Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland.
Phys Chem Chem Phys. 2018 Jul 18;20(28):19057-19070. doi: 10.1039/c8cp03309a.
We construct a one-bead-per-residue coarse-grained dynamical model to describe intrinsically disordered proteins at significantly longer timescales than in the all-atom models. In this model, inter-residue contacts form and disappear during the course of the time evolution. The contacts may arise between the sidechains, the backbones or the sidechains and backbones of the interacting residues. The model yields results that are consistent with many all-atom and experimental data on these systems. We demonstrate that the geometrical properties of various homopeptides differ substantially in this model. In particular, the average radius of gyration scales with the sequence length in a residue-dependent manner.
我们构建了一个单残基/单链节的粗粒化动力学模型，用于描述在比全原子模型显著更长的时间尺度下的无规卷曲蛋白质。在该模型中，残基间的相互作用在时间演化过程中形成和消失。这些相互作用可以发生在侧链之间、主链之间，或者侧链和主链之间。该模型的结果与这些系统的许多全原子和实验数据一致。我们证明了在该模型中，各种同聚肽的几何性质有很大的差异。特别是，转动半径的平均值与序列长度以残基依赖性的方式相关。
