Studies Of The Deleterious SNPs In The ATP-binding Cassette (ABC) Transporter Superfamily

It is generally said that the deleterious (or functional) SNPs always change the structure and functional activities of proteins or the expression of them, and cause various diseases. The deleterious SNPs in ABC (ATP-binding cassette) transporters may cause deleterious effects on them, and are close association with many serious diseases. According to the characteristics of ABC transporters, using building models in silico and experimental analysis, the deleterious SNPs in the ABC transporters have been explored in this work.In the theoretical study, the results are as follows: I. Applying the RPLS (ridge partial least square) and LDA (linear discriminant analysis) methods, we have developed the computational models to analyze the deleterious nsSNPs in the transporters and predict ones in ABCB (ATP-binding cassette B) transporters of interest. The prediction accuracy of two models for the training (762 nsSNPs) are more over 84%. Meanwhile, 28 nsSNPs in the ABCB proteins were always predicted to be deleterious. II. The silico models based on RPLS and cross-validation methods have been proposed to analyze the pathogenicity of missense mutations in the ABC transporters. The 5286 missense mutations, located on the quite different length of proteins, were selected to build the models. The accuracy were 82.2% (training: 4098 nsSNPs) and 81.4% (test: 752 nsSNPs), respectively. Moreover, 234 missense mutations were always analyzed to be of the pathogenicity among the ABC proteins.In the experimental analysis, the distribution of the functional MDR3435C>T (ABCB1) genotypes in 265 healthy subjects, which were selected from 2836 Chinesesamples of Han nationality, was studied. In this part, the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay has been applied to assess 3435C>T genotypes. The genotype frequencies are: CC 32% (n = 85), CT 48% (n = 127) and TT 20% (n = 53), which is the first report in the Chinese samples.In conclusion, the evolutionary-conservation features and secondary structural features of the proteins were applied in this work. Moreover, it is always difficult to build the related models for the transmembrane and glycoproteins with the large molecular weight. Therefore, the models were built not only based on the deleterious nsSNPs in the transporters as datasets, but also based on ones of the non-transporters in the large proteins as datasets too. The high predicting accuracy was got for the deleterious nsSNPs model in the ABC transporters using different theoretic methods. On the other hand, we obtained the data about the distribution of the functional MDR1/ABCB1 3435C>T in the healthy Chinese Han samples because there has been a lack of data about them. The above studies are the exploratory attempts for validating the results of the theoretic models, exploring the pathogenesis of the diseases caused by ABC transporters and the therapy of them, and especially for improving the levels of individual treatments in our country.