Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India.
J Chem Phys. 2012 Aug 7;137(5):055102. doi: 10.1063/1.4739421.
Water-mediated protein-carbohydrate interaction is a complex phenomenon responsible for different biological processes in cellular environment. One of the unexplored but important issues in this area is the role played by water during the recognition process and also in controlling the microscopic properties of the complex. In this study, we have carried out atomistic molecular dynamics simulations of a protein-carbohydrate complex formed between the hyaluronan binding domain of the murine Cd44 protein and the octasaccharide hyaluronan in explicit water. Efforts have been made to explore the heterogeneous influence of the complex on the dynamic properties of water present in different regions around it. It is revealed from our analyses that the heterogeneous dynamics of water around the complex are coupled with differential time scales of formation and breaking of hydrogen bonds at the interface. Presence of a highly rigid thin layer of motionally restricted water molecules bridging the protein and the carbohydrate in the common region of the complex has been identified. Such water molecules are expected to play a crucial role in controlling properties of the complex. Importantly, it is demonstrated that the formation of the protein-carbohydrate complex affects the transverse and longitudinal degrees of freedom of the interfacial water molecules in a heterogeneous manner.
水介导的蛋白质-碳水化合物相互作用是一种复杂的现象，它负责细胞环境中不同的生物学过程。在这个领域中，一个尚未被探索但很重要的问题是水在识别过程中以及在控制复合物微观性质方面所起的作用。在这项研究中，我们在明确的水中对鼠 Cd44 蛋白的透明质酸结合结构域与八糖透明质酸之间形成的蛋白质-碳水化合物复合物进行了原子分子动力学模拟。我们努力探索了复合物对其周围不同区域的水中动态特性的不均匀影响。我们的分析表明，复合物周围水的不均匀动力学与界面处氢键形成和断裂的不同时间尺度相关联。在复合物的共同区域中，存在一层高度刚性的运动受限水分子薄带，将蛋白质和碳水化合物连接起来。可以预期，这些水分子将在控制复合物的性质方面发挥关键作用。重要的是，研究表明，蛋白质-碳水化合物复合物的形成以不均匀的方式影响界面水分子的横向和纵向自由度。
