Skliros Aris, Jernigan Robert L, Kloczkowski Andrzej
L. H. Baker Center for Bioinformatics and Biological Statistics, Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
J Chem Theory Comput. 2010 Oct 12;6(10):3249-3258. doi: 10.1021/ct1001413.
We approximate the loop motions of various proteins by using a coarse-grained model and the theory of rubberlike elasticity of polymer chains. The loops are considered as chains where only the first and the last residues thereof are tethered by their connections to the main structure; while within the loop, the loop residues are connected only to their sequence neighbors. We applied these approximate models to five proteins. Our approximation shows that the loop motions can usually be computed locally which shows these motions are robust and not random. But most interestingly, the new method presented here can be used to compute the likely motions of loops that are missing in the structures.
我们通过使用粗粒度模型和聚合物链的类橡胶弹性理论来近似各种蛋白质的环运动。环被视为链，其中只有其第一个和最后一个残基通过与主结构的连接而固定；而在环内，环残基仅与其序列相邻残基相连。我们将这些近似模型应用于五种蛋白质。我们的近似结果表明，环运动通常可以在局部进行计算，这表明这些运动是稳健的而非随机的。但最有趣的是，这里提出的新方法可用于计算结构中缺失的环的可能运动。
