Prediction of protein domain boundaries from sequence alone
Prediction of protein domain boundaries from sequence alone
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DOI：
10.1110/ps.0233103
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发表时间：
2003-04-01
期刊：
影响因子：
8
通讯作者：
Melnik, BS
中科院分区：
文献类型：
--
作者：
Galzitskaya, OV;Melnik, BS
我们在这里提出了一种简单的方法来识别未知三维结构的蛋白质中的结构域边界。我们的方法基于一个假设，即蛋白质链中一个区域的高侧链熵必须由该区域内的高残基相互作用能来补偿，这可能与球的结构良好的部分相关，即与结构域单元相关。对于蛋白质结构域，这意味着结构域边界是由侧链熵值较小的氨基酸残基决定的，而侧链熵值与侧链大小有关。一方面，结构域边界上较高的Ala和Gly含量导致结构域间主链的构象熵较高。另一方面，Pro残基的存在导致结构域相对取向的铰链形成。该方法应用于从SCOP数据库中提取的具有两个连续结构域的646个蛋白，成功率为63%。我们还报道了用同样的方法预测CASP5靶点的结构域边界。
We present here a simple approach to identify domain boundaries in proteins of an unknown three-dimensional structure. Our method is based on the hypothesis that a high-side chain entropy of a region in a protein chain must be compensated by a high-residue interaction energy within the region, which could correlate with a well-structured part of the globule, that is, with a domain unit. For protein domains, this means that the domain boundary is conditioned by amino acid residues with a small value of side chain entropy, which correlates with the side chain size. On the one hand, relatively high Ala and Gly content on the domain boundary results in high conformational entropy of the backbone chain between the domains. On the other hand, the presence of Pro residues leads to the formation of hinges for a relative orientation of domains. The method was applied to 646 proteins with two contiguous domains extracted from the SCOP database with a success rate of 63%. We also report the prediction of domain boundaries for CASP5 targets obtained with the same method.