Bioinformatics Centre, Bose Institute, Kolkata, India.
J Mol Graph Model. 2012 Sep;38:211-9. doi: 10.1016/j.jmgm.2012.05.004. Epub 2012 Jun 9.
Comparative molecular dynamics simulations of Ca²⁺ dependent psychrophilic type II antifreeze protein (AFP) from herring (Clupea harengus) (hAFP) and Ca²⁺ dependent type II antifreeze protein from long snout poacher (Brachyopsis rostratus) (lpAFP) have been performed for 10 ns each at five different temperatures. We have tried to investigate whether the Ca²⁺ dependent protein obtains any advantage in nature over the independent one. To this end the dynamic properties of these two proteins have been compared in terms of secondary structure content, molecular flexibility, solvent accessibility, intra molecular hydrogen bonds and protein-solvent interactions. At 298 and 373 K the flexibility of the Ca²⁺ independent molecule is higher which indicates that Ca²⁺ could contribute to stabilize the structure. The thermal unfolding pathways of the two proteins have also been monitored. The rate of unfolding is similar up to 373 K, beyond that hAFP shows faster unfolding than lpAFP. The essential subspaces explored by the simulations of hAFP and lpAFP at different temperatures are significantly different as revealed from principal component analysis. Our results may help in understanding the role of Ca²⁺ for hAFP to express antifreeze activity. Furthermore our study may also help in elucidating the molecular basis of thermostability of two structurally similar proteins, which perform the same function in different manner, one in presence of Ca²⁺, and the other in absence of the same.
对来自鲱鱼（Clupea harengus）的 Ca²⁺依赖型 II 型抗冻蛋白（AFP）和长吻拟鲿（Brachyopsis rostratus）的 Ca²⁺依赖型 II 型抗冻蛋白（lpAFP）进行了 10 ns 的比较分子动力学模拟，每个蛋白在五个不同温度下进行。我们试图研究 Ca²⁺依赖型蛋白是否在自然界中比独立型蛋白具有优势。为此，我们比较了这两种蛋白的二级结构含量、分子柔性、溶剂可及性、分子内氢键和蛋白-溶剂相互作用等方面的动态特性。在 298 和 373 K 下，Ca²⁺非依赖型分子的柔性更高，这表明 Ca²⁺可能有助于稳定结构。还监测了两种蛋白的热解折叠途径。在 373 K 以下，解折叠速率相似，超过 373 K 后，hAFP 的解折叠速度比 lpAFP 快。主成分分析表明，在不同温度下模拟 hAFP 和 lpAFP 时所探索的基本子空间明显不同。我们的结果可能有助于理解 Ca²⁺对 hAFP 表达抗冻活性的作用。此外，我们的研究还可能有助于阐明两种结构相似的蛋白的热稳定性的分子基础，这两种蛋白以不同的方式执行相同的功能，一种在 Ca²⁺存在下，另一种在缺乏 Ca²⁺的情况下。
