Oroguchi Tomotaka, Ikeguchi Mitsunori, Ota Motonori, Kuwajima Kunihiro, Kidera Akinori
Department of Physics, Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan.
J Mol Biol. 2007 Aug 31;371(5):1354-64. doi: 10.1016/j.jmb.2007.06.023. Epub 2007 Jun 14.
Molecular dynamics simulations of protein unfolding were performed at an elevated temperature for the authentic and recombinant forms of goat alpha-lactalbumin. Despite very similar three-dimensional structures, the two forms have significantly different unfolding rates due to an extra N-terminal methionine in the recombinant protein. To identify subtle differences between the two forms in the highly stochastic kinetics of unfolding, we classified the unfolding trajectories using the multiple alignment method based on the analogy between the biological sequences and the molecular dynamics trajectories. A dendrogram derived from the multiple trajectory alignment revealed a clear difference in the unfolding pathways of the authentic and recombinant proteins, i.e. the former reached the transition state in an all-or-none manner while the latter unfolded less cooperatively. It was also found in the classification that the two forms of the protein shared a common transition state structure, which was in excellent agreement with the transition state structure observed experimentally in the Phi-value analysis.
在升高的温度下对山羊α-乳白蛋白的天然形式和重组形式进行了蛋白质解折叠的分子动力学模拟。尽管两种形式的三维结构非常相似，但由于重组蛋白中额外的N端甲硫氨酸，它们具有明显不同的解折叠速率。为了识别两种形式在高度随机的解折叠动力学中的细微差异，我们基于生物序列与分子动力学轨迹之间的类比，使用多重比对方法对解折叠轨迹进行了分类。从多重轨迹比对得出的树状图揭示了天然蛋白和重组蛋白解折叠途径的明显差异，即前者以全或无的方式达到过渡态，而后者的解折叠协同性较低。在分类中还发现，两种形式的蛋白质共享一个共同的过渡态结构，这与Phi值分析中实验观察到的过渡态结构非常一致。
