的这种负相关性不仅被发现用于β-链，而且用于α-螺旋。如果残基具有高RCO或低RCO，则β-链的预测准确度较低，这对应于蛋白质复合物中不同链的β-链形成β-折叠的情况。本研究得出与以往研究相反结论的原因进行了分析。蛋白质折叠的影响进行了讨论。
The influence of long-range residue interactions on defining secondary structure in a protein has long been discussed and is often cited as the current limitation to accurate secondary structure prediction. There are several experimental examples where a local sequence alone is not sufficient to determine its secondary structure, but a comprehensive survey on a large data set has not yet been done. Interestingly, some earlier studies denied the negative effect of long-range interactions on secondary structure prediction accuracy. Here, we have introduced the residue contact order (RCO), which directly indicates the separation of contacting residues in terms of the position in the sequence, and examined the relationship between the RCO and the prediction accuracy. A large data set of 2777 nonhomologous proteins was used in our analysis. Unlike previous studies, we do find that prediction accuracy drops as residues have contacts with more distant residues. Moreover, this negative correlation between the RCO and the prediction accuracy was found not only for beta-strands, but also for alpha-helices. The prediction accuracy of beta-strands is lower if residues have a high RCO or a low RCO, which corresponds to the situation that a beta-sheet is formed by beta-strands from different chains in a protein complex. The reason why the current study draws the opposite conclusion from the previous studies is examined. The implication for protein folding is also discussed.