Analysis of 3D structural differences in the IgG-binding domains based on the interresidue average-distance statistics
Analysis of 3D structural differences in the IgG-binding domains based on the interresidue average-distance statistics
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DOI：
10.1007/s00726-008-0082-1
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发表时间：
2008-10-01
期刊：
影响因子：
3.5
通讯作者：
Kikuchi, Takeshi
中科院分区：
文献类型：
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作者：
Kikuchi, Takeshi
众所周知，葡萄球菌蛋白A的免疫球蛋白结合域折叠成3α螺旋束结构，而链球菌蛋白G的免疫球蛋白结合域形成(α+β)结构。最近，他等人。(生物化学44：14055-14061,2005年)从蛋白A和蛋白G的野生型菌株中获得了这些蛋白的突变。这些突变体被称为蛋白质A219和蛋白质G311，结果表明，这两个突变体具有不同的三维结构，即3α螺旋束结构和(α+β)结构，尽管它们具有很高的序列同源性(59%)。我们研究的目的是阐明这种3D结构差异是如何在同源性较高的序列中编码的。为了解决这个问题，我们引入了一种基于残基间平均距离统计构建的预测接触图来预测蛋白质的折叠特性。我们将该地图称为平均距离地图(ADM)。此外，残基间距离的统计可以转换为有效的残基间势。利用这个有效的残基间势，我们计算了蛋白质在随机构象中的每个残基的接触频率，得到了与Phi值相似的值。我们将每个残基的这种接触频率称为p(Mu)值。蛋白质的p(Mu)值与PHI值的比较表明，p(Mu)值揭示了折叠起始部位的信息。利用这些技术，我们试图提取蛋白质A219和蛋白质G311在其氨基酸序列中编码的三维结构差异的信息。结果表明，ADM分析和p(Mu)值分析预测了折叠起始位置的信息，可以用来检测两种蛋白质的三维差异。
It is well-known that the IgG-binding domain from staphylococcal protein A folds into a 3 alpha helix bundle structure, while the IgG-binding domain of streptococcal protein G forms an (alpha + beta) structure. Recently, He et al. (Biochemistry 44:14055-14061, 2005) made mutants of these proteins from the wild types of protein A and protein G strains. These mutants are referred to as protein A219 and protein G311, and it was showed that these two mutants have different 3D structures, i.e., the 3 alpha helix bundle structure and the (alpha + beta) structure, respectively, despite the high sequence identity (59%). The purpose of our study was to clarify how such 3D structural differences are coded in the sequences with high homology. To address this problem, we introduce a predicted contact map constructed based on the interresidue average-distance statistics for prediction of folding properties of a protein. We refer to this map as an average distance map (ADM). Furthermore, the statistics of interresidue distances can be converted to an effective interresidue potential. We calculated the contact frequency of each residue of a protein in random conformations with this effective interresidue potential, and then we obtained values similar to phi values. We refer to this contact frequency of each residue as a p(mu) value. The comparison of the p(mu) values to the phi values for a protein suggests that p(mu) values reveal the information on the folding initiation site. Using these techniques, we try to extract the information on the difference in the 3D structures of protein A219 and protein G311 coded in their amino acid sequences in the present work. The results show that the ADM analyses and the p(mu) value analyses predict the information of folding initiation sites, which can be used to detect the 3D difference in both proteins.