Prabhu N Prakash, Bhuyan Abani K
School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
Biochemistry. 2006 Mar 21;45(11):3805-12. doi: 10.1021/bi0521137.
Delineating the determinants of folding of small proteins is essential for decoding the folding code. By considering the literature data for the folding of 45 two-state proteins that differ widely in sequence, structure, and function, this work suggests two empirical relations for the prediction of the folding rate. One relation is based on the content of secondary structure elements, and the other uses the number of residues of each of the following types: hydrophobic, positively charged, and negatively charged. Both relations incorporate the chain length as an indirect descriptor. The correlation between experimental values for folding rates and free energy is poor, providing little support to the "stability gap" hypothesis based on the folding of simple lattice and off-lattice polymers. The average rate-determining barrier height for these two-state proteins is much larger than the small barriers for the transition-state ensemble envisaged by theoretical models.
描绘小蛋白质折叠的决定因素对于解读折叠密码至关重要。通过考虑45种在序列、结构和功能上差异很大的两态蛋白质折叠的文献数据，这项工作提出了两个用于预测折叠速率的经验关系。一个关系基于二级结构元件的含量，另一个使用以下类型的每种残基的数量：疏水、带正电荷和带负电荷。这两个关系都将链长作为间接描述符纳入其中。折叠速率的实验值与自由能之间的相关性很差，几乎没有支持基于简单晶格和非晶格聚合物折叠的“稳定性差距”假设。这些两态蛋白质的平均速率决定势垒高度远大于理论模型设想的过渡态系综的小势垒。
