An In-Depth Analysis of Neuropilin 1
Nicole Dano and Jessica Hrnciar
Date Published: December, 14 2020
Protein Structure
Source: "Chimera Structure Viewer" (11)
The structure we used is the Neuropilin-1/VEGF-A complex, and the PDB ID is 4DEQ (12). We used chimera to visualize the 3D structure and beta sheets are in purple, helices are in red, and coils are in gray. In our image, neuropilin-1 is bound to the phosphate ion, and VEGF-A is the structure above it. We were unable to find a structure of human NRP1 alone, so we chose this complex. It is very common for NRP1 to bind VEGF-1, and they bind with a high affinity, so this structure is a very common complex (13). This structure shows positions 274-429 of NRP1, so it is not inclusive of the whole protein (14). The structure of NRP1 is primarily beta sheets and coils, with very few helices. There are 9 helices and 41 beta-sheets. The C terminus of NRP-1 has an arginine binding cleft consisting of three loops that are highly conserved (15).
Secondary Structure
As mentioned above, the secondary structure of NRP1 is primarily beta-sheets, with very few helices. In the image provided from UniProt, the sheets are represented with green, the helices are represented with blue, and coils/turns are represented with pink (14). This diagram makes it easy to visualize that NRP1 primarily consists of sheets, and the exact locations and length of sheets are also provided on UniProt. NRP1 is made up of only one polypeptide chain, so it does not have a quaternary structure.
Through the NCBI conserved domains page, we were able to determine the binding sites of our protein (16). All of the binding sites on this database are within the F5/8 type C domain; 3 sugar-binding sites in the first F5/8 type C domain and 3 sugar-binding sites in the second F5/8 type C domain. The sugar-binding sites are Threonine-316, Alanine-344, Tyrosine-353, Histidine-478, Glycine 503, and Valine 510 (16). In addition to binding sites, heterodimerization interaction locations were also provided, and they all occur within the CUB domain. These locations are Proline-36, Tyrosine-38, Threonine-40, Methionine-60, Histidine-74, Proline-111, Serine-135, Arginine-137,Glutamic acid-139, Isoleucine-140, Serine-155, Valine-157, Lysine-159, isoleucine- 186, Serine 191, Arginine -235, Serine-259, Asparagine-261, Serine-263, Valine-164 (16). Our protein also contains a glycosylation point at position 31 (12). Our protein also contains 4 disulfide linkages. These occur between C6-C155 and C170-C188, C173-C190, and C199-C213 (12).
Functional Domains
CUB Domain
Source: "Chimera Structure Viewer" (11)
Neuropilin-1 contains two CUB Domains, which occur in tandem. These domains are about 110 amino acids in length and it is an extracellular domain (18). This domain has four highly conserved cysteine residues that form two disulfide bonds that are characteristic of this domain (18). The Cub domain is shown in blue in the image above, and it is mostly made up of beta-sheets, forming a structure referred to as a beta-barrel. This domain mediates binding to semaphorin molecules (14). Both of the isoforms we provided detailed information about have two CUB domains. For isoform a the domain is from amino acids 27-138 and 147-262 (8). For isoform i the Cub domain is found in the same location as isoform a.
The functions of the CUB domain consist of complement activation, axon guiding, angiogenesis, cell signaling, tumor suppression, and many others (18). These functions are directly related to NRP1 functions. NRP1 has been found to be strongly involved in the major biological processes of axon guidance and angiogenesis. Our protein function page goes into more detail about NRP1’s role in these processes.
F5/8 Type C Domain
Source: "Chimera Structure Viewer/Pfam" (11)
This domain is also known as FA58C or C1/C2, and it is found twice in tandem in Neuropilin-1. It is a cell surface carbohydrate-binding domain, and it also binds heparin and VEGF (14). This domain is about 150 amino acids in length and its secondary structure contains a helix and coils (19, 20). The structure is shown in the image above and it is highlighted blue, which shows the structure in 3D. Both isoform a and isoform i contain two F5/8 type C domains. For isoform a, they are located from amino acids 290-421 and 446-580 (8). For isoform i the two F5/8 type C domains are found in the same locations.
The functions of the F5/8 type C domain can include a role in coagulation because they are found in most coagulation factor proteins. Within their role in coagulation, this domain is responsible for binding anionic phospholipids on the surface of cells (19). Another function of this domain is binding carbohydrates, heparin, and VEGF. This directly relates to their role in NRP1. In NRP1 the F5/8 type C domains contain all the sugar-binding sites, so this where sugars and other molecules interact with neuropilin-1. This domain facilitates that interaction. Also, NRP-1 binds VEGF often and with a high affinity, and this domain makes that possible (13). It is important for NRP1 and VEGF to interact because it promotes cell migration and signaling (21). These functions of NRP1 will be further discussed on our protein function page.
MAM Domain
Source: "Chimera Structure Viewer" (11)- we used PDB ID:5L73 to better highlight the MAM domain (22).
The MAM domain is found once in the neuropilin 1 protein. This domain is about 170 amino acids long and it is mainly found in the extracellular portion of proteins (23). The secondary structure is mainly beta sheets and its structure is highlighted in blue in the image above. This domain consists of a beta-sandwich made up of five antiparallel strands which are rotated away from each other (16). This domain contains four highly conserved cysteine residues that form two disulfide linkages. Only isoform a contains this domain, and it is found from amino acids 650-811(8).
The functions of the MAM domain include homodimerization in the phosphatase ectoprotein, but its main function is cell adhesion in most other proteins (16). Cell adhesion is one of the main processes NRP1 is involved in. The MAM domain helps the NRP1 protein perform cell-to-cell adhesion, but since this domain is not found in all isoforms this shows the different functions of the different isoform protein products (8). Our gene protein function page provides more information on the functional roles of NRP1.