Sandbox 35
From Proteopedia
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| + | <Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Insert optional scene name here' /> | ||
| + | ==Adenylate Kinase== | ||
| + | Adenylate kinase, also known as "ADK", is an enzyme which speeds up the reaction that includes the interconversion of adenine nucleotides. The protein's flexibility allows it to bind to certain substrates known as ligands. Adenylate kinase is known for influencing cellular energy homeostasis. | ||
| - | = '''Papain''' = | ||
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| - | ==Introduction== | ||
| - | [[Image:Papain_cartoon.png|200px|left|thumb|Cartoon Peak at Pepsin]] | ||
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| - | DID YOU KNOW? | ||
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| - | <scene name='Sandbox_35/Papain/1'>Papain</scene>. Meat tenderizer. Old time home remedy for insect, jellyfish, and stingray stings<ref>[http://www.ameriden.com/products/advanced-digestive-enzyme/] Ameridan International</ref>. Who would have thought that a sulfhydryl protease from the latex of the papaya fruit, ''Carica papaya'' and ''Vasconcellea cundinamarcensis'' would have such a practical application beyond proteopedia? | ||
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| - | This protease belongs to an extended family of aminopeptidases, dipeptidyl peptidases, endopeptidases, and other enzymes having both exo- and endo-peptidase activity. The inactivated zymogen with N-terminal propeptide regions - providing stability in alkaline environments and enabling proper folding - is activated through removal of the propeptide regions. <ref>PMID: 7845226</ref><ref>PMID: 12188906</ref> | ||
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| - | Papain. Lights. Camera. Action! | ||
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| - | <Structure load='9pap' size='500' frame='true' align='right' caption='Structure of Papain (PDB entry [[9PAP]])' scene='Sandbox_35/Papain/1'/> | ||
==Structure== | ==Structure== | ||
| - | + | The <scene name='Sandbox_35/Secondary_structure_colored/1'>secondary structure</scene> of Adenylate Kinase has alpha helicies (purple) and beta sheets (dark pink) that circle around and enclose the non-hydrolysable part of the protein,(seen in the center). This is known as the ligand, which does not experience hydrolysis. These alpha helicies and beta sheets are known as the "backbone" of the protein. | |
| - | <scene name='Sandbox_35/ | + | One of the main components of protein structure are the <scene name='Sandbox_35/Secondary_h_bonds2/1'>hydrogen bonds</scene> which are shown in green on this structure. The hydrogen bonds form links between adjacent amino acids, contributing to the protein structure and fold. Hydrogen bonding is an excellent stabilizing factor for the protein! The hydrogen bonds on the beta sheets are in an anti-parallel configuration, which offers stability for the protein. |
| - | + | ==Hydrophobic and Hydrophilic Residue Composition== | |
| - | + | Adenylate kinase is composed of both hydrophobic and hydrophilic residues, and folds accordingly to obtain the optimum environments for the nature of both kinds of residues. The <scene name='Sandbox_35/Secondary_hydrophobs_only_gre/1'>hydrophobic residues</scene> shown in grey are buried within the folded protein, away from contact with the solvent. This action represents the hydrophobic effect taking place, which is mainly driven by entropy. Surrounding the outside of the protein are the <scene name='Sandbox_35/Secondary_hphobic_and_hphilic/1'>hydrophilic residues</scene> (dark green). These residues are polar and can be in caontact with the surrounding solvent in the protein's environment. These residues can either be charged or uncharged, can hydrogen bond with water, and are generally more soluble. They cover the hydrophobic amino acid residues to protect them from the solvent. | |
| - | + | ==Water and Solvent== | |
| - | <scene name='Sandbox_35/ | + | Water is very important when it comes to protein folding and structure. It determines the conformation of exposed side chains, stabilizes the ends of secondary structures, and occupy positions at active sites where they influence substrate binding and sometimes catalysis. Adenylate kinase in <scene name='Sandbox_35/Secondary_with_water_molecules/1'>solvent</scene> is mostly surrounded by water molecules around the exterior area of the protein; However, it also can utilizes the water molecules to increase efficent substrate binding. The water molecules (light blue) surround the outside of the protein, interacting with the polar hydrophilic residues. However, some water molecules are seen in contact with the ligand (light green center) where the molecules are influencing catalysis. |
| - | + | ==Adenylate Kinase and The Ligand== | |
| - | + | The ligand(dark pink) in the center of the protein has specific residues surrounding it that are also known as the <scene name='Sandbox_35/Secondary_with_ligand_in_cente/1'>ligand contacts</scene>. These residues have polar-charged side chains, which stabilize the ligand. The ligand in Adenylate kinase is a molecule which is able to bind to the protein's specific active site. | |
| - | + | ==Catalytic Residues== | |
| - | + | The <scene name='Sandbox_35/Secondary_catalytic_residues/1'>catalytic residues</scene> (black) are found in the center of the protein, lining the active site where the ligand binds. These residues, also known as "active site residues", help with recognition of the ligand. The ligand binds with the protein in various ways: hydrogen bonds, hydrophobic interactions, temporary covalent interactions, or a mixture of the mentioned methods. The catalytic residues assist the reaction by acting as proton donors or acceptors. In the big picture, all of this helps the enzyme protein lower the activation energy of the ligand to speed up the reaction efficiently. | |
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Current revision
| Please do NOT make changes to this Sandbox. Sandboxes 30-60 are reserved for use by Biochemistry 410 & 412 at Messiah College taught by Dr. Hannah Tims during Fall 2012 and Spring 2013. |
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Contents |
Adenylate Kinase
Adenylate kinase, also known as "ADK", is an enzyme which speeds up the reaction that includes the interconversion of adenine nucleotides. The protein's flexibility allows it to bind to certain substrates known as ligands. Adenylate kinase is known for influencing cellular energy homeostasis.
Structure
The of Adenylate Kinase has alpha helicies (purple) and beta sheets (dark pink) that circle around and enclose the non-hydrolysable part of the protein,(seen in the center). This is known as the ligand, which does not experience hydrolysis. These alpha helicies and beta sheets are known as the "backbone" of the protein. One of the main components of protein structure are the which are shown in green on this structure. The hydrogen bonds form links between adjacent amino acids, contributing to the protein structure and fold. Hydrogen bonding is an excellent stabilizing factor for the protein! The hydrogen bonds on the beta sheets are in an anti-parallel configuration, which offers stability for the protein.
Hydrophobic and Hydrophilic Residue Composition
Adenylate kinase is composed of both hydrophobic and hydrophilic residues, and folds accordingly to obtain the optimum environments for the nature of both kinds of residues. The shown in grey are buried within the folded protein, away from contact with the solvent. This action represents the hydrophobic effect taking place, which is mainly driven by entropy. Surrounding the outside of the protein are the (dark green). These residues are polar and can be in caontact with the surrounding solvent in the protein's environment. These residues can either be charged or uncharged, can hydrogen bond with water, and are generally more soluble. They cover the hydrophobic amino acid residues to protect them from the solvent.
Water and Solvent
Water is very important when it comes to protein folding and structure. It determines the conformation of exposed side chains, stabilizes the ends of secondary structures, and occupy positions at active sites where they influence substrate binding and sometimes catalysis. Adenylate kinase in is mostly surrounded by water molecules around the exterior area of the protein; However, it also can utilizes the water molecules to increase efficent substrate binding. The water molecules (light blue) surround the outside of the protein, interacting with the polar hydrophilic residues. However, some water molecules are seen in contact with the ligand (light green center) where the molecules are influencing catalysis.
Adenylate Kinase and The Ligand
The ligand(dark pink) in the center of the protein has specific residues surrounding it that are also known as the . These residues have polar-charged side chains, which stabilize the ligand. The ligand in Adenylate kinase is a molecule which is able to bind to the protein's specific active site.
Catalytic Residues
The (black) are found in the center of the protein, lining the active site where the ligand binds. These residues, also known as "active site residues", help with recognition of the ligand. The ligand binds with the protein in various ways: hydrogen bonds, hydrophobic interactions, temporary covalent interactions, or a mixture of the mentioned methods. The catalytic residues assist the reaction by acting as proton donors or acceptors. In the big picture, all of this helps the enzyme protein lower the activation energy of the ligand to speed up the reaction efficiently.
