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| + | <Structure load='1ake' size='500' frame='true' align='right' caption='Adenylate kinase' scene='Sandbox_36/Adenylate_kinase/4' /> |
| + | =Background= |
| + | Adenylate kinase is an important protein found within the bacterium, Yersinia pestis, the culprit of the bubonic plagues. According to Relationship between bacterial virulence and nucleotide metabolism: a mutation in the adenylate kinase gene renders Yersinia pestis avirulent, by Munier-Lehmann H et al., a mutant form of adenylate kinase was able to be digested and was unable to infect mice. <scene name='Sandbox_36/Adenylate_kinase/4'>Adenylate kinase</scene> is a phosphotransferase protein, that catalyzes the reaction of adenosine triphosphate (ATP) and adenosine monophosphate (AMP), to form two molecules of adenosine diphosphate (ADP). |
| + | =Structure= |
| + | In the <scene name='Sandbox_36/Crystal_structure/1'>crystal structure</scene>, adenylate kinase dimerizes because of interactions with another molecule of adenylate kinase, that are not existent within a living organism. It is actually comprised of just one <scene name='Sandbox_36/Rainbow_map/1'>amino acid chain</scene>, which is highlighted from N-terminus to C-terminus, blue to red, respectively. |
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- | =Lysozyme= | + | Adenylate kinase's <scene name='Sandbox_36/Secondary_structure_of_ak/1'>secondary structural characteristics</scene> consist of twelve (12) alpha helices, shown in brown, and seven (7) beta sheets, shown in blue. <scene name='Sandbox_36/The_bonds_of_backbone/1'>Hydrogen bonds</scene>, shown as black, dashed lines, hold together the secondary structural features of adenylate kinase. Most of the beta sheets, in this protein, are aligned parallel to one another. This is evident by the presence of an angle of the hydrogen bonds between the sheets; antiparallel sheets have parallel hydrogen bonding. |
| + | =Interactions= |
| + | Here the <scene name='Sandbox_36/Hydrophobic_residues_alone/1'>hydrophobic</scene> residues are pictured in light grey, and in this scene the <scene name='Sandbox_36/Charged_and_polar/1'>hydrophilic</scene> (charged, polar) residues are pictured in brown. In this representation both the <scene name='Sandbox_36/Residues_together/1'>hydrophobic and hydrophilic</scene> residues are shown in the same colors as previously. It can be seen that there is a cleft in the protein, which is lined with hydrophilic residues. This is most likely the area in which the substrates and/or ligand enter into the active site. It can also be noted that both hydrophobic and hydrophilic residues come in contact with the ligand, which is expected. |
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- | ==Overview== | + | Here the <scene name='Sandbox_36/Water/1'>solvent</scene>, represented by dark grey spheres, is displayed. The placement of the solvent molecules help to confirm the prediction of the location of entry for substrates and ligands, in the cleft. The solvent is mainly on the exterior of the protein; it cannot be found in the "spaces" of the protein. This is because there actually are not any "spaces" the solvent to fit into the protein, as can be seen in this <scene name='Sandbox_36/Adenylate_kinase_space_fill/1'>space filling</scene> model of adenylate kinase. |
- | Lysozyme is an enzyme that inhibits the growth of bacteria through lysis of the cell wall. It can be found in salvia, tears, other bodily secretions. Lysozyme is also present in high concentrations in hen egg whites. Lysozymes small size and high stability makes it ideal for protein structure and function research. Furthermore, the enzyme is easy to purify from egg whites and easy to crystallize, unlike most proteins.
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- | ==Structure== | + | In this scene, the interactions between the <scene name='Sandbox_36/Ligand_interactions/1'>residues and ligand</scene> are represented. Anionic side chains are red, cationic side chains are blue, and histidine residues are light blue. Most of the residues that interact with the ligand are cationic, or positive, which makes sense because the ligand contains many negatively charged phosphate groups. The <scene name='Sandbox_36/Catalytic_residues/1'>catalytic residues</scene>, pictured in brown, are focused towards the center of the ligand. This also matches the data, as the purpose of adenylate kinase is to transfer a phosphate group from ATP to AMP. |
| + | =Resources= |
| + | [http://www.ncbi.nlm.nih.gov/pubmed www.ncbi.nlm.nih.gov/pubmed] |
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- | <applet load='3IJU'' size='300' frame='true' align='right' caption='Egg White Lysozyme ' />
| + | [http://www.ebi.ac.uk/pdbsum/ www.ebi.ac.uk/pdbsum/] |
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- | The lysozyme used to analyze structural features was isolated from the eggs of ''Gallus gallus''(chicken). Alternatives names for this lysozyme include 1,4-beta-N-acetylmuramidase C, Allergen Gal d IV, Allergen=Gal d 4. The European Commission number, or EC number, is 3.2.1.17. The sequence consists of 147 amino acids with a molecular weight of 16kD <ref> Lysozyme cprecursor - gallus gallus (chicken). (2010, October 5). Retrieved from http://www.uniprot.org/uniprot/P00698 </ref>. Lysozyme is <scene name='Sandbox_36/Composition/1'>composed</scene>of carbon(gray), nitrogen(blue), oxygenpurple) and sulfur(yellow). This <scene name='Sandbox_36/Composition/2'>surface view</scene> shows the ellipsoidal shape, which has the dimension 30 x 30 x 45 Angstroms. The dominate feature, the cleft for substrate binding, is also clear in this figure.
| + | [http://www.wikipedia.org/ www.wikipedia.org/] |
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- | ===Secondary Structure===
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- | ''Gallus gallus'' egg white lysozyme has an alpha+beta fold, consisting of eight alpha helices and a three-stranded antiparallel beta sheet. There is also a large amount of random coils and beta turns. Click <scene name='Sandbox_36/Secondary/3'>view</scene> to visualize the cartoon portrayal of the enzyme with alpha helices and beta sheets highlighted. The alpha helices are in green and the beta sheets in blue. The random coils are gray. Click <scene name='Sandbox_36/Secondary/5'>view</scene> for the rainbow color ordered cartoon chain from N to C terminals. Depending on where it was isolated from, not all lysozyme molecules will have the same number of alpha helices and beta sheets.
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- | ===Disulfide and Hydrogen Bonds===
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- | Disulfide bonds are formed by the oxidation of two cysteine residues to form a covalent sulphur-sulphur bond <ref> Day, A. (1996). Disulphide bonds. Retrieved from http://www.cryst.bbk.ac.uk/PPS2/projects/day/TDayDiss/DisulphideBonds.html </ref>. These interactions are not as important for stability, as they are for insuring correct folding patterns.
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- | Lysozyme has four disulphide bonds connecting the <scene name='Sandbox_36/Bonds/1'>backbone</scene> of the molecule, which are highlighted in yellow. There are also four disulphide bonds in between the <scene name='Sandbox_36/Bonds/2'>side chains</scene>, highlighted in red. The residues surrounding the side chain disulphide bonds are highlighted in yellow.
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- | Hydrogen bonds are essential to protein structure, forming an attractive force between the hydrogen attached to an electronegative atom of one molecule and an electronegative atom of a different molecule<ref> Ophardt, C. (2003). Intermolecular forces: hydrogen bonds. Retrieved from http://www.elmhurst.edu/~chm/vchembook/161Ahydrogenbond.html </ref>. The enzyme has many hydrogen bonds connecting the <scene name='Sandbox_36/Cartoon/3'>backbone</scene>, these are highlighted red. The hydrogen bonds, in yellow, between the <scene name='Sandbox_36/Cartoon/5'>side chains</scene> are also numerous.
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- | ===Active Site===
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- | The large cleft that transverses the side of lysozyme is the active site. The two amino acids residues that interact with the bound substrate are Asp52 and Glu35. The lysozyme as <scene name='Sandbox_36/Lysozyme/4'>cartoon</scene> and <scene name='Sandbox_36/Lysozyme/3'>backbone</scene> representations show Asp52, in green, and Glu35, in purple, branching off in the ball and stick form. The openness of the secondary representation does not allow cleft identification. The cleft, however, can be viewed from the tertiary structures
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- | <scene name='Sandbox_36/Lysozyme/5'>surface</scene> view of the enzyme. This view also has the green Asp52 and purple Glu35 visible.
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- | The peptidoglycan that binds in the lysis reaction is considered a ligand of lysozyme. Lysozyme has no natural ligands.
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- | ===Polar vs Nonpolar Residues===
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- | The hydrophobic collapse is the driving force behind protein folding. The nonpolar residues minimize there contact with water by compacting into a hydrophobic core. For this reason the hydrophobic effect is the major determinant of protein structure and has the greatest influence of stability.
