On the significance of alternating patterns of polar and non-polar residues in beta-strands
On the significance of alternating patterns of polar and non-polar residues in beta-strands
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DOI：
10.1016/s0022-2836(02)00973-7
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发表时间：
2002-10-25
影响因子：
5.6
通讯作者：
Gregoret, LM
中科院分区：
文献类型：
--
作者：
Mandel-Gutfreund, Y;Gregoret, LM
关于β链中蛋白质序列的一个常见假设是它们具有极性和非极性残基的交替模式。据认为，这种模式反映了β-折叠上氨基酸残基侧链的内部/外部几何形状。在这里，我们研究了简单的疏水性模式在已知结构的蛋白质和淀粉样蛋白的序列中的平行和反平行β-折叠的流行。在1911个非同源蛋白质结构中计算了32种可能的五肽二元模式（极性（P）/非极性（N））的出现。尽管它们倾向于在实验设计的蛋白质中聚集，但纯粹交替的疏水/极性模式（PNPNP和NPNPN）在β折叠中最常见，通常发生在反平行链中。五肽二元模式的总体分布在平行和反平行片内的链中显著不同。在这两种类型的片，互补的模式（其中疏水性和极性残基彼此配对）相关联的优先。我们没有发现交替模式在淀粉样蛋白或直接参与淀粉样蛋白形成的短片段中是常见的。然而，我们确实注意到淀粉样蛋白生成序列和平行链中的模式之间存在一些相似之处。(C)2002爱思唯尔科技有限公司。保留所有权利。
A common assumption about protein sequences in beta-strands is that they have alternating patterns of polar and non-polar residues. It is thought that such patterns reflect the interior/exterior geometry of amino acid residue side-chains on a beta-sheet. Here we study the prevalence of simple hydrophobicity patterns in parallel and antiparallel beta-sheets in proteins of known structure and in the sequences of amyloidogenic proteins. The occurrence of 32 possible pentapeptide binary patterns (polar (P)/nonpolar (N)) is computed in 1911 non-homologous protein structures. Despite their tendency to aggregate in experimentally designed proteins, the purely alternating hydrophobic/polar patterns (PNPNP and NPNPN) are most frequent in beta-sheets, typically occurring in antiparallel strands. The overall distribution of the pentapeptide binary patterns is significantly different in strands within parallel and antiparallel sheets. In both types of sheets, complementary patterns (where the hydrophobic and polar residues pair with one another) associate preferentially. We do not find alternating patterns to be common in amyloidogenic proteins or in short fragments involved directly in amyloid formation. However, we do note some similarities between patterns present in amyloidogenic sequences and those in parallel strands. (C) 2002 Elsevier Science Ltd. All rights reserved.