OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method
OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method
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OMPcontact：一种外膜蛋白桶间残留物接触预测方法
DOI：
10.1089/cmb.2015.0236
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发表时间：
2017-03
影响因子：
1.7
通讯作者：
王晗
中科院分区：
文献类型：
--
作者：
王晗
在两种跨膜蛋白中，外膜蛋白（OMPs）具有多种重要的生化功能，包括底物转运和被动营养吸收和摄入。因此，它们的3D结构有望揭示这些功能。由于实验结构的缺乏，预测的三维结构更适合OMP研究，而桶间残基接触成为最显著的特征之一，通过描述OMP的结构信息提高了预测精度。为了准确预测OMP结构，我们探索了一种OMP桶间残留物接触预测方法：OMPcontact。在该方法中集成了多种OMP特异性特征，包括残基进化协变、基于拓扑结构的跨膜片段相对残基位置、OMP脂质层可及性和残基进化保守性。这些特征描述了残基对在不同方面的性质：序列、结构、进化和生物化学。在3个残基的滑动窗口内，支持向量机（SVM）可以使用上述特征准确地确定筒间接触残基对。一个5倍的交叉评估过程中应用的测试OMPcontact性能对非冗余OMP集与75个样本内。试验比较了四种进化协变方法，并筛选分析了适用于枪管间接触预测的进化协变方法。结果表明，该方法不仅能有效地实现预测，而且能可靠地对残基对的可能性进行评分。这有望改善OMP三级结构预测。因此，OMPcontact将有助于编制外膜蛋白的结构普查。
In the two transmembrane protein types, outer membrane proteins (OMPs) perform diverse important biochemical functions, including substrate transport and passive nutrient uptake and intake. Hence their 3D structures are expected to reveal these functions. Because experimental structures are scarce, predicted 3D structures are more adapted to OMP research instead, and the inter-barrel residue contact is becoming one of the most remarkable features, improving prediction accuracy by describing the structural information of OMPs. To predict OMP structures accurately, we explored an OMP inter-barrel residue contact prediction method: OMPcontact. Multiple OMP-specific features were integrated in the method, including residue evolutionary covariation, topology-based transmembrane segment relative residue position, OMP lipid layer accessibility, and residue evolution conservation. These features describe the properties of a residue pair in different respects: sequential, structural, evolutionary, and biochemical. Within a 3-residues slide window, a Support Vector Machine (SVM) could accurately determinate the inter-barrel contact residue pair using above features. A 5-fold cross-valuation process was applied in testing the OMPcontact performance against a non-redundant OMP set with 75 samples inside. The tests compared four evolutionary covariation methods and screen analyzed the adaptive ones for inter-barrel contact prediction. The results showed our method not only efficiently realized the prediction, but also scored the possibility for residue pairs reliably. This is expected to improve OMP tertiary structure prediction. Therefore, OMPcontact will be helpful in compiling a structural census of outer membrane protein.
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DOI：
10.1002/prot.20195
发表时间：
2004-10
期刊：
Proteins: Structure
影响因子：
--
作者：
S. Shacham;Y. Marantz;S. Bar-Haim;O. Kalid;D. Warshaviak;N. Avisar;B. Inbal;Alexander Heifetz;M. Fichman;M. Topf;Z. Naor;S. Noiman;O. Becker
通讯作者：
S. Shacham;Y. Marantz;S. Bar-Haim;O. Kalid;D. Warshaviak;N. Avisar;B. Inbal;Alexander Heifetz;M. Fichman;M. Topf;Z. Naor;S. Noiman;O. Becker
影响因子：
3
作者：
Eickholt J;Cheng J
通讯作者：
Cheng J
基于预测拓扑结构的跨膜蛋白比对和折叠识别。
影响因子：
3.7
作者：
Wang H;He Z;Zhang C;Zhang L;Xu D
通讯作者：
Xu D
影响因子：
14.9
作者：
Tegge AN;Wang Z;Eickholt J;Cheng J
通讯作者：
Cheng J
影响因子：
5.8
作者：
Di Lena, Pietro;Nagata, Ken;Baldi, Pierre
通讯作者：
Baldi, Pierre