Development of a structure based protein function prediction method: Calcium binding protein

Chem-Bio Informatics Journal

Tadashi Ando¹  Toshiyuki Meguro¹  Takeo Asaoka¹  Ichiro Yamato¹ 

[1] Tokyo University of Science

关键词: protein local structures;    タンパク質局�?立体構�?�;    calcium binding protein;    Ca2+結合タンパク質;    EF-hand calcium binding site;    EF-ハンドCa2+結合部位;    amino acid propensity;    アミノ酸使用傾向;    distance distribution;    距離分布;   

DOI  :  10.1273/cbij.3.96

学科分类：生物化学/生物物理

来源: Chem-Bio Informatics Society

【 摘 要 】

References(21)Cited-By(3)Three-dimensional local structures located near active sites are responsible for protein functions. To predict protein functions, we developed a method to extract three-dimensional structural characteristics of functions. We chose EF-hand calcium binding proteins as the model target. We defined a local structure as the structure within 12Å from an arbitrary Asp(Cα). Analysis of the amino acid propensities in the active sites showed that there were clear preferences for certain amino acids to locate at the binding sites. Furthermore, the analysis of the distributions of the distances between Asp(Cα) and any other amino acids(Cα) showed that there were preferred distances for respective amino acids. Using such structural data, we derived a DB (distance based) score and a DPB (distance and propensity based) score for the prediction of functional sites. A search for EF-hand calcium binding sites was performed to test the method. EF-hand calcium binding sites were successfully predicted. Key Words: protein local structures, calcium binding protein, EF-hand calcium binding site, amino acid propensity, distance distribution

【 授权许可】

Unknown