An In-Depth Analysis of Neuropilin 1
Nicole Dano and Jessica Hrnciar
Date Published: December, 14 2020
Discussion and Conclusions
At the conclusion of this project, the objectives stated were all successfully met. By just starting with a partial protein sequence a protein was able to be successfully identified. From the protein information, the gene which encodes for the protein was discovered, and this was all thanks to the help of bioinformatics tools and databases. This project has served as an irreplaceable learning experience. Not only did we learn about the specifics of the neuropilin-1 gene and protein, but we also learned our way around many different bioinformatics tools and how to apply them.
The Gene
We were able to determine that the neuropilin-1 gene encodes for the protein we were given. AceView provided isoform-specific information-including that neuropilin-1 has 30 different isoforms. All of these isoforms were unique- they varied based on their length, number of exons, expression levels, and other features. Since there are so many isoforms of this gene, there was a lot of overlap in the coding sequences, but this still resulted in a variety of different protein products. The developmental related differential gene expression was also identified, which revealed this gene’s expression in different stages of fetal development. The use of different bioinformatics tools allowed us to make all these discoveries and map out neuropilin-1 gene.
Protein Structure
Once we had a thorough understanding of the gene, it was important for us to look at the protein product it encoded. It was hard to find a complete structure of NRP-1, and the best structure we were able to identify was NRP-1 in complex with VEGFA. We were also able to visualize the structure of the domains found in our protein- CUB, F5/8 type C, and MAM. The structure typically implies function, and we were able to better understand NRP-1 function by interpreting its structure.
Protein Function
The major functions of NRP-1 include axon guidance, angiogenesis, cell adhesion, and HTLV-1 infection among others. These functions give NRP-1 a role in many different biochemical pathways- such as axon repulsion and the entry of HTLV1 into a CD4 T cell. These functions also correlate to where the protein is localized within a cell. NRP1 is mainly seen in the plasma membrane or extracellular space. NRP1 is also found to interact with several other proteins, most commonly VEGFA, ITGA5, AGER, FLNA, and KDR.
Mutations and Diseases
NRP1 has been shown to be involved in many different diseases, mostly where it acts as a receptor. NRP1 plays a role in glioma, HTLV1, leukemia, Sars-CoV-2, and congenital heart defects. Mutations in NRP1 can be harmful since this protein is so widespread in the body.