Benyamini Hadar, Shulman-Peleg Alexandra, Wolfson Haim J, Belgorodsky Bogdan, Fadeev Ludmila, Gozin Michael
Bioinformatics Unit, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
Bioconjug Chem. 2006 Mar-Apr;17(2):378-86. doi: 10.1021/bc050299g.
The unique properties of fullerenes have raised the interest of using them for biomedical applications. Within this framework, the interactions of fullerenes with proteins have been an exciting research target, yet little is known about how native proteins can bind fullerenes, and what is the nature of these interactions. Moreover, though some proteins have been shown to interact with fullerenes, up to date, no crystal structure of such complexes was obtained. Here we report docking studies aimed at examining the interactions of fullerene in two forms (C60 nonsubstituted fullerene and carboxyfullerene) with four proteins that are known to bind fullerene derivatives: HIV protease, fullerene-specific antibody, human serum albumin, and bovine serum albumin. Our work provides docking models with detailed binding pockets information, which closely match available experimental data. We further compare the predicted binding sites using a novel multiple binding site alignment method. A high similarity between the physicochemical properties and surface geometry was found for fullerene's binding sites of HIV protease and the human and bovine serum albumins.
富勒烯的独特性质引发了将其用于生物医学应用的兴趣。在此框架内，富勒烯与蛋白质的相互作用一直是一个令人兴奋的研究目标，但对于天然蛋白质如何结合富勒烯以及这些相互作用的本质是什么，人们知之甚少。此外，尽管一些蛋白质已被证明可与富勒烯相互作用，但截至目前，尚未获得此类复合物的晶体结构。在此我们报告对接研究，旨在研究两种形式的富勒烯（C60 未取代富勒烯和羧基富勒烯）与四种已知可结合富勒烯衍生物的蛋白质之间的相互作用：HIV 蛋白酶、富勒烯特异性抗体、人血清白蛋白和牛血清白蛋白。我们的工作提供了具有详细结合口袋信息的对接模型，这些模型与现有的实验数据密切匹配。我们进一步使用一种新颖的多结合位点比对方法比较预测的结合位点。发现 HIV 蛋白酶以及人血清白蛋白和牛血清白蛋白的富勒烯结合位点在物理化学性质和表面几何形状方面具有高度相似性。
