Sandbox 39

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<Structure load='1AKE' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />
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=Description=
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Adenylate kinase, commonly known as ADK, is a phosphotransferase enzyme. It has two important roles in various organisms. First, ADK plays an important role in nucleotide metabolism and synthesis. It also has a role in cellular energetics and homeostasis by phosphotransfer networks. Adenylate kinase catalyzes the reaction that forms ADP. The reaction is ATP + AMP = 2 ADP. In this catalyzed reaction, ADK molecules bind to AMP molecules and increase its binding affinity for ATP over other phosphate groups. However, adenylate kinase is also found in other molecules such as bacteria and yeast. ADK plays similar roles in bacteria and yeast, in that it involves cellular metabolism and energy. The following images highlight the structure of Adenylate kinase from ''Yersinia pestis'', commonly known as yeast.
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== '''LYSOZYME''' ==
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=Structure=
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ADK is a protein made up of 214 amino acids. The <scene name='Sandbox_39/Adenylate_kinase_main_chain2/1'>mainchain</scene> of adenylate kinase can be seen here in purple with the ligand in the middle of the protein. The <scene name='Sandbox_39/Adenylate_kinase_beta_sheets2/1'>secondary structure</scene> contains 12 alpha helices (light blue) and 7 beta sheets (yellow). The <scene name='Sandbox_39/Adenylate_kinase_hbonds2/1'>backbone hydrogen bonds</scene> hold the protein together and give it shape. The <scene name='Sandbox_39/Adenylate_kinase_hydro_resid4/1'>hydrophobic residues</scene> are located towards the center of the protein, away from water. These residues are responsible for the overall conformation of the protein because of their "water fearing" nature. The <scene name='Sandbox_39/Adenylate_kinase_philic_resid2/1'>hydrophilic residues</scene> are located mainly on the surface or outside of the protein where they will have contact with water and other molecules. The hydrophilic residues that are inside the enzyme are necessary for the enzyme to open its active site and allow substrate in. The <scene name='Sandbox_39/Adenylate_kinase_ligand/1'>ligand</scene> is located in the center of protein. The ligand has six <scene name='Sandbox_39/Adenylate_kinase_cat_residues/1'>catalytic residues</scene> that allow it to bind to ADK's target protein (catalytic residues shown in white within the green ligand). These catalytic residues are known as the active site. The catalytic residues consist of arginine, aspartic acid, and lysine. The <scene name='Sandbox_39/Adenylate_kinase_solv_w_lig/1'>ligand has minimal water contact</scene> because it is located in the center of the protein (ligand is orange and water is displayed by space filling model). It is important to be shielded from water so that nothing interferes with the active site of the protein. The waters that are found in the interior are a result of the hydrophobic residues that are also found there. The ligands and catalytic residues of adenylate kinase are highly conserved throughout various organisms. This conservation indicates their importance to the protein's enzymatic function.
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Lysozyme is a powerful [[enzyme]] of biological significance found in abundance in tears, saliva, and human milk. It is also known as muramidase, or [[glycocide hydrolase]].
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=References=
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It is known for damaging bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins. In this way, lysozyme is efficient in lysing the cell walls of both bacteria and fungi.
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http://www.pnas.org/content/102/2/303.full
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A simple cartoon structure of lysozyme can be seen below. The secondary structures can be seen in blue, and the salt bridges are highlighted in yellow. The following sections will highlight different subsections of the lysozyme protein using colors and labels through the program Jmol.
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http://www.uniprot.org/uniprot/O69172
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http://www.biomedcentral.com/1471-2199/13/31/abstract
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= Secondary Structure =
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The structure of lysozyme with its <scene name='Sandbox_39/Secondary_structure/1'>Secondary Structure</scene> highlighted in yellow and pink can be seen to your left. The structures highlight the alpha helicies, and the yellow lines highlight the beta-pleated sheets. Lysozyme contains five alpha helicies and five beta-pleated sheets. Three of the beta-pleated sheets are antiparallel to one another, and the other two are separate from each other.
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= Hydrophobicity =
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Lysozyme contain both hydrophobic, or water-hating, regions and hydrophillic, or water-loving, regions, referred to overall as <scene name='Sandbox_39/Hydrophobicity/2'>Hydrophobicity</scene> . These regions can be displayed with the hydrophobic regions in gray and the polar, hydrophillic regions in purple. This coloration highlights the location of these regions, showing the majority of the hydrophobic regions are inside of the protein and the majority of the hydrophillic regions are on the outside of the molecule.
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= Ligands =
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A <scene name='Sandbox_39/Ligands_1/1'>ligand</scene> is a protein that is able to bind to the active site of an enzyme to form a biologically relevant complex. Lysozyme reaction is hydrolysis of the beta (1-4) glycosidic bond between N-acetylglucosamine sugar (NAG) and N-acetylmuramic acid sugar (NAM). Lysozyme very specific active site, which can bind only six sugar rings from a polysaccharide chain and hydrolyze them, so these six sugar rings represent the ligand of lysozyme.
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= Charged Residues =
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The charged residues, or the most polar portions of the molecule, are seen highlighted to the right in the space-filling model. The blue <scene name='Sandbox_39/Charges/1'>charges</scene> represent cations, and the red charges represent anions. The <scene name='Sandbox_39/Charged_and_polar_residues/1'>charged and polar residues</scene> can also be seen, with the charged residues the same as above and the polar residues in purple. It is important to note that these residues are found almost exclusively on the outside of the protein to increase its interaction of water.
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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.

Insert caption here

Drag the structure with the mouse to rotate

Description

Adenylate kinase, commonly known as ADK, is a phosphotransferase enzyme. It has two important roles in various organisms. First, ADK plays an important role in nucleotide metabolism and synthesis. It also has a role in cellular energetics and homeostasis by phosphotransfer networks. Adenylate kinase catalyzes the reaction that forms ADP. The reaction is ATP + AMP = 2 ADP. In this catalyzed reaction, ADK molecules bind to AMP molecules and increase its binding affinity for ATP over other phosphate groups. However, adenylate kinase is also found in other molecules such as bacteria and yeast. ADK plays similar roles in bacteria and yeast, in that it involves cellular metabolism and energy. The following images highlight the structure of Adenylate kinase from Yersinia pestis, commonly known as yeast.

Structure

ADK is a protein made up of 214 amino acids. The of adenylate kinase can be seen here in purple with the ligand in the middle of the protein. The contains 12 alpha helices (light blue) and 7 beta sheets (yellow). The hold the protein together and give it shape. The are located towards the center of the protein, away from water. These residues are responsible for the overall conformation of the protein because of their "water fearing" nature. The are located mainly on the surface or outside of the protein where they will have contact with water and other molecules. The hydrophilic residues that are inside the enzyme are necessary for the enzyme to open its active site and allow substrate in. The is located in the center of protein. The ligand has six that allow it to bind to ADK's target protein (catalytic residues shown in white within the green ligand). These catalytic residues are known as the active site. The catalytic residues consist of arginine, aspartic acid, and lysine. The because it is located in the center of the protein (ligand is orange and water is displayed by space filling model). It is important to be shielded from water so that nothing interferes with the active site of the protein. The waters that are found in the interior are a result of the hydrophobic residues that are also found there. The ligands and catalytic residues of adenylate kinase are highly conserved throughout various organisms. This conservation indicates their importance to the protein's enzymatic function.

References

http://www.pnas.org/content/102/2/303.full

http://www.uniprot.org/uniprot/O69172

http://www.biomedcentral.com/1471-2199/13/31/abstract

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