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タイトル
  • en Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands
作成者
アクセス権 open access
権利情報
主題
  • NDC 460
内容注記
  • Abstract en Background: Structural genomics approaches, particularly those solving the 3D structures of many proteins with unknown functions, have increased the desire for structure-based function predictions. However, prediction of enzyme function is difficult because one member of a superfamily may catalyze a different reaction than other members, whereas members of different superfamilies can catalyze the same reaction. In addition, conformational changes, mutations or the absence of a particular catalytic residue can prevent inference of the mechanism by which catalytic residues stabilize and promote the elementary reaction. A major hurdle for alignment-based methods for prediction of function is the absence (despite its importance) of a measure of similarity of the physicochemical properties of catalytic sites. To solve this problem, the physicochemical features radially distributed around catalytic sites should be considered in addition to structural and sequence similarities. Results: We showed that radial distribution functions (RDFs), which are associated with the local structural and physicochemical properties of catalytic active sites, are capable of clustering oxidoreductases and transferases by function. The catalytic sites of these enzymes were also characterized using the RDFs. The RDFs provided a measure of the similarity among the catalytic sites, detecting conformational changes caused by mutation of catalytic residues. Furthermore, the RDFs reinforced the classification of enzyme functions based on conventional sequence and structural alignments. Conclusions: Our results demonstrate that the application of RDFs provides advantages in the functional classification of enzymes by providing information about catalytic sites.
出版者 en BioMed Central
日付
    Issued2012-04-26
言語
  • eng
資源タイプ journal article
出版タイプ VoR
資源識別子 HDL http://hdl.handle.net/2115/50022
関連
  • isIdenticalTo DOI https://doi.org/10.1186/1472-6807-12-5
収録誌情報
    • PISSN 1472-6807
      • en BMC Structural Biology
      • 巻12 開始ページ5
ファイル
    • fulltext BMCSB12_5.pdf
    • 832.19 KB (application/pdf)
      • Issued2012-04-26
コンテンツ更新日時 2023-07-26