Prediction of Protein-Protein Binding Interactions in Dimeric Coiled Coils by Information Contained in Folding Energy Landscapes.
Prediction of Protein-Protein Binding Interactions in Dimeric Coiled Coils by Information Contained in Folding Energy Landscapes.
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DOI：
10.3390/ijms22031368
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发表时间：
2021-01-29
影响因子：
5.6
通讯作者：
Bjelic S
中科院分区：
文献类型：
--
作者：
Georgoulia PS;Bjelic S
卷曲螺旋代表了两个相互作用的蛋白质伙伴之间形成的复合物的最简单形式。他们的广泛研究导致了旨在研究和设计复杂形成相互作用的各种方法的发展。尽管在预测蛋白质复合物的结合亲和力方面取得了进展，特别是针对卷曲螺旋的结合亲和力，但仍然存在许多挑战。在这项工作中，我们探索二聚体卷曲线圈折叠能量景观中包含的信息是否可用于预测结合相互作用。使用已发布的 SYNZIP 数据集，我们从氨基酸序列开始，同时折叠和对接大约 1000 个卷曲线圈二聚体。对折叠能量景观的评估表明，基于最低能量结构的簇计算数量的模型显示了与实验确定的蛋白质相互作用相关的信号。尽管揭示的相关性很弱，但我们证明这种相关性是存在的；然而，还需要做更多的工作来确定是否可以对所提出的模型进行进一步改进。
Coiled coils represent the simplest form of a complex formed between two interacting protein partners. Their extensive study has led to the development of various methods aimed towards the investigation and design of complex forming interactions. Despite the progress that has been made to predict the binding affinities for protein complexes, and specifically those tailored towards coiled coils, many challenges still remain. In this work, we explore whether the information contained in dimeric coiled coil folding energy landscapes can be used to predict binding interactions. Using the published SYNZIP dataset, we start from the amino acid sequence, to simultaneously fold and dock approximately 1000 coiled coil dimers. Assessment of the folding energy landscapes showed that a model based on the calculated number of clusters for the lowest energy structures displayed a signal that correlates with the experimentally determined protein interactions. Although the revealed correlation is weak, we show that such correlation exists; however, more work remains to establish whether further improvements can be made to the presented model.
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影响因子：
15
作者：
Reinke, Aaron W.;Grant, Robert A.;Keating, Amy E.
通讯作者：
Keating, Amy E.
影响因子：
5.6
作者：
Rao, F;Caflisch, A
通讯作者：
Caflisch, A
影响因子：
4.7
作者：
Thompson, Kenneth Evan;Bashor, Caleb J.;Lim, Wendell A.;Keating, Amy E.
通讯作者：
Keating, Amy E.
DOI：
10.1107/s0365110x53001964
发表时间：
1953-01-01
期刊：
ACTA CRYSTALLOGRAPHICA
影响因子：
--
作者：
CRICK, FHC
通讯作者：
CRICK, FHC
影响因子：
8
作者：
Chen, Jieming;Sawyer, Nicholas;Regan, Lynne
通讯作者：
Regan, Lynne