内在无序蛋白的校正Langevin动力学模拟
Calibrated Langevin dynamics simulations of intrinsically disordered proteins
摘要：
我们进行了广泛的粗粒度（CG）朗之万动力学模拟的内在无序蛋白（IDPs），具有波动的构象统计之间的排除体积随机游走和崩溃的小球。我们的CG模型包括排斥立体，有吸引力的疏水，和残基之间的静电相互作用，并校准到一个大的收集的单分子荧光共振能量转移数据的36对残基间的分离在5个IDP：$α$ -，$β$ -，和$γ$ -突触核蛋白，微管相关蛋白$τ$，和胸腺素原$α$。我们发现，我们的CG模型是能够概括的平均残基间的分离，无论选择的疏水性尺度，这表明，我们的校准模型可以鲁棒地捕捉构象动态的IDPs。然后，我们采用我们的模型来研究11个已知的IDP的回转半径与化学距离的缩放。我们发现平均电荷和疏水性空间中折叠蛋白质和IDP之间分界线的距离与回转半径与蛋白质化学距离的标度指数之间存在强相关性。
英文摘要：
We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules. Our CG model includes repulsive steric, attractive hydrophobic, and electrostatic interactions between residues and is calibrated to a large collection of single-molecule fluorescence resonance energy transfer data on the inter-residue separations for 36 pairs of residues in five IDPs: $α$-, $β$-, and $γ$-synuclein, the microtubule-associated protein $τ$, and prothymosin $α$. We find that our CG model is able to recapitulate the average inter-residue separations regardless of the choice of the hydrophobicity scale, which shows that our calibrated model can robustly capture the conformational dynamics of IDPs. We then employ our model to study the scaling of the radius of gyration with chemical distance in 11 known IDPs. We identify a strong correlation between the distance to the dividing line between folded proteins and IDPs in the mean charge and hydrophobicity space and the scaling exponent of the radius of gyration with chemical distance along the protein.
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