Construction And Preliminary Analyses Of The Database Of Copper-chelating Proteins

In recent years, evidence has been gathered to suggest that the dysfunction of the neural system such as Alzheimer's disease and prion disease is relevant to the abnormal metabolism of metal ions especially the transitional ones, e.g. copper and iron. However, the disorders of the metal-chelating proteins are the direct causes to the abnormal transport of ions. Many intensive researches have been carried out on the age-associated diseases and the metal-chelating proteins. Thus, we constructed a database of the copper-chelating proteins (DCCP) with methods in Bioinformatics. Although there are some databases where some samples of copper-chelating proteins have been involved, the information is not enough and the rate of update is very slowly. The most one is lacking the ample structural files and yet DCCP can complement these. Based on the construction of DCCP, the preliminary analyses on the data are done and they may be helpful to the discovery of the new drugs to the treatment of the neurodegenerative diseases.The data in DCCP are derived from GenBank, PIR, SWISS-PROT and PDB, the famous centers in Bioinformatics worldwide and they are organized by the LAMP strategy which means Apache, MySQL and PHP are run on the Linux platform. Then a database comes into being.The information from PDB database including the structural files, the localizations of proteins, sequences and the binding sites with copper ion is involved in DCCP. One of the marked properties is the homology modeling to the non-structural proteins in the DCCP₁D. The newly predicted structures may be helpful to the drug discovery. Moreover, the known networks of copper transporting in yeast cell are also contained in DCCP. They are available in the website (http://sdbi.sdut.edu.cn/DCCP/cn/index.php) and can be accessible freely.The copper-chelating proteins are much different from the non-metal-chelating proteins in the function. The analyses of the amino acid contents of different properties and (3-sheet hydrophobicity are done between the data in DCCP₃D and the comparison of the same number of samples selected randomly from SWISS-PROT database. However, the result assumes that there is no visible difference between the two kinds of proteins. Hence, it may besignificant to keep the stability of the species in the course of evolution.The secondary structure prediction is based on the analyses of the primary sequences. The constitutions and the contents of the protein both influence the prediction accuracy. The prediction accuracies are obviously lower than those for common proteins by 10%, suggesting that the existing secondary-structure-predicting softwares are not very appropriate in predicting the secondary structures of metalloproteins.The copper-chelating proteins play important roles in the course of redox, electron transport and metal ions transport. It is speculated that there exits cooperative evolution among those function-associated proteins. The elementary evolutionary analyses verify that SOD and its chaperone CCS which have a tight contact with SOD evolve cooperatively and that prion protein may have no direct interaction with them.In brief, at the base of the construction of the database, the primary sequence analyses, the evaluation to the existing secondary-structure-predicting softwares, the modeling of the three dimensional structures, the functional classification and the evolutionary analyses will be helpful to the basic researches on the copper-chelating proteins and the applied researches on the therapy of the diseases.