Bovine chymosin: a computational study of recognition and binding of bovine kappa-casein.
Bovine chymosin: a computational study of recognition and binding of bovine kappa-casein.
复制标题
牛凝乳酶：牛卡帕酪蛋白识别和结合的计算研究。
作者：
David S. Palmer;A. U. Christensen;J. Sørensen;L. Çelik;K. B. Qvist;B. Schiøtt
牛凝乳酶是一种天冬氨酸蛋白酶，可选择性地切割牛奶蛋白卡帕酪蛋白。这种酶在奶酪生产中被广泛用于促进牛奶凝固。我们利用配体对接、构象搜索算法和分子动力学模拟，建立了牛kappa-酪蛋白与牛凝乳酶络合的残基97-112模型。与有限的实验证据一致，该模型表明底物以扩展构象结合，在可剪键的两侧带电残基对稳定结合姿态起重要作用。Lys111和Lys112被观察到与凝乳酶的n端结构域结合，取代了一个保守的水分子。kappa-酪蛋白中的一组组氨酸和脯氨酸残基（His98-Pro99-His100-Pro101-His102）结合到该蛋白的c端结构域，其中邻近的保守精氨酸残基（Arg97）对稳定结合姿态很重要。在18 ns的分子动力学模拟中，催化位点（包括催化水分子）在先前提出的一般酸/碱催化机理的起始构象中是稳定的。
Bovine chymosin is an aspartic protease that selectively cleaves the milk protein kappa-casein. The enzyme is widely used to promote milk clotting in cheese manufacturing. We have developed models of residues 97-112 of bovine kappa-casein complexed with bovine chymosin, using ligand docking, conformational search algorithms, and molecular dynamics simulations. In agreement with limited experimental evidence, the model suggests that the substrate binds in an extended conformation with charged residues on either side of the scissile bond playing an important role in stabilizing the binding pose. Lys111 and Lys112 are observed to bind to the N-terminal domain of chymosin displacing a conserved water molecule. A cluster of histidine and proline residues (His98-Pro99-His100-Pro101-His102) in kappa-casein binds to the C-terminal domain of the protein, where a neighboring conserved arginine residue (Arg97) is found to be important for stabilizing the binding pose. The catalytic site (including the catalytic water molecule) is stable in the starting conformation of the previously proposed general acid/base catalytic mechanism for 18 ns of molecular dynamics simulations.