Huang Ji-Tao, Cheng Jin-Pei
College of Chemistry and State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China.
Proteins. 2007 Jul 1;68(1):218-22. doi: 10.1002/prot.21411.
Folding kinetics of proteins is governed by the free energy and position of transition states. But attempts to predict the position of folding transition state on reaction pathway from protein structure have been met with only limited success, unlike the folding-rate prediction. Here, we find that the folding transition-state position is related to the secondary structure content of native two-state proteins. We present a simple method for predicting the transition-state position from their alpha-helix, turn and polyproline secondary structures. The method achieves 81% correlation with experiment over 24 small, two-state proteins, suggesting that the local secondary structure content, especially for content of alpha-helix, is a determinant of the solvent accessibility of the transition state ensemble and size of folding nucleus.
蛋白质的折叠动力学受过渡态的自由能和位置支配。但与折叠速率预测不同，从蛋白质结构预测反应途径上折叠过渡态的位置仅取得了有限的成功。在这里，我们发现折叠过渡态的位置与天然两态蛋白质的二级结构含量有关。我们提出了一种从其α螺旋、转角和多聚脯氨酸二级结构预测过渡态位置的简单方法。该方法在24种小型两态蛋白质上与实验的相关性达到81%，这表明局部二级结构含量，特别是α螺旋的含量，是过渡态集合体溶剂可及性和折叠核大小的决定因素。
