Specificity versus stability in computational protein design
Specificity versus stability in computational protein design
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DOI：
10.1073/pnas.0506124102
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发表时间：
2005-09-06
影响因子：
11.1
通讯作者：
Sauer, RT
中科院分区：
文献类型：
--
作者：
Bolon, DN;Grant, RA;Sauer, RT
蛋白质-蛋白质相互作用可以通过使用最大化期望结构稳定性的积极策略和/或寻求破坏竞争状态的消极策略来计算设计。在这里，我们比较了这些方法在将蛋白质同源二聚体重组为异源二聚体方面的功效。稳定性设计蛋白（仅阳性设计）在实验上比特异性设计异二聚体（阳性和阴性设计）更稳定。相比之下，只有特异性设计蛋白在溶液中以异质二聚体的形式组装，而稳定性设计蛋白则形成异质二聚体和异质二聚体的混合物。工程蛋白的实验稳定性与计算稳定性大致相关，特异性设计的异源二聚体的晶体结构显示了大部分预测的侧链包装相互作用，并且与野生型结构的主链构象难以区分。这些结果表明，设计模拟捕获了稳定性和结构的重要特征，并表明当竞争状态在结构空间中接近时，负设计对于获得特异性至关重要。
Protein-protein interactions can be designed computationally by using positive strategies that maximize the stability of the desired structure and/or by negative strategies that seek to destabilize competing states. Here, we compare the efficacy of these methods in reengineering a protein homodimer into a heterodimer. The stability-design protein (positive design only) was experimentally more stable than the specificity-design heterodimer (positive and negative design). By contrast, only the specificity-design protein assembled as a homogenous heterodimer in solution, whereas the stability-design protein formed a mixture of homodimer and heteroclimer species. The experimental stabilities of the engineered proteins correlated roughly with their calculated Stabilities, and the crystal structure of the specificity-design heterodimer showed most of the predicted side-chain packing interactions and a mainchain conformation indistinguishable from the wild-type structure. These results indicate that the design simulations capture important features of both stability and structure and demonstrate that negative design can be critical for attaining specificity when competing states are close in structure space.