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Structural and Functional Analysis of Deleterious Nonsynonymous Single Nucleotide Polymorphisms in PAH Associated with Phenylketonuria

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Along with the completion of human genome project, major interest in human genetics is to distinguish mutations that are functionally neutral from those that contribute to disease. Understanding human genetic variation through Single Nucleotide Polymorphisms (SNPs) is currently believed to reveal the cause of individual susceptibility to disease and the large variation observed in response to treatment. It is important to determine whether nonsynonymous (ns) mutations in the coding regions of human genes are responsible for phenotypic differences between humans. The main goal of this work reported here is to predict the deleterious nsSNPs, so that the number of SNPs screened for association with disease can be reduced to those that most likely alter gene function. In this paper, we present a strategy of bioinformatics tools to analyze the SNPs that can alter the expression and function of PAH gene responsible candidate for causing Phenylketonuria (PKU) as a pipeline and for providing a guide to experimental work. We applied both structural (Polymorphism Phenotyping) and evolutionary based methods (Sorting Intolerant from Tolerant) to assess potential functional effects of SNPs. PupaSuite tool predicted the phenotypic effect of SNPs on the structure and function of the affected protein. Structure analysis was carried out with the major mutation that occurred in the native protein coded by PAH gene. The native and mutant modeled proteins were further analyzed for FOLD-X, solvent accessibility and secondary structure to check the stability of the proteins. The SNPs reported here will be potential candidates for future studies in PKU.
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Document Type: Research Article

Publication date: 2009-09-01

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