Conformations of amino acids in proteins
Conformations of amino acids in proteins
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DOI：
10.1107/s0907444902003359
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发表时间：
2002-05-01
期刊：
影响因子：
--
通讯作者：
Ohlson, T
中科院分区：
文献类型：
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作者：
Hovmöller, S;Zhou, T;Ohlson, T
用 Ramachandran 图分析了 PDB 1042 个蛋白质亚基中 237 384 个氨基酸的主链构象。拉马钱德兰经验图的人口稠密地区与所有地区的经典图都显着不同。 α 螺旋中的所有氨基酸均位于非常窄的 phi、psi 角度范围内。多达 40% 的氨基酸都存在于这个人口最多的区域，但仅覆盖了 Ramachandran 图的 2%。 β-折叠区域清楚地分为两个不同的区域。这些不是由平行和反平行β链产生的，它们具有非常相似的构象。一个β区主要来自无规卷曲的氨基酸。拉马钱德兰图中的第三个也是最小的人口稠密区域，通常表示为左手 α 螺旋，其位置与拉马钱德兰最初提出的位置不同。 20 种氨基酸中的每一种都有其独特的拉马钱德兰图。大多数甘氨酸具有被认为不太受欢迎的构象。这些结果可能有助于检查 PDB 中的二级结构分配和预测蛋白质折叠。
The main-chain conformations of 237 384 amino acids in 1042 protein subunits from the PDB were analyzed with Ramachandran plots. The populated areas of the empirical Ramachandran plot differed markedly from the classical plot in all regions. All amino acids in alpha-helices are found within a very narrow range of phi, psi angles. As many as 40% of all amino acids are found in this most populated region, covering only 2% of the Ramachandran plot. The beta-sheet region is clearly subdivided into two distinct regions. These do not arise from the parallel and antiparallel beta-strands, which have quite similar conformations. One beta region is mainly from amino acids in random coil. The third and smallest populated area of the Ramachandran plot, often denoted left-handed alpha-helix, has a different position than that originally suggested by Ramachandran. Each of the 20 amino acids has its own very characteristic Ramachandran plot. Most of the glycines have conformations that were considered to be less favoured. These results may be useful for checking secondary-structure assignments in the PDB and for predicting protein folding.