Robust folding of a de novo designed ideal protein even with most of the core mutated to valine.
Robust folding of a de novo designed ideal protein even with most of the core mutated to valine.
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从头设计的理想蛋白质的稳健折叠即使大多数核心突变为Valine。
DOI：
10.1073/pnas.2002120117
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发表时间：
2020-12-08
影响因子：
11.1
通讯作者：
Koga N
中科院分区：
文献类型：
--
作者：
Koga R;Yamamoto M;Kosugi T;Kobayashi N;Sugiki T;Fujiwara T;Koga N
与天然存在的蛋白质相比，从头设计的蛋白质表现出极高的热稳定性的显着特性。设计的蛋白质针对折叠进行了完全优化；主链结构是通过使用一组将局部主链结构与优选的三级基序相关联的规则来创建的，并且侧链被设计为有利于局部主链结构和整个三级结构。在这里，我们发现一种从头设计的蛋白质，经过突变以大部分缬氨酸残基填充核心，即使其核心堆积减少和松弛，仍然具有折叠能力并显示出高稳定性（Tm = 106 °C）。这一结果支持了局部主链结构对蛋白质折叠的重要性。蛋白质设计为我们对蛋白质折叠的理解提供了严格的考验。我们之前描述了设计通过一致的局部和非局部相互作用稳定的理想蛋白质结构的原则，基于一组将局部主链结构与三级包装基序相关的规则。这些原理使得设计具有各种拓扑且具有高热稳定性的蛋白质结构成为可能。尽管传统上认为紧密疏水核心堆积等非局部相互作用对于蛋白质折叠和稳定性至关重要，但我们之前的研究提出的规则表明局部主链结构对蛋白质折叠的重要性。在这项研究中，我们通过将其中一种设计的大疏水残基（Leu、Ile）广泛突变为较小疏水残基（Val），研究了从头设计的蛋白质折叠对疏水核心减少的稳健性。令人惊讶的是，即使在10个Leu和Ile残基突变为Val后，这种核心大部分由Val填充的突变体也被发现不处于熔球状态，并且折叠成与原始设计相同的骨架结构，具有很高的稳定性。这些结果表明局部主链结构对设计蛋白质的折叠能力和高热稳定性的重要性，并提出了一种工程热稳定天然蛋白质的方法。
De novo designed proteins exhibit a remarkable property of extremely high thermal stability compared with naturally occurring proteins. The designed proteins are completely optimized for folding; the backbone structures are created by using a set of rules that relate local backbone structures to preferred tertiary motifs and the side chains are designed to favor both the local backbone structures and the entire tertiary structures. Here, we found that one of the de novo designed proteins, which was mutated to fill the core with mostly valine residues, still has the folding ability and shows high stability (Tm = 106 °C) even with its reduced and loosened core packing. This result supports the importance of local backbone structures to protein folding. Protein design provides a stringent test for our understanding of protein folding. We previously described principles for designing ideal protein structures stabilized by consistent local and nonlocal interactions, based on a set of rules relating local backbone structures to tertiary packing motifs. The principles have made possible the design of protein structures having various topologies with high thermal stability. Whereas nonlocal interactions such as tight hydrophobic core packing have traditionally been considered to be crucial for protein folding and stability, the rules proposed by our previous studies suggest the importance of local backbone structures to protein folding. In this study, we investigated the robustness of folding of de novo designed proteins to the reduction of the hydrophobic core, by extensive mutation of large hydrophobic residues (Leu, Ile) to smaller ones (Val) for one of the designs. Surprisingly, even after 10 Leu and Ile residues were mutated to Val, this mutant with the core mostly filled with Val was found to not be in a molten globule state and fold into the same backbone structure as the original design, with high stability. These results indicate the importance of local backbone structures to the folding ability and high thermal stability of designed proteins and suggest a method for engineering thermally stabilized natural proteins.
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影响因子：
64.8
作者：
通讯作者：
--
影响因子：
64.8
作者：
Chevalier A;Silva DA;Rocklin GJ;Hicks DR;Vergara R;Murapa P;Bernard SM;Zhang L;Lam KH;Yao G;Bahl CD;Miyashita SI;Goreshnik I;Fuller JT;Koday MT;Jenkins CM;Colvin T;Carter L;Bohn A;Bryan CM;Fernández-Velasco DA;Stewart L;Dong M;Huang X;Jin R;Wilson IA;Fuller DH;Baker D
通讯作者：
Baker D
影响因子：
14.8
作者：
Huang PS;Feldmeier K;Parmeggiani F;Velasco DAF;Höcker B;Baker D
通讯作者：
Baker D
影响因子：
15
作者：
HO, SP;DEGRADO, WF
通讯作者：
DEGRADO, WF
DOI：
10.1126/science.aad8036
发表时间：
2016-05-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jacobs TM;Williams B;Williams T;Xu X;Eletsky A;Federizon JF;Szyperski T;Kuhlman B
通讯作者：
Kuhlman B