User:Jessica Dempsey/sandbox1

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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Function

Saporin is a ribosome-inactivating protein (RIP); alone, saporin does not selectively inactive ribosomes but rather conjugate with other molecules like peptides ^[3]. Saponaria officinalis is the plant from which saporin is extracted ^[4]. Type I and type II RIPS exist. Of these types, saporin is a type I. Ribosome inactivating proteins catalyze a cleavages N-glycosidic bond that is formed between the ribosome and adenine ^[5]. This adenine has the role of binding EF-1 and EF-2 to a ribosome ^[5]. EF stands for elongation factor. Since adenine no longer has a bond to the ribosome, the elongation step in translation cannot occur because the elongation factors cannot bind to just the ribosome. The specific elongation factor that is inhibited is elongation factor 2, which causes irreversible damage and disallows protein synthesis ^[4].

Disease

Relevance

Structural highlights

Type 1 RIPS are monomeric, meaning they have one part ^[6]. Saporin-S6 at maturity is 256 amino acids long ^[4]. While saporin consists of different residues and molecules, there is only one Chain A in it, and thus is monomeric. Chain A is a polypeptide weighing 30 KDa ^[7]. This chain consists of beta-sheets and alpha-helixes. The β-sheets make up the N-terminal domain, while the 𝛼-helix portion is the C-terminal domain ^[5]. In the figure of Chain A, the 𝛼-helices are spiral-shaped strands, while the β-sheets are more of a flat strand.

There is an active site within this chain that consists of five residues. These residues are Tyr⁷², Tyr¹²⁰, Glu¹⁷⁶, Arg¹⁷⁹, and Trp²⁰⁸ ^[4]. Other RIPs also have these same residues in their active sites. The saporin active has Glu¹⁷⁶, Arg¹⁷⁹, and Trp²⁰⁸ in the exact same position as the other ribosome-inactivating proteins. There is a difference in Tyr⁷², which has different side-chain conformations in RIPs and thus is not the same in saporin and other RIPs. This Tyr⁷² is the residue that interacts with the adenine in the cleavage of adenine and the ribosome ^[5].

Saporin can also be complexed with other inhibitors. One of these is cyclic tetranucleotide inhibitor in complex with saporin-L1. This can be used because the cyclic tetranucleotide can take the place of the recognition loop for saporin of 28S rRNA ^[8]. It is also interesting to note that Ricin can also be complex with other inhibitors like saporin. Saporin is a homologue of Ricin A-Chain which means they are similar in structure ^[8]. This ability also allows for saporin-S6 to be conjugated with specific targeting proteins, and thus the saporin-S6 is able to be delivered to the cell. This happens due to the antibodies and is referred to as an immunotoxin ^[4]. The antibodies are recognized by the cell, and the cell binds them. Since the saporin-S6 is in complex with the antibody, it is also taken to the cell. Some other carries can also be used, such as growth factors, antigens, and growth hormones ^[4].

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

Medical Uses

Medical uses for saporin have been studied as well. Most notably, the use of saporin as an anti-tumor agent or anti-cancer agent. Research has been done to determine if and how saporin could be used to treat cancer. Cancer treatments include many things, some of which are tumor debulking surgeries and chemotherapy. Although toxins like saporin can cause cell death, if saporin can be used to target cancer, it would kill off cancer cells. The delivery of drugs to a specific tissue can be used to avoid healthy tissue but harm the diseased tissue or cancer tissue ^[9]. Saporin is toxic to cancer cells due to its level of enzymatic activity and saponin’s resistance to conjugation. This toxicity causes apoptosis, cell death to the targeted cancer cells ^[7]. Assays of saporin-S6’s ability to induce apoptosis and necrosis are also being studied ^[4]. Saporin-S6 has been used in mice to study its effects on tumors and cancers. Mice were injected with saporin-S6 at a dose that was non-lethal to them. They were then left and later examined for tumors throughout their bodies. The best results were in the liver, but then no tumors were reported 14 days after the initial saporin-S6 injection ^[4].

One way that has been researched to treat cancer with saporin is by using an amino-terminal fragment (ATF) and fusing it with saporin (SAP) ^[9]. The specific ATF used was the human urokinase-type plasminogen activator (uPA) which is the ligand to the urokinase plasminogen activator receptor (uPAR). This means that uPAR will bind uPA, and if saporin is fused with uPA, it will also be bound to the uPAR. This is important because uPAR is upregulated, increasing its levels in cancer cells ^[9]. With increased levels, it means that more uPA will be in the cancer cell and again more saporin since the saporin is bounded to the uPA. This particular study found that the ATF-SAP was able to get into the cancer cells and kill the cells in cancer cells. Although, with lower and undetectable levels of uPAR, there was no effect on cancer with ATF-SAP ^[9]. Saporin can be bound to other molecules to make it effective for specific things in the body. Although, there need to be appropriate levels of what is being targeted, or the saporin won't be able to get to where it needs to be to achieve the goal.