High-resolution structure prediction of β-barrel membrane proteins
High-resolution structure prediction of β-barrel membrane proteins
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β-桶膜蛋白的高分辨率结构预测
DOI：
10.1073/pnas.1716817115
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发表时间：
2018
期刊：
影响因子：
--
通讯作者：
Hammad Naveed
中科院分区：
文献类型：
--
作者：
Wei Tian;Meishan Lin;Ke Tang;Jie Liang;Hammad Naveed
意义 β-桶膜蛋白（βMP）因其在生物纳米技术中的巨大潜力而受到越来越多的关注。然而，众所周知，它们的结构很难通过实验确定。在这里，我们开发了一种方法来实现 βMP 结构的精确预测，包括那些以前从未尝试过预测的结构。该方法具有通用性，可应用于βMPs的全基因组结构预测，这将有助于βMPs的生物纳米技术和成药性研究。 β-桶膜蛋白（βMP）发挥着重要作用，但对其结构的了解有限。我们开发了一种方法来预测它们的 3D 结构。我们准确预测链寄存器并构建 βMP 的跨膜 (TM) 结构域，包括以前从未尝试过预测的蛋白质。我们的方法还可以准确预测具有有限数量序列的蛋白质家族和具有新颖折叠的蛋白质的结构。预测的 TM 结构域结构与实验解析的 TM 结构域结构之间的平均主链 rmsd 为 3.48 Å，这比最近的研究有了显着改进 (>3 Å)。对于具有 NMR 结构的 βMP，预测与实验解析结构之间的偏差与 NMR 结构之间的差异相似，表明预测精度很高。此外，我们现在可以准确地对非 TM 域中的扩展 β-桶和环进行建模，将结构预测的总体覆盖率提高了 30% 以上。我们的方法是通用的，可以应用于βMPs的全基因组结构预测。
Significance β-Barrel membrane proteins (βMPs) are drawing increasing attention because of their promising potential in bionanotechnology. However, their structures are notoriously hard to determine experimentally. Here we develop a method to achieve accurate prediction of βMP structures, including those for which no prediction has been attempted before. The method is general and can be applied to genome-wide structural prediction of βMPs, which will enable research into bionanotechnology and drugability of βMPs. β-Barrel membrane proteins (βMPs) play important roles, but knowledge of their structures is limited. We have developed a method to predict their 3D structures. We predict strand registers and construct transmembrane (TM) domains of βMPs accurately, including proteins for which no prediction has been attempted before. Our method also accurately predicts structures from protein families with a limited number of sequences and proteins with novel folds. An average main-chain rmsd of 3.48 Å is achieved between predicted and experimentally resolved structures of TM domains, which is a significant improvement (>3 Å) over a recent study. For βMPs with NMR structures, the deviation between predictions and experimentally solved structures is similar to the difference among the NMR structures, indicating excellent prediction accuracy. Moreover, we can now accurately model the extended β-barrels and loops in non-TM domains, increasing the overall coverage of structure prediction by >30%. Our method is general and can be applied to genome-wide structural prediction of βMPs.
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影响因子：
5.6
作者：
Naveed, Hammad;Jimenez-Morales, David;Tian, Jun;Pasupuleti, Volga;Kenney, Linda J.;Liang, Jie
通讯作者：
Liang, Jie
影响因子：
5.6
作者：
Gessmann D;Mager F;Naveed H;Arnold T;Weirich S;Linke D;Liang J;Nussberger S
通讯作者：
Nussberger S
影响因子：
17.1
作者：
Fahie M;Chisholm C;Chen M
通讯作者：
Chen M
影响因子：
15
作者：
Cierpicki, Tomasz;Liang, Binyong;Bushweller, John H.
通讯作者：
Bushweller, John H.
影响因子：
17.1
作者：
Ayub M;Stoddart D;Bayley H
通讯作者：
Bayley H