De novo design of knotted tandem repeat proteins.
De novo design of knotted tandem repeat proteins.
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DOI：
10.1038/s41467-023-42388-y
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发表时间：
2023-10-24
影响因子：
16.6
通讯作者：
Bradley, Philip
中科院分区：
文献类型：
--
作者：
Doyle, Lindsey A.;Takushi, Brittany;Kibler, Ryan D.;Milles, Lukas F.;Orozco, Carolina T.;Jones, Jonathan D.;Jackson, Sophie E.;Stoddard, Barry L.;Bradley, Philip
从头开始的蛋白质设计方法可以创造出自然界中还没有见过的折叠蛋白质。这些方法主要集中在优化设计序列和预期构象之间的兼容性，而没有明确考虑蛋白质折叠途径。深度打结的蛋白质，其拓扑结构可能会引入大量的折叠障碍，因此代表了蛋白质设计的一个有趣的测试案例。在这里，我们报告了我们尝试设计具有三叶(31)和五叶油(51)打结拓扑的蛋白质。我们扩展了前面描述的串联重复蛋白设计算法，以构建深度打结的骨架和匹配设计的重复序列(三叶虫的N = 3个重复序列和五叶虫的N = 5个重复序列)。我们通过X射线结晶学确认了三叶设计的预期构象，并在此报告了该蛋白质的结构、稳定性和折叠行为。五叶草设计错误地折叠成不对称结构(尽管有5倍对称序列)；四个重复-重复单元中的两个与设计的骨架匹配，而另外两个分叉形成局部接触，导致三叶草而不是五叶草打结的拓扑结构。我们的结果也为打结蛋白质的折叠提供了见解。这项研究报告了成功的三叶打结蛋白质折叠的从头设计，其晶体结构与预期的三叶打结拓扑结构非常一致。
De novo protein design methods can create proteins with folds not yet seen in nature. These methods largely focus on optimizing the compatibility between the designed sequence and the intended conformation, without explicit consideration of protein folding pathways. Deeply knotted proteins, whose topologies may introduce substantial barriers to folding, thus represent an interesting test case for protein design. Here we report our attempts to design proteins with trefoil (31) and pentafoil (51) knotted topologies. We extended previously described algorithms for tandem repeat protein design in order to construct deeply knotted backbones and matching designed repeat sequences (N = 3 repeats for the trefoil and N = 5 for the pentafoil). We confirmed the intended conformation for the trefoil design by X ray crystallography, and we report here on this protein’s structure, stability, and folding behaviour. The pentafoil design misfolded into an asymmetric structure (despite a 5-fold symmetric sequence); two of the four repeat-repeat units matched the designed backbone while the other two diverged to form local contacts, leading to a trefoil rather than pentafoil knotted topology. Our results also provide insights into the folding of knotted proteins. This study reports the successful de novo design of a trefoil knotted protein fold for which the crystal structure agrees closely with the intended trefoil knot topology.
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DOI：
10.1007/978-1-62703-691-7_18
发表时间：
2014
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
--
作者：
Dyer, Kevin N;Hammel, Michal;Rambo, Robert P;Tsutakawa, Susan E;Rodic, Ivan;Classen, Scott;Tainer, John A;Hura, Greg L
通讯作者：
Hura, Greg L
金黄色葡萄球菌块状因子A是一种激活细菌粘附力的力敏感分子开关。
DOI：
10.1073/pnas.1718104115
发表时间：
2018-05-22
影响因子：
11.1
作者：
Herman-Bausier P;Labate C;Towell AM;Derclaye S;Geoghegan JA;Dufrêne YF
通讯作者：
Dufrêne YF
影响因子：
3.9
作者：
Zuo, Jiacheng;Zhan, Denghuang;Xia, Jiahao;Li, Hongbin
通讯作者：
Li, Hongbin
影响因子：
64.8
作者：
BRYANT, TN;WATSON, HC;WENDELL, PL
通讯作者：
WENDELL, PL
影响因子：
8.6
作者：
Hugel, T;Rief, M;Netz, RR
通讯作者：
Netz, RR