Computational design of receptors for an organophosphate surrogate of the nerve agent soman
Computational design of receptors for an organophosphate surrogate of the nerve agent soman
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DOI：
10.1073/pnas.0401309101
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发表时间：
2004-05-25
影响因子：
11.1
通讯作者：
Hellinga, HW
中科院分区：
文献类型：
--
作者：
Allert, M;Rizk, SS;Hellinga, HW
我们报告的可溶性蛋白质受体的计算设计频哪醇甲基膦酸（PMPA），主要水解产物的神经毒剂梭曼。使用最近开发的计算蛋白质设计技术，两个周质结合蛋白，葡萄糖结合蛋白和核糖结合蛋白的配体结合口袋，被转换为结合PMPA，而不是它们的同源糖。这些设计在亲本蛋白中引入9-12个突变。12个测试的20个设计表现出PMPA依赖的荧光报告的发射强度的变化与45 nM和10 μ M之间的亲和力。通过丙氨酸扫描诱变在两种设计中确定了单个残基对配体结合的贡献，并且与分子模型一致。这些结果表明，可以成功地预测设计的受体与根本改变的结合特异性和亲和力的竞争对手或超过那些的亲本蛋白质。这些设计在亲本支架、序列多样性和对接配体的方向上各不相同，这表明设计问题的可能解决方案的数量很大并且是简并的。这一观察结果对生物功能的随机过程的起源有影响。这里报道的设计受体可能具有实用性的荧光生物传感器监测神经毒剂的发展。
We report the computational design of soluble protein receptors for pinacolyl methyl phosphonic acid (PMPA), the predominant hydrolytic product of the nerve agent soman. Using recently developed computational protein design techniques, the ligand-binding pockets of two periplasmic binding proteins, glucose-binding protein and ribose-binding protein, were converted to bind PMPA instead of their cognate sugars. The designs introduce 9-12 mutations in the parent proteins. Twelve of 20 designs tested exhibited PMPA-dependent changes in emission intensity of a fluorescent reporter with affinities between 45 nM and 10 muM. The contributions to ligand binding by individual residues were determined in two designs by alanine-scanning mutagenesis, and are consistent with the molecular models. These results demonstrate that designed receptors with radically altered binding specificities and affinities that rival or exceed those of the parent proteins can be successfully predicted. The designs vary in parent scaffold, sequence diversity, and orientation of docked ligand, suggesting that the number of possible solutions to the design problem is large and degenerate. This observation has implications for the genesis of biological function by random processes. The designed receptors reported here may have utility in the development of fluorescent biosensors for monitoring nerve agents.