Zhang Hua, Zhang Tuo, Chen Ke, Shen Shiyi, Ruan Jishou, Kurgan Lukasz
Nankai University, Tianjin, People's Republic of China.
Proteins. 2009 Aug 15;76(3):617-36. doi: 10.1002/prot.22375.
We investigate the relationship between the flexibility, expressed with B-factor, and the relative solvent accessibility (RSA) in the context of local, with respect to the sequence, neighborhood and related concepts such as residue depth. We observe that the flexibility of a given residue is strongly influenced by the solvent accessibility of the adjacent neighbors. The mean normalized B-factor of the exposed residues with two buried neighbors is smaller than that of the buried residues with two exposed neighbors. Inclusion of RSA of the neighboring residues (local RSA) significantly increases correlation with the B-factor. Correlation between the local RSA and B-factor is shown to be stronger than the correlation that considers local distance- or volume-based residue depth. We also found that the correlation coefficients between B-factor and RSA for the 20 amino acids, called flexibility-exposure correlation index, are strongly correlated with the stability scale that characterizes the average contributions of each amino acid to the folding stability. Our results reveal that the predicted RSA could be used to distinguish between the disordered and ordered residues and that the inclusion of local predicted RSA values helps providing a better contrast between these two types of residues. Prediction models developed based on local actual RSA and local predicted RSA show similar or better results in the context of B-factor and disorder predictions when compared with several existing approaches. We validate our models using three case studies, which show that this work provides useful clues for deciphering the structure-flexibility-function relation.
我们在局部范围内,相对于序列、邻域以及诸如残基深度等相关概念,研究了用B因子表示的柔韧性与相对溶剂可及性(RSA)之间的关系。我们观察到,给定残基的柔韧性受到相邻近邻溶剂可及性的强烈影响。具有两个埋藏近邻的暴露残基的平均归一化B因子小于具有两个暴露近邻的埋藏残基的平均归一化B因子。纳入相邻残基的RSA(局部RSA)显著增加了与B因子的相关性。结果表明,局部RSA与B因子之间的相关性强于考虑基于局部距离或体积的残基深度的相关性。我们还发现,20种氨基酸的B因子与RSA之间的相关系数,即柔韧性-暴露相关指数,与表征每种氨基酸对折叠稳定性平均贡献的稳定性量表密切相关。我们的结果表明,预测的RSA可用于区分无序和有序残基,并且纳入局部预测的RSA值有助于更好地区分这两种类型的残基。与几种现有方法相比,基于局部实际RSA和局部预测RSA开发的预测模型在B因子和无序预测方面显示出相似或更好的结果。我们使用三个案例研究验证了我们的模型,结果表明这项工作为解读结构-柔韧性-功能关系提供了有用的线索。