用蒙特卡洛方法估计蛋白质折叠速率

Estimation of protein folding rate by the Monte Carlo method

采用蛋白质残基间的非局域接触距离构造接触得分函数,将蛋白质结构映射为接触得分序列。假设接触是独立形成的,应用蒙特卡洛方法对146个蛋白质的实验折叠速率值进行了估计,结果显示,蒙特卡洛步骤数与折叠速率之间存在良好的相关性,拟合优度达到0.69。进一步,若仅保留那些由特定氨基酸参与的非局域接触得分,认为这些接触在折叠过程中扮演了重要角色,此时蒙特卡洛步骤数与折叠速率之间的相关性将提高到0.72。结果表明,由特定残基参与形成的非局域接触数量是决定蛋白质折叠速率的主要因素。

The non-local contact distance between protein residues was used to construct a contact score function that maps protein structures to contact score sequences.Assuming that contacts are formed independently,the experimental folding rate values for 146 proteins were estimated by applying the Monte Carlo method,and the results showed a good correlation between the number of Monte Carlo steps and the folding rate,with a goodness of fit of 0.69.Further,if only those non-local contact scores involving specific amino acids were retained,and these contacts were considered to play an important role in the folding process,the correlation between the number of Monte Carlo steps and the folding rate would increase to 0.72.The results suggest that the number of non-local contacts formed by the involvement of specific residues is a major factor in determining the rate of protein folding.