Hall Benjamin A, Sansom Mark S P
Department of Biochemistry & Oxford Centre for Integrative Systems Biology, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
J Chem Theory Comput. 2009 Sep 8;5(9):2465-71. doi: 10.1021/ct900140w.
Coarse-grained molecular dynamics (CG-MD) may be applied as part of a multiscale modeling approach to protein-protein interactions. The cohesin-dockerin interaction provides a valuable test system for evaluation of the use of CG-MD, as structural (X-ray) data indicate a dual binding mode for the cohesin-dockerin pair. CG-MD simulations (of 5 μs duration) of the association of cohesin and dockerin identify two distinct binding modes, which resemble those observed in X-ray structures. For each binding mode, ca. 80% of interfacial residues are predicted correctly. Furthermore, each of the binding modes identified by CG-MD is conformationally stable when converted to an atomistic model and used as the basis of a conventional atomistic MD simulation of duration 20 ns.
粗粒度分子动力学（CG-MD）可作为蛋白质-蛋白质相互作用多尺度建模方法的一部分加以应用。内聚蛋白-锚定蛋白相互作用为评估CG-MD的使用提供了一个有价值的测试系统，因为结构（X射线）数据表明内聚蛋白-锚定蛋白对存在双重结合模式。对内聚蛋白和锚定蛋白缔合进行的5微秒时长的CG-MD模拟确定了两种不同的结合模式，这与在X射线结构中观察到的模式相似。对于每种结合模式，约80%的界面残基能够被正确预测。此外，当将由CG-MD确定的每种结合模式转换为原子模型，并用作时长为20纳秒的传统原子分子动力学模拟的基础时，每种结合模式在构象上都是稳定的。
