Hu Xiaozhen, Wang Huanchen, Ke Hengming, Kuhlman Brian
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USA.
Structure. 2008 Dec 10;16(12):1799-805. doi: 10.1016/j.str.2008.09.013.
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 wild-type 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.
球状β折叠蛋白质的从头设计在很大程度上仍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向设计，即明确识别在采用不期望的构象时能量较差的序列。我们测试了是否可以使用一种不包括明确负向设计的设计算法来重新设计天然存在的β折叠蛋白质腱生蛋白的序列。变性实验表明，设计的蛋白质比野生型蛋白质显著更稳定，并且一种设计的晶体结构与设计模型紧密匹配。这些结果表明，创建折叠良好的β三明治蛋白质不需要广泛的负向设计。然而，需要注意的是，负向设计元素可能编码在从野生型蛋白质保留下来的蛋白质主链构象中。