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- | Understanding the polar and nonpolar areas of a molecule gives an understanding of where water can and will interact. This <scene name='Sandbox_36/Polar_vs_nonpolar/1'>figure</scene> visualizes the polar(red) and nonpolar(white) regions of the secondary structure. Using the same labeling, the polar and nonpolar residues are represented in this ball and stick <scene name='Sandbox_36/Polar_vs_nonpolar/2'>figure</scene>. Through these depictions of lysozyme it is apparent the hydrophobic, nonpolar residues favor the inside of the molecule and the hydrophilic, polar residues tend to stay on the outside. The active site residues are highlighted in this polar vs nonpolar dot <scene name='Sandbox_36/Polar_vs_nonpolar/7'>representation</scene>. Viewing this depiction makes it clear that Asp52, in yellow, is in a highly polar, hydrophilic area. While Glu35, in green, is located in more of a nonpolar, hydrophobic region. In the lysis reaction, this placement of Glu35 in a hydrophobic area makes it possible for protonation at a neutral pH, because the dissociation is suppressed.
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- | The charged residues are also located on the outside of the enzyme. This <scene name='Sandbox_36/dot fill/8'>TextToBeDisplayed</scene> representation shows the positive, acidic residues in red and the negative, basic residues in blue. Research has shown that charged residues are major determinants of the transmembrane orientation.
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- | ==Function==
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- | Lysozyme’s main function is to protect from infection. The enzyme is a general non-specific organism defense effective against gram positive bacteria. Lysozyme degrades the polysaccharides found in cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins<ref>Lysozyme. (2008). Retrieved from http://lysozyme.co.uk/</ref>. X-ray crystallography has shown that the binding of lysozyme and the substrates slightly deforms both structures. The binding first distorts the fourth hexose in the chain to the half chair conformation <ref>Voet, D, G., J, & W., C. (2008). Fundamentals of biochemistry: life at the molecular level. John Wiley & Sons Inc</ref>. This imposes a strain on the C-O bond on the ring-4 side of the oxygen bridge between rings 4 and 5<ref>Kimball, J. (2010, May 26). Enzymes. Retrieved from http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Enzymes.html#lysozyme</ref>. The polysaccharide is broken at this point and a molecule of water is inserted between the two hexoses. The reaction mechanism is shown below.
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- | [[Image:Lys.gif]]
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- | ==History==
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- | Laschtschenko first described lysozyme in chicken eggs in 1909. In 1919, Bloomfield reported the enzyme in saliva. Not until its discovery by Alexander Fleming in 1922 was lysozyme officially named and understood<ref> Worthington, K. (2010). Lysozyme. Retrieved from http://www.worthington-biochem.com/ly/default.html </ref>. Researching medical antibiotics, Fleming tested human mucus on a live culture. To his surprise, it successfully killed the bacteria. The phenomena was carefully analyzed and, shortly after, proven that lysozyme was the main active enzyme. Fleming had discovered one of the human body’s natural defenses against infection. Lysozyme could not successfully be used as an antibiotic, however, because its large size inhibits transportation through cells<ref>Goodsell, D. (2000, September). Lysozyme. Retrieved from http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb9_1.html</ref>. The enzyme has been put to good use, being the source of much protein structure and function research.
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- | As mentioned earlier lysozyme can be purified from hen egg-whites and crystallized quite simply. This has made it the best object for X-Ray analysis for many years. The X-Ray beam diffraction of lysozyme crystals has an extremely high resolution, reaching 0.94 Angstroms. In 1965 David Chilton Phillips successfully solved the structure through X-Ray analysis with 2 angstrom resolution<ref>Lysozyme. (2008). Retrieved from http://lysozyme.co.uk/</ref>. Lysozyme was the first enzyme ever to have its structure solved. A year later, the mechanism was explained. Today lysozyme is still being used in research and is commercially valuable enzyme used for many purposes, including the treatment of ulcers and infections, and as a food and drug preservative.
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- | ==References==
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- | <references/>
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Adenylate kinase is an important protein found within the bacterium, Yersinia pestis, the culprit of the bubonic plagues. According to Relationship between bacterial virulence and nucleotide metabolism: a mutation in the adenylate kinase gene renders Yersinia pestis avirulent, by Munier-Lehmann H et al., a mutant form of adenylate kinase was able to be digested and was unable to infect mice. is a phosphotransferase protein, that catalyzes the reaction of adenosine triphosphate (ATP) and adenosine monophosphate (AMP), to form two molecules of adenosine diphosphate (ADP).
In the , adenylate kinase dimerizes because of interactions with another molecule of adenylate kinase, that are not existent within a living organism. It is actually comprised of just one , which is highlighted from N-terminus to C-terminus, blue to red, respectively.
Adenylate kinase's consist of twelve (12) alpha helices, shown in brown, and seven (7) beta sheets, shown in blue. , shown as black, dashed lines, hold together the secondary structural features of adenylate kinase. Most of the beta sheets, in this protein, are aligned parallel to one another. This is evