Makhlynets O V, Korendovych I V
Syracuse University, Syracuse, NY, United States.
Syracuse University, Syracuse, NY, United States.
Methods Enzymol. 2016;580:191-202. doi: 10.1016/bs.mie.2016.05.055. Epub 2016 Jun 29.
Nature facilitates chemical transformations with exceptional selectivity and efficiency. Despite a tremendous progress in understanding and predicting protein function, the overall problem of designing a protein catalyst for a given chemical transformation is far from solved. Over the years, many design techniques with various degrees of complexity and rational input have been developed. Minimalist approach to protein design that focuses on the bare minimum requirements to achieve activity presents several important advantages. By focusing on basic physicochemical properties and strategic placing of only few highly active residues one can feasibly evaluate in silico a very large variety of possible catalysts. In more general terms minimalist approach looks for the mere possibility of catalysis, rather than trying to identify the most active catalyst possible. Even very basic designs that utilize a single residue introduced into nonenzymatic proteins or peptide bundles are surprisingly active. Because of the inherent simplicity of the minimalist approach computational tools greatly enhance its efficiency. No complex calculations need to be set up and even a beginner can master this technique in a very short time. Here, we present a step-by-step protocol for minimalist design of functional proteins using basic, easily available, and free computational tools.
自然界能以极高的选择性和效率促进化学反应。尽管在理解和预测蛋白质功能方面取得了巨大进展，但为特定化学反应设计蛋白质催化剂的整体问题远未解决。多年来，已开发出许多具有不同程度复杂性和合理输入的设计技术。专注于实现活性的最低要求的简约蛋白质设计方法具有几个重要优点。通过关注基本的物理化学性质以及仅对少数高活性残基进行策略性定位，人们可以在计算机上可行地评估非常多种可能的催化剂。更一般地说，简约方法寻求的仅仅是催化的可能性，而不是试图识别可能的最具活性的催化剂。即使是利用引入非酶蛋白或肽束中的单个残基的非常基本的设计也具有惊人的活性。由于简约方法固有的简单性，计算工具极大地提高了其效率。无需设置复杂的计算，即使是初学者也能在很短的时间内掌握这项技术。在此，我们使用基本、易于获得且免费的计算工具，给出一份功能性蛋白质简约设计的分步方案。
