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首页> 外文期刊>Journal of Biomolecular Structure and Dynamics >Underlying hydrophobic sequence periodicity of protein tertiary structure.
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Underlying hydrophobic sequence periodicity of protein tertiary structure.

机译：蛋白质三级结构的潜在疏水序列周期性。

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摘要

Hydropathy plots or window averages over local stretches of the sequence of residue hydrophobicity have revealed patterns related to various protein tertiary structural features. This has enabled identification of regions of the sequence that are at the surface or within the interior of globular soluble proteins, regions located within the lipid bilayer of transmembrane proteins, portions of the sequence that characterize repeating motifs, as well as motifs that usefully characterize different protein structural families. This, therefore, provides one example of the generally expressed maxim that "sequence determines structure". On the other hand, a number of previous investigations have shown the rapidly varying values of residue hydrophobicity along the sequence to be distributed approximately randomly. So one might question just how much of the sequence actually determines structure. It is, therefore, of interest to extract that part of this rapidly varying distribution of residue hydrophobicity that is responsible for the longer wavelength variations that correlate with protein tertiary structural features and to determine their prevalence within the entire distribution. This is accomplished by a finite Fourier analysis of the sequence of residue hydrophobicity and of a new measure of residue distance from the protein interior. Calculations are performed on a number of globins, immunoglobulins, cuprodoxins, and papain-like structures. The spectral power of the Fourier amplitudes of the frequencies extracted, whose inverse transforms underlie the windowed values of residue hydrophobicity is shown to be a small fraction of the total power of the hydrophobicity distribution and thereby consistent with a distribution that might appear to be predominantly random. The wide range of sequence identity between proteins having the same fold, all exhibiting similar small fractions of power amplitude that correlate with the longer wavelength inside-to-outside excursions of the amino acid residues, supports the general contention that close sequence identity is an expression of a close evolutionary relationship rather than an expression of structural similarity. Practical implications of the present analysis for protein structure prediction and engineering are also described.
机译：残基疏水性序列的局部延伸上的亲水性图或窗均值揭示了与各种蛋白质三级结构特征有关的模式。这使得能够鉴定位于球状可溶性蛋白的表面或内部的序列区域，位于跨膜蛋白脂质双分子层内的区域，表征重复基序的序列部分以及有用地表征不同基序的基序。蛋白质结构家族。因此，这提供了通常表达的格言的一个例子，即“顺序决定结构”。另一方面，许多先前的研究表明，残基疏水性沿序列的迅速变化的值近似随机地分布。因此，人们可能会质疑到底有多少序列实际上决定了结构。因此，感兴趣的是提取残留疏水性这种迅速变化的分布的那部分，该部分负责与蛋白质三级结构特征相关的更长的波长变化，并确定它们在整个分布中的普遍性。这是通过对残基疏水性序列和距蛋白质内部残基距离的新度量进行有限傅里叶分析来完成的。对许多球蛋白，免疫球蛋白，铜氧还蛋白和木瓜蛋白酶样结构进行计算。提取频率的傅立叶振幅的频谱功率，其逆变换位于残留疏水性窗口值的基础上，显示为疏水性分布总功率的一小部分，因此与似乎主要是随机的分布一致。具有相同倍数的蛋白质之间的序列同一性范围广，均显示出相似的小幅度功率振幅，与氨基酸残基的更长波长的内外偏移相关，支持普遍的观点，即紧密序列同一性是一种表达紧密的进化关系，而不是结构相似性的表达。还介绍了本分析对蛋白质结构预测和工程化的实际意义。

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