脯氨酸肽键数据集的构建

Constituting of a prolyl peptide bond dataset

由分辨率<0.25nm,同一性(identity)<30％的2401条肽链中计算提取了全部顺式与反式脯氨酸肽键的位置,数目分别为1221个与26401个,从而建立了一个较大规模的脯氨酸肽键数据集。统计分析了该数据集的基本特征:肽键N端残基的分布、N端残基的二面角统计、在二级结构中的分布情况、顺式肽键在脯氨酸肽键中所占比例。此数据集对于进一步研究顺反X-Pro肽键的结构、与氨基酸序列之间的关系,以及肽链折叠动力学具有重要作用。

Peptidyl-prolyl cis/trans isomerization is of considerable biological significance and prolyl residue plays an important role in the final structure of proteins. In order to analyze the prolyl peptide bond in the peptide chain. A large prolyl peptide bond dataset is needed. A PDB code list was used in this work, which was provided by PISCES. All structures in this list had resolution better than 0. 25nm. Sequence identity between each pair of the sequences was less than 30% . The number of chains in the list was 2401. Several FORTRAN programs by ourselves were used to do the calculating and analyzing. A large prolyl peptide bond dataset was constituted. The number of cis peptide bonds is 1221 and that of trans peptide bonds is 26401. Some characters of the dataset were analyzed, including the distribution of the residues of the peptide bonds' N-terminal, the statistic of dihedral angel, the distribution of cis peptide bonds in different secondary structure, the proportion of cis peptide bonds. The dataset maybe was important to those researches such as the structure of X -Pro peptide bond, the relation between amino acid sequence and structure, peptide chain folding kinetics.