A dissection of specific and non-specific protein - Protein interfaces
A dissection of specific and non-specific protein - Protein interfaces
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DOI：
10.1016/j.jmb.2003.12.073
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发表时间：
2004-02-27
影响因子：
5.6
通讯作者：
Janin, J
中科院分区：
文献类型：
--
作者：
Bahadur, RP;Chakrabarti, P;Janin, J
我们比较了蛋白质数据库中报道的晶体结构中特异性和非特异性蛋白质-蛋白质相互作用的界面的几何和物理化学性质。特异性相互作用由70种蛋白质-蛋白质复合物和122种同源二聚体蛋白质中的亚基接触来说明;非特异性相互作用由188对单体蛋白质来说明，这些单体蛋白质形成晶体包装接触，选择这些接触来掩埋超过800埃（2）的蛋白质表面。这些对中的大多数具有2重对称性，并形成“晶体二聚体”，其不能基于界面尺寸或对称性与真实的二聚体区分开。大晶体堆积界面的化学和氨基酸组成类似于蛋白质溶剂可接近的表面。这些界面比同二聚体中的疏水性更低，并且包含更少的完全掩埋的原子。我们开发了一个残基倾向得分和疏水相互作用得分，以评估偏好中看到的化学和氨基酸组成的不同类型的接口，我们得出的指数来评估原子包装，我们发现是不那么紧凑的非特异性比在特定的接口。我们测试这些参数的能力，以确定同源二聚体蛋白质的晶体结构，并表明，一个简单的组合的非极性界面面积和掩埋的界面原子的分数分配的四级结构的同源二聚体的88%和77%的单体在我们的数据集正确。当考虑界面的残留倾向评分时，这些成功率增加到93-95%。(C)2004 Elsevier Ltd.保留所有权利。
We compare the geometric and physical-chemical properties of interfaces involved in specific and non-specific protein-protein interactions in crystal structures reported in the Protein Data Bank. Specific interactions are illustrated by 70 protein-protein complexes and by subunit contacts in 122 homodimeric proteins; non-specific interactions are illustrated by 188 pairs of monomeric proteins making crystal-packing contacts selected to bury more than 800 A(2) of protein surface. A majority of these pairs have 2-fold symmetry and form "crystal dimers" that cannot be distinguished, from real dimers on the basis of the interface size or symmetry The chemical and amino acid compositions of the large crystal-packing interfaces resemble the protein solvent-accessible surface. These interfaces are less hydrophobic than in homodimers and contain much fewer fully buried atoms. We develop a residue propensity score and a hydrophobic interaction score to assess preferences seen in the chemical and amino acid compositions of the different types of interfaces, and we derive indexes to evaluate the atomic packing, which we find to be less compact at nonspecific than at specific interfaces. We test the capacity of these parameters to identify homodimeric proteins in crystal structures, and show that a simple combination of the non-polar interface area and the fraction of buried interface atoms assigns the quaternary structure of 88% of the homodimers and 77% of the monomers in our data set correctly. These success rates increase to 93-95% when the residue propensity score of the interfaces is taken into consideration. (C) 2004 Elsevier Ltd. All rights reserved.