User:Jerrica Flakes/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.

Introduction

The protein that I chose to research Phospholipase A2 (3VBZ), and it is in many snake venoms, but I will be focusing on the Australian Taipan (Oxyuranus microlepidotus) venom. The Australian Taipan has one of the most potent neurotoxic and hemotoxic, which will cause a swift death. A neurotoxin damages the nervous system, which will cease communication between cells. Hemotoxin destroys red blood cells meaning clotting will not occur, the carrying of oxygen throughout the body will stop, tissue damage and many other body functions will not happen anymore. “Hemotoxic venoms affect the circulatory system by causing hemolysis and venous or arterial thrombosis. Cardiotoxicity is secondary to organ degeneration, generalized tissue damage, and hyperkalemia”^[3]( Epidemiology of Cardiovascular Toxin). Hemolysis is when a red blood cell is destroyed, and hemoglobin is released into the blood plasma. Since hemoglobin carries oxygen, that means the body will not receive oxygen anymore. Along with oxygen being deprived of the body, arterial and venous thrombosis occurs, which means blood clots will form in arteries and veins. This will lead to the death of tissue and organ degeneration. Venom is the ultimate defense from predators for snakes, and venom/venom glands evolved in snakes before fangs. Venom has become stronger because the predators and prey have become more resistant to it, and now venom from the Australian Taipan can kill any organism. According to Elmen and Zimmer, the way venom evolved is through gene recruitment, which means once a gene duplicates, it is moved to a new part of the body. In snakes, the proteins crotamine and kallikrein originated in the pancreas and were recruited to the mouth, giving the snake an offensive and defensive advantage. Based on the effects of the venom for the Australian Taipan, I can assume that the Australian Taipan’s venom protein could have originated from 3FTx (effects neurotoxins found in the head), Acetylcholinesterase (disrupts nerve impulses found in the muscle), ADAM (Tissue decay comes from the lungs), and crotamine and kallikrein (comes from the pancreas and it affects muscle decay and the destruction of red blood cells) (324). It is incredible how some snake toxins that affect an organism’s body’s specific functions come from that particular body part. For example, 3FTx protein is a neurotoxin that was recruited from the brain. Phospholipase A2 origin is also in the pancreas. Recently Phospholipase is found in many mammals (including humans) and plants (which can help neutralize PLA2 in venom), but what makes it dangerous in the snake is the different subunits (α,β, and γ) in other species.

About Stucture

Phospholipase A2 (PLA2)/ has two chains, A and B. It has a sequence length of one-hundred eighteen amino acids, and by using X-ray diffraction, the resolution of the protein is 1.76Å. That is a pretty okay resolution, and the means the data collected will be pretty accurate. The researchers on the protein database state, “Although no correlation has been reported between neurotoxicity and enzymatic activity, toxicity increases with structural complexity and phospholipase A2 oligomers show 10‐fold lower LD50 values compared to their monomeric counterparts” (Cendron, L., Micetic, I., Polverino, P., Beltramini, M., Paoli). So the more complex a toxic protein, the more lethal it is. The oligomer if PLA2 is lower than the lethal dose is because oligomers have a lower molecular weight and fewer repeating units. In humans and mammals, PLA2 is used as a metabolizing catalyst for phospholipids. PLA2 critical structure has six disulfide bonds (R-S-S-R) at 28-44, 26-118, 43-99, 50-92, 60-85, and 78-80. Also, there is a disulfide bridge (Cys-S-S-Cys) at the 11-17 position. The for the PLA2 location is His-48 and Asp-93 ((*have a highlighted active site where it probably shows the Ca+2 in the active site, and maybe one without it in the active site)), and Ca+2 turns on the active site, which then attaches to the binding loop, the enzyme goes through hydrolysis. It uses H2O (water) to take away a proton to break the SN-2 ester bond apart. This reaction will make the pH between seven and nine. PLA2 will bind to the phospholipid bilayer membrane and has electrostatic (van der Waals) and hydrophobic interactions. During the electrostatic interactions, they attract each other, making it either particle positive or article negative. For hydrophobic interaction occur at Leu-2, Phe-5, Trb-19, Tyr-52, and Tyr-69. These amino acids, once they come into contact with the phospholipid membrane, wrap around the acyl chain (R1-C=O) of the lipid substrate, and this. The amino acids bind to the membrane, and the rest of the chain is in the lipid water interface. There are two types for PLA’s: Type I (Old world snakes: snakes and cobras) and Type II (New world snakes: rattlesnakes), and the Australian Taipan is a Type II snake. The venom for Type I and II are very similar, but there are a few differences. For Type I, there is an additional C-terminal, and because of this extra terminal, there are a few more disulfide bonds, which have a different arrangement. Type II has a Lys-49 instead of Asp-49 making it unable to bind Ca+2 to the active sites. A taipoxin is both a neurotoxin and a myotoxin. The complex of the taipoxin is a 1:1:1 of (in purple), neutral (in reddish-purple), and acidic γ-taipoxin (not shown in this crystal structure model). All three are in PLA2 when it is secreted (sPLA2) into another organism. The α-taipoxin subunit has 119 amino acids (Asn-Leu-Leu-Gln), and it the “toxic” part of the protein because it is 10% taipoxin. The neutral β-taipoxin subunit is 118 amino acids (Asn-Leu-Val-Gln), and γ-taipoxin subunit is the largest, and it has 133 amino acids (Ser-Glu-Iln-Pro). Going through the whole process, we first start with the Australian Taipan biting a predator, prey, or person. The fangs release the Type II venom and secrete it into the organism’s body, and this frees PLA2 (sPLA2 is “secreted” PLA2). Since it is a taipoxin, it first binds to the nerve terminals and hydrolyzes by binding Ca+2 to the active site ate His-48 and Asp-99. The plasma membrane uses water to take away a proton and breaks the SN2 ester bonds, raising the pH. This reaction will turn the phospholipid into lysophospholipid and fatty acids. When the sPLA2 is attaching to the phospholipid, only a few carbons and amino acids will bind by wrapping around the acyl chain, which has a Ca+2 in the active site/loop. Resulting in an unbalance with developing vesicles for exocytosis. Since the vesicle and the membrane are damaged, it becomes hard for myoglobin and hemoglobin to stay on the extracellular matrix, cut the transport of oxygen to the body, and leading to severe myotoxicity and neurotoxicity. This will lead to the organism experiencing hyperkalemia (the potassium in your blood skyrockets) and myglobinuria (myoglobin dramatically falls and can end up in urine). The peripheral nervous system (every nerve outside the brain and spinal cord) will begin to shut down because the sPLA2 will target the mortar nerve terminal and motor axon terminal and block communication between the cells. Due to sPLA2 binding to the nerves, this will lead to rapid paralysis of the neuromuscular junction meaning the muscles will not begin to work. PLA2 affects and kills the cell and will block communication to muscle cells, which leads to the muscle cells dying. The body will shut down in a matter of thirty minutes after the bite.

For a more general description there are several good references including.