Routine phasing of coiled-coil protein crystal structures with AMPLE.
Routine phasing of coiled-coil protein crystal structures with AMPLE.
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DOI：
10.1107/s2052252515002080
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发表时间：
2015-03-01
期刊：
影响因子：
3.9
通讯作者：
Rigden DJ
中科院分区：
文献类型：
--
作者：
Thomas JM;Keegan RM;Bibby J;Winn MD;Mayans O;Rigden DJ
AMPLE通过从头算结构预测的分子替换，解决了80%的不同结构的大组螺旋蛋白靶点。成功的目标包括多达253个残基，衍射只有2.9 Å分辨率的情况和含有其他折叠或DNA的蛋白质的大分子复合物。盘绕的蛋白质折叠是自然界中最丰富的。这些褶皱由长缠绕的α-螺旋组成，结构简单，但矛盾的是，它们的晶体结构很难用分子替代技术来解决。AMPLE程序可以在不存在同源蛋白质结构的情况下，利用从头算搜索模型通过分子替换来求解晶体结构。AMPLE已经在一个大而多样的线圈晶体结构测试集上进行了基准测试，并发现解决了80%的所有情况。成功的包括链长高达253个残基的结构和分辨率低至2.9 Å，大大扩展了通常由从头算方法处理的尺寸和分辨率的限制。两个大分子复合物的结构，其中一个包括DNA，也成功地解决了使用他们的盘绕线圈组件。通过与使用单一结构或理想聚丙氨酸螺旋的相位尝试进行比较，证明了从头算模型和集成搜索模型的使用都有助于AMPLE的成功。这些成功表明，分子置换与AMPLE应该是选择的方法，为晶体图形阐明一个卷曲的线圈结构。此外，AMPLE可能能够利用复合材料中线圈线圈的存在，为相位提供方便的途径。
AMPLE solved 80% of a large set of coiled-coil protein targets of diverse architectures by molecular replacement with ab initio structure predictions. Successes included targets of up to 253 residues, cases of diffraction to only 2.9 Å resolution and macromolecular complexes containing proteins with other folds or DNA. Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The program AMPLE can solve crystal structures by molecular replacement using ab initio search models in the absence of an existent homologous protein structure. AMPLE has been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable by ab initio methodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both the ab initio modelling and the use of ensemble search models contribute to the success of AMPLE by comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement with AMPLE should be the method of choice for the crystallographic elucidation of a coiled-coil structure. Furthermore, AMPLE may be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.