盐和突变对U1A蛋白与U1小核RNA茎环II结合速率影响的预测
Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop II.
作者信息
Qin Sanbo, Zhou Huan-Xiang
机构信息
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA.
出版信息
J Phys Chem B. 2008 May 15;112(19):5955-60. doi: 10.1021/jp075919k. Epub 2007 Dec 22.
Abstract
We have developed a computational approach for predicting protein-protein association rates (Alsallaq and Zhou, Structure 2007, 15, 215). Here we expand the range of applicability of this approach to protein-RNA binding and report the first results for protein-RNA binding rates predicted from atomistic modeling. The system studied is the U1A protein and stem/loop II of the U1 small nuclear RNA. Experimentally it was observed that the binding rate is significantly reduced by increasing salt concentration while the dissociation changes little with salt concentration, and charges distant from the binding site make marginal contribution to the binding rate. These observations are rationalized. Moreover, predicted effects of salt and charge mutations are found to be in quantitative agreement with experimental results.
摘要
我们开发了一种用于预测蛋白质-蛋白质结合速率的计算方法（Alsallaq和Zhou，《结构》，2007年，第15卷，第215页）。在此，我们将该方法的适用范围扩展到蛋白质-RNA结合，并报告了通过原子模型预测的蛋白质-RNA结合速率的首批结果。所研究的系统是U1A蛋白和U1小核RNA的茎环II。实验观察到，随着盐浓度的增加，结合速率显著降低，而解离速率随盐浓度变化不大，且远离结合位点的电荷对结合速率的贡献很小。这些观察结果得到了合理的解释。此外，发现盐和电荷突变的预测效应与实验结果在数量上一致。
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