Investigation of the effect of pd1.1, pd1.5, and pd1.9 mutations on pd1 gene function with a system biology approach

Programmed cell death 1 (pd1) is an immune-inhibitory receptor that is expressed in activated T cells. This gene may play a role in inhibition of actual anti- microbial and anti-tumor immunity. In human, this gene is located on the long arm of chromosome 2. This gene has many variations that three of which are more common. This study was aimed to investigate the influence of pd1.1, pd1.5, and pd1.9 variations on function of pd1gene based on a bioinformatics approach. In this study, the EPD and PROMO webserver was used to evaluate the pd1.1 variation as a promoter mutation. It has been detected in the promoter region by EPD, while the transcription factor arrangement was evaluated by the PROMO server. But, some bioinformatics tools such as ProtScale – ExPASy and Ramachandran plot assay web servers were used to evaluate the effects of codding polymorphisms. Obtained data from EPD showed that the promoter of pd1 contains 60 nucleotides. Evaluation of upstream of pd1 revealed that the number of transcription factors could alter the pd1.1 variation. With regard to the pd1.5 polymorphisms, the result showed that it is considered as a synonymous variation, but the pd1.9 was known as a nonsynonymous mutation. Thus, the pd1.9 could alter the hydrophobicity and Ramachandran plots of PD1. The pd1.5 mutation may impact the expression of the pd1gene because it changes the transcription factor arrangement on the upstream of pd1. Also, the pd1.9 substitution could alter the hydrophobicity and Ramachandran plots of protein.