ACS Chem Biol. 2012 Jan 20;7(1):150-4. doi: 10.1021/cb200363r. Epub 2011 Oct 18.
In cases where binding ligands of proteins are not easily available, structural analogues are often used. For example, in the analysis of proteins recognizing different methyl-lysine residues in histones, methyl-lysine analogues based on methyl-amino-alkylated cysteine residues have been introduced. Whether these are close enough to justify quantitative interpretation of binding experiments is however questionable. To systematically address this issue, we developed, applied, and assessed a hybrid computational/experimental approach that extracts the binding free energy difference between the native ligand (methyl-lysine) and the analogue (methyl-amino-alkylated cysteine) from a thermodynamic cycle. Our results indicate that measured and calculated binding differences are in very good agreement and therefore allow the correction of measured affinities of the analogues. We suggest that quantitative binding parameters for defined ligands in general can be derived by this method with remarkable accuracy.
在难以获得蛋白质结合配体的情况下，通常会使用结构类似物。例如，在分析识别组蛋白中不同甲基赖氨酸残基的蛋白质时，已经引入了基于甲基氨基烷基化半胱氨酸残基的甲基赖氨酸类似物。然而，这些类似物是否足够接近，以至于可以对结合实验进行定量解释是值得怀疑的。为了系统地解决这个问题，我们开发、应用和评估了一种混合计算/实验方法，该方法从热力学循环中提取天然配体（甲基赖氨酸）和类似物（甲基氨基烷基化半胱氨酸）之间的结合自由能差异。我们的结果表明，测量和计算的结合差异非常吻合，因此可以校正类似物的测量亲和力。我们建议，通常可以通过这种方法以显著的准确性得出定义配体的定量结合参数。
