Computer-Based Redesign of a β Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo β Sheet Design
Computer-Based Redesign of a β Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo β Sheet Design
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DOI：
10.1016/j.str.2008.09.013
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发表时间：
2008-12-10
期刊：
影响因子：
5.7
通讯作者：
Kuhlman, Brian
中科院分区：
文献类型：
--
作者：
Hu, Xiaozhen;Wang, Huanchen;Kuhlman, Brian
球状β-折叠蛋白的从头设计在很大程度上仍然是一个未解决的问题。目前尚不清楚大多数设计失败是因为设计的序列在目标构象中没有有利的能量，还是应该更多地强调负设计，即当采用不希望的构象时，明确识别能量较差的序列。我们测试了是否可以用一种不包括显式负设计的设计算法来重新设计自然产生的β-折叠蛋白tenascin的序列。变性实验表明，这些设计明显比野生型蛋白更稳定，其中一个设计的晶体结构与设计模型非常吻合。这些结果表明，产生折叠良好的β-夹心蛋白并不需要广泛的负设计。然而，重要的是要注意，负设计元件可能编码在从野生型蛋白质中保存的蛋白质骨架的构象中。
The de novo design of globular beta sheet proteins remains largely an unsolved problem. It is unclear whether most designs are failing because the designed sequences do not have favorable energies in the target conformations or whether more emphasis should be placed on negative design, that is, explicitly identifying sequences that have poor energies when adopting undesired conformations. We tested whether we could redesign the sequence of a naturally occurring beta sheet protein, tenascin, with a design algorithm that does not include explicit negative design. Denaturation experiments indicate that the designs are significantly more stable than the wildtype protein and the crystal structure of one design closely matches the design model. These results suggest that extensive negative design is not required to create well-folded beta sandwich proteins. However, it is important to note that negative design elements may be encoded in the conformation of the protein backbone which was preserved from the wild-type protein.