Fractal dimension of an intrinsically disordered protein: Small-angle X-ray scattering and computational study of the bacteriophage λ N protein
Fractal dimension of an intrinsically disordered protein: Small-angle X-ray scattering and computational study of the bacteriophage λ N protein
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DOI：
10.1002/pro.739
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发表时间：
2011-12-01
期刊：
影响因子：
8
通讯作者：
Goldenberg, David P.
中科院分区：
文献类型：
--
作者：
Johansen, Daniel;Trewhella, Jill;Goldenberg, David P.
利用小角度x射线散射（SAXS）对噬菌体λ N蛋白进行了表征，该蛋白是一种具有转录抗终止因子功能的107残基内在无序蛋白（IDP）。SAXS数据用于估计在各种溶液条件下的平均旋转半径和分形维数，分形维数是蛋白质内部缩放特性的度量。在没有变性剂的情况下，旋转半径为38 +/- 3.5埃，分形维数为1.76 +/- 0.05，略大于排除体积的良好溶剂化聚合物的预测值（1.7）。尿素的加入对旋转半径和分形维数的影响都不明显，进一步说明在没有变性剂的情况下，蛋白质得到了广泛的展开和良好的溶剂化。NaCl或D2O的加入促进了聚合，但不影响单体形式的性质。实验的SAXS谱也与可调节溶剂化能项的随机卷曲多肽计算模型预测的结果进行了比较。实验数据与模型拟合较好，溶剂化能接近于零。这些结果表明，λ N蛋白是广泛的IDPs中扩展的成员之一，很可能是因为其高含量的带电残基和大的净电荷（在中性pH下为+ 15）。构象集合的扩展性质可能在促进蛋白质与动态转录复合物的其他组分的相互作用中发挥作用。
Small-angle X-ray scattering (SAXS) was used to characterize the bacteriophage lambda N protein, a 107 residue intrinsically disordered protein (IDP) that functions as a transcriptional antitermination factor. The SAXS data were used to estimate both the average radius of gyration and the fractal dimension, a measure of the protein's internal scaling properties, under a variety of solution conditions. In the absence of denaturants, the radius of gyration was 38 +/- 3.5 angstrom and the fractal dimension was 1.76 +/- 0.05, slightly larger than the value predicted for a well-solvated polymer with excluded volume (1.7). Neither the radius of gyration nor the fractal dimension changed significantly on the addition of urea, further indicating that the protein is extensively unfolded and well solvated in the absence of denaturant. The addition of NaCl or D2O was found to promote aggregation, but did not appear to affect the properties of the monomeric form. The experimental SAXS profiles were also compared with those predicted by a computational model for a random-coil polypeptide, with an adjustable solvation energy term. The experimental data were well fit to the model with the solvation energy close to zero. These results indicate that the lambda N protein is among the more expanded members of the broad class of IDPs, most likely because of its high content of charged residues and a large net charge (+ 15 at neutral pH). The expanded nature of the conformational ensemble may play a role in facilitating the interactions of the protein with other components of the dynamic transcriptional complex.