Nadra Alejandro D, Serrano Luis, Alibés Andreu
Departamentos de Química Biológica y Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina.
Methods Enzymol. 2011;498:3-18. doi: 10.1016/B978-0-12-385120-8.00001-2.
With the advent of Synthetic Biology, a field between basic science and applied engineering, new computational tools are needed to help scientists reach their goal, their design, optimizing resources. In this chapter, we present a simple and powerful method to either know the DNA specificity of a wild-type protein or design new specificities by using the protein design algorithm FoldX. The only basic requirement is having a good resolution structure of the complex. Protein-DNA interaction design may aid the development of new parts designed to be orthogonal, decoupled, and precise in its target. Further, it could help to fine-tune the systems in terms of specificity, discrimination, and binding constants. In the age of newly developed devices and invented systems, computer-aided engineering promises to be an invaluable tool.
随着合成生物学这一基础科学与应用工程之间领域的出现，需要新的计算工具来帮助科学家实现他们的目标，即进行设计并优化资源。在本章中，我们介绍一种简单而强大的方法，用于了解野生型蛋白质的DNA特异性或通过使用蛋白质设计算法FoldX设计新的特异性。唯一的基本要求是拥有复合物的高分辨率结构。蛋白质-DNA相互作用设计可能有助于开发旨在具有正交性、解耦性且对其靶标精确的新部件。此外，它有助于在特异性、区分能力和结合常数方面对系统进行微调。在新开发的设备和发明的系统的时代，计算机辅助工程有望成为一种非常有价值的工具。
