MMSB, UMR 5086 CNRS/Univ. Lyon I, Institut de Biologie et Chimie des Protéines , 7 passage du Vercors , Lyon 69367 , France.
J Phys Chem B. 2019 Feb 14;123(6):1294-1301. doi: 10.1021/acs.jpcb.8b11913. Epub 2019 Feb 6.
We analyze the capacity of normal mode analysis in internal coordinates' space to generate large-amplitude structural deformations that can describe the conformational changes occurring upon the binding of proteins to other species. We also analyze how many modes need to be studied to capture a given transition and whether a combination of two modes is better than using a single mode. The technique is tested on known unbound-to-bound structural transitions for a set of single- or multidomain proteins. The results suggest that this approach is a promising way to generate structures for protein docking or for more refined molecular dynamics simulations.
我们分析了在内部坐标空间中的正常模式分析生成大振幅结构变形的能力，这些变形可以描述蛋白质与其他物种结合时发生的构象变化。我们还分析了需要研究多少模式才能捕捉到给定的转变，以及使用两个模式的组合是否优于使用单个模式。该技术已在一组单域或多域蛋白质的已知非键合到键合的结构转变上进行了测试。结果表明，这种方法是生成蛋白质对接或更精细的分子动力学模拟结构的有前途的方法。
