The role played by environmental residues on sidechain torsional angles within homologous families of proteins: A new method of sidechain modeling
The role played by environmental residues on sidechain torsional angles within homologous families of proteins: A new method of sidechain modeling
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环境残基对蛋白质同源家族中侧链扭转角的作用：侧链建模的新方法
DOI：
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发表时间：
1998
期刊：
影响因子：
--
通讯作者：
H. Umeyama
中科院分区：
文献类型：
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作者：
K. Ogata;H. Umeyama
我们研究了蛋白质数据库(PDB)中同源蛋白质家族中每个残基的侧链构象保守性，并利用这些信息进行了侧链建模。信息由从许多蛋白质家族获得的保守的侧链扭角的概率表示，这些概率是计算由于结构比对而在拓扑等价位置上的一对残基的概率。获得了一对相同氨基酸和一对不同氨基酸的概率。对同一对氨基酸残基进行了环境残留量与概率波动的相关性检验，对不同氨基酸对进行了简单概率计算。从同一对氨基酸的分析结果来看，除丙氨酸、甘氨酸和Pro外，17种氨基酸可分为受环境残留物影响的和不受环境残留物影响的两种类型。根据对不同氨基酸对的结果，在假设大残基如Trp、Phe和Tyr在同源蛋白质家族中扭转角保持不变的情况下，进行了替换。我们对11个已知蛋白质分别进行了侧链建模，这些蛋白质来自它们的天然骨架和建模骨架。对于天然脊骨，χ-1角在30°以内的正确率分别为67%和80%。对于建模的骨架，所有和核心残基的正确χ1角的百分比分别为60%和72%。为了估计预测侧链构象准确度的上限，我们研究了高度相似的蛋白质具有90%的序列一致性和2.5%的X射线分辨率的侧链扭转角守恒的可能性。在这些蛋白质中，83%的侧链构象对于χ1角是保守的。蛋白质31：355-369,1998。©1998 Wiley-Liss，Inc.
We investigated the conservation of sidechain conformation for each residue within a homologous family of proteins in the Protein Data Bank (PDB) and performed sidechain modeling using this information. The information was represented by the probability of conserved sidechain torsional angles obtained from many families of proteins, and these were calculated for a pair of residues at topologically equivalent positions as a result of structural alignment. Probabilities were obtained for a pair of same amino acids and for a pair of different amino acids. The correlation between environmental residues and the fluctuation of probability was examined for the pair of same amino acid residues, and the simple probability was calculated for the pair of different amino acids. From the results on the same amino acid pairs, 17 amino acids, except for Ala, Gly, and Pro, were divided into two types: those that were influenced and those that were not influenced by the environmental residues. From results on different amino acid pairs, a replacement between large residues, such as Trp, Phe, and Tyr, was performed assuming conservation of their torsional angles within a homologous family of proteins. We performed sidechain modeling for 11 known proteins from their native and modeled backbones, respectively. With the native backbones, the percentage of the χ1 angle correct within 30° was found to be 67% and 80% for all and core residues, respectively. With the modeled backbones, the percentage of the correct χ1 angle was found to be 60% and 72% for all and core residues, respectively. To estimate an upper limit on the accuracy for predicting sidechain conformations, we investigated the probability of conserved sidechain torsional angles for highly similar proteins having > 90% sequence identity and <2.5‐Å X‐ray resolution. In those proteins, 83% of the sidechain conformations were conserved for the χ1 angle. Proteins 31:355–369, 1998. © 1998 Wiley‐Liss, Inc.
影响因子：
5.6
作者：
Bower, MJ;Cohen, FE;Dunbrack, RL
通讯作者：
Dunbrack, RL
影响因子：
5.6
作者：
LEVITT, M
通讯作者：
LEVITT, M