title: ETMB-RBF: discrimination of metal-binding sites in electron transporters based on RBF networks with PSSM profiles and significant amino acid pairs.
abstract: BACKGROUND
  Cellular respiration is the process by which cells obtain energy from glucose and is a very important biological process in living cell. As cells do cellular respiration, they need a pathway to store and transport electrons, the electron transport chain. The function of the electron transport chain is to produce a trans-membrane proton electrochemical gradient as a result of oxidation-reduction reactions. In these oxidation-reduction reactions in electron transport chains, metal ions play very important role as electron donor and acceptor. For example, Fe ions are in complex I and complex II, and Cu ions are in complex IV. Therefore, to identify metal-binding sites in electron transporters is an important issue in helping biologists better understand the workings of the electron transport chain.
  
  
  METHODS
  We propose a method based on Position Specific Scoring Matrix (PSSM) profiles and significant amino acid pairs to identify metal-binding residues in electron transport proteins.
  
  
  RESULTS
  We have selected a non-redundant set of 55 metal-binding electron transport proteins as our dataset. The proposed method can predict metal-binding sites in electron transport proteins with an average 10-fold cross-validation accuracy of 93.2% and 93.1% for metal-binding cysteine and histidine, respectively. Compared with the general metal-binding predictor from A. Passerini et al., the proposed method can improve over 9% of sensitivity, and 14% specificity on the independent dataset in identifying metal-binding cysteines. The proposed method can also improve almost 76% sensitivity with same specificity in metal-binding histidine, and MCC is also improved from 0.28 to 0.88.
  
  
  CONCLUSIONS
  We have developed a novel approach based on PSSM profiles and significant amino acid pairs for identifying metal-binding sites from electron transport proteins. The proposed approach achieved a significant improvement with independent test set of metal-binding electron transport proteins.
authors: Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan. yien@csie.org
authors: Yu-Yen
authors: YY
authors: Ou
authors: Shu-An
authors: SA
authors: Chen
authors: Sheng-Cheng
authors: SC
authors: Wu
mesh_terms: D000596:Amino Acids / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites; D004579:Electron Transport; D004583:Electrons; D008670:Metals / Q000737:chemistry* / Q000378:metabolism*; D056510:Position-Specific Scoring Matrices
chemical_list: D000596:Amino Acids; D008670:Metals
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