Kopecký Vladimír, Ettrich Rüdiger, Pazderka Tomáš, Hofbauerová Kateřina, Řeha David, Baumruk Vladimír
Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, CZ-12116, Prague 2, Czech Republic.
Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zámek 136, CZ-37333, Nové Hrady, Czech Republic.
J Mol Recognit. 2016 Feb;29(2):70-9. doi: 10.1002/jmr.2496. Epub 2015 Sep 24.
Ligand binding of neutral progesterone, basic propranolol, and acidic warfarin to human α1-acid glycoprotein (AGP) was investigated by Raman spectroscopy. The binding itself is characterized by a uniform conformational shift in which a tryptophan residue is involved. Slight differences corresponding to different contacts of the individual ligands inside the β-barrel are described. Results are compared with in silico ligand docking into the available crystal structure of deglycosylated AGP using quantum/molecular mechanics. Calculated binding energies are -18.2, -14.5, and -11.5 kcal/mol for warfarin, propranolol, and progesterone, respectively. These calculations are consistent with Raman difference spectroscopy; nevertheless, minor discrepancies in the precise positions of the ligands point to structural differences between deglycosylated and native AGP. Thermal dynamics of AGP with/without bounded warfarin was followed by Raman spectroscopy in a temperature range of 10-95 °C and analyzed by principal component analysis. With increasing temperature, a slight decrease of α-helical content is observed that coincides with an increase in β-sheet content. Above 45 °C, also β-strands tend to unfold, and the observed decrease in β-sheet coincides with an increase of β-turns accompanied by a conformational shift of the nearby disulfide bridge from high-energy trans-gauche-trans to more relaxed gauche-gauche-trans. This major rearrangement in the vicinity of the bridge is not only characterized by unfolding of the β-sheet but also by subsequent ligand release. Hereby, ligand binding alters the protein dynamics, and the more rigid protein-ligand complex shows an improved thermal stability, a finding that contributes to the reported chaperone-like function of AGP.
通过拉曼光谱研究了中性孕酮、碱性普萘洛尔和酸性华法林与人α1-酸性糖蛋白(AGP)的配体结合情况。配体结合本身的特征是涉及色氨酸残基的一致构象变化。描述了与β桶内各个配体不同接触相对应的细微差异。将结果与使用量子/分子力学对去糖基化AGP的可用晶体结构进行的计算机模拟配体对接进行了比较。华法林、普萘洛尔和孕酮的计算结合能分别为-18.2、-14.5和-11.5千卡/摩尔。这些计算结果与拉曼差光谱一致;然而,配体精确位置的微小差异表明去糖基化AGP和天然AGP之间存在结构差异。在10-95°C的温度范围内,通过拉曼光谱跟踪了有/无结合华法林的AGP的热动力学,并通过主成分分析进行了分析。随着温度升高,观察到α-螺旋含量略有下降,这与β-折叠含量的增加相吻合。在45°C以上,β-链也趋于展开,观察到的β-折叠减少与β-转角的增加相吻合,同时附近二硫键的构象从高能反式- gauche-反式转变为更松弛的gauche- gauche-反式。桥附近的这种主要重排不仅以β-折叠的展开为特征,还以随后的配体释放为特征。因此,配体结合改变了蛋白质动力学,更刚性的蛋白质-配体复合物表现出更高的热稳定性,这一发现有助于报道的AGP的伴侣样功能。