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. Due to its antibacterial effects, it is a strong component of the innate immune system, and is an important part of an infant's diet to ward off diarrheal diseases.
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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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<applet load='1hew' size='350' frame='true' align='left' caption='' />
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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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= 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. The model to your left shows a space-filling model of lysozyme, with the protein distinguishable in brown and the ligand distinguishable in green.
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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. The lysozyme then distorts the fourth sugar in the six membered sugar, producing stress on the molecule and breaking the glycosidic bond.
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The amino acid side-chains glutamic acid 35 (Glu35) and aspartate 52 (Asp52) have been found to be critical to the activity of this enzyme. Glu35 acts as a proton donor to the glycosidic bond, cleaving the C-O bond in the substrate, whereas Asp52 acts as a nucleophile to generate a glycosyl enzyme intermediate. The glycosyl enzyme intermediate then reacts with a water molecule, to give the product of hydrolysis and leaving the enzyme unchanged.
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<applet load='1hew' size='350' frame='true' align='right' caption='' />
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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> . The hydrophilic effect, or the desire for proteins to be at a specific position regarding water, is the single most important determinant of protein folding. 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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Here, lysozyme can also be seen interacting with <scene name='Sandbox_39/Water/1'>water</scene>, demonstrating how water remains almost exclusively on the outside of the molecule where the polar residues reside.
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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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<applet load='1hew' size='350' frame='true' align='left' caption='' />
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= Composition of Lysozyme =
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All proteins consist of carbon, hydrogen, nitrogen, oxygen, and sulfur, as do most organic molecules. Enzymes are composed in such a way as to maximize their reactivity with their desired substrate, increasing the efficiency of biological reactions. The <scene name='Sandbox_39/Elements/1'>composition of lysozyme</scene> can be seen on the left, with the carbon atoms outlined in gray, oxygen atoms in red, nitrogen atoms in blue, sulfur atoms in yellow, and the three-letter abbreviation for the <scene name='Sandbox_39/Amino_acid_residues/1'>amino acid residues</scene> in purple.
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Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.
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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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