Evidence for nonrandom hydrophobicity structures in protein chains.
Evidence for nonrandom hydrophobicity structures in protein chains.
复制标题
蛋白质链中非随机疏水性结构的证据。
DOI：
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发表时间：
1995
影响因子：
11.1
通讯作者：
F. Potthast
中科院分区：
文献类型：
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作者：
A. Irback;C. Peterson;F. Potthast
蛋白质是否起源于氨基酸的随机序列的问题得到解决。通过沿着蛋白质链沿着氨基酸的二元疏水分配形成的阻断和随机游走值进行统计分析。从疏水性的随机分布这些变量的理论预期进行比较与功能蛋白质。基于SWISS-PROT数据库中蛋白质的结果令人信服地表明，蛋白质中的氨基酸序列与随机序列的预期序列在统计学上显著不同。通过对随机游动进行傅立叶变换，可以获得分布非随机性的额外证据。我们还分析了只含有两种氨基酸类型（疏水性和亲水性）的合成模型的结果。在结晶学和动力学行为方面具有良好折叠性质的合理标准，分离出折叠良好的序列。对折叠良好的序列进行相同的统计分析表明，与功能蛋白质的随机性有类似的偏差。从随机性的偏差可以被解释为起源于一个伊辛自旋模型的疏水性方面的关系。我们的研究结果，这不同于以前的一些调查，使用其他方法，可能会有影响如何允许相对于序列特异性蛋白质折叠过程是只有序列与非随机疏水性分布折叠好。其他分布产生的能量景观具有较差的折叠特性，因此没有在进化中幸存下来。
The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along the protein chains. Theoretical expectations of these variables from random distributions of hydrophobicities are compared with those obtained from functional proteins. The results, which are based upon proteins in the SWISS-PROT data base, convincingly show that the amino acid sequences in proteins differ from what is expected from random sequences in a statistically significant way. By performing Fourier transforms on the random walks, one obtains additional evidence for nonrandomness of the distributions. We have also analyzed results from a synthetic model containing only two amino acid types, hydrophobic and hydrophilic. With reasonable criteria on good folding properties in terms of thermodynamical and kinetic behavior, sequences that fold well are isolated. Performing the same statistical analysis on the sequences that fold well indicates similar deviations from randomness as for the functional proteins. The deviations from randomness can be interpreted as originating from anticorrelations in terms of an Ising spin model for the hydrophobicities. Our results, which differ from some previous investigations using other methods, might have impact on how permissive with respect to sequence specificity protein folding process is-only sequences with nonrandom hydrophobicity distributions fold well. Other distributions give rise to energy landscapes with poor folding properties and hence did not survive the evolution.