結構字元應用於蛋白質骨架重建之研究

The Study of Protein Backbone Reconstruction by Applying Structural Alphabet

葉融(Jung Yeh) ； 董其樺(Chi-Hua Tung)

《Journal of Information Technology and Applications(資訊科技與應用期刊)》 9卷1期 (2015/03) Pp. 1-7

https://doi.org/10.6302/JITA.201503_9(1).0001

摘要

在蛋白質資料庫（Protein Data Bank, PDB）中會常見一種僅含Cα原子座標的蛋白質結構或是骨架結構出現問題的蛋白質。為了解決這種蛋白質立體結構不完整的問題，已發展出許多快速蛋白質骨架重建的演算法。但由於這些重建結構的準確度尚有改進空間，本研究因而對此設計出一個骨架重建演算法，稱為REconstructing protein Backbone using Structural Alphabet, REBSA。REBSA採用前人所用之Kappa角與Alpha角分群及結構字元（Structural Alphabet），用拼圖的方式將兩Cα原子間的C、O與N三個原子的座標從空間上的各種位置與位向，透過旋轉和平移準確地疊合，讓一個原本只有含Cα原子結構的蛋白質最終被重建成具有完整骨架結構的蛋白質。研究結果顯示，與其他方法相比，REBSA有更高的準確度，可增進結構重建後的RMSD平均值最多0.07Å。我們相信本研究對分子生物學及結構生物學等相關領域具有顯著貢獻。

關鍵字

結構字元 ； 結構疊合 ； 蛋白質骨架重建 ； 結構生物資訊

並列摘要

In the Protein Data Bank (PDB), there are problems about certain proteins containing Cα-only atomic coordinates and disordered backbone conformation. For proteins whose structures are still incomplete, many algorithms have been developed to fast reconstruction of protein backbone using Cα-only atomic coordinates. However, the accuracy of reconstructing structures still need to be improved. In this study, we design a novel backbone reconstruction algorithm, named as REconstructing protein Backbone using Structural Alphabet (REBSA). REBSA applies previous studies of Kappa-Alpha angle and Structural Alphabet to superimpose local structure accurately for C, O and N atoms between two Cα atoms through rotation and translation matrix. The purpose of this research is to rebuild the complete backbone structure of a protein with the Cα-only atomic structure. The results show that REBSA has higher accuracy compared with other methods. The improvement of average RMSD may be up to 0.07Å. We believe that this study may provide significant contribution to molecular biology and structural biology.

並列關鍵字

Structural Alphabet ； superimpose ； protein backbone reconstruction ； structural bioinformatics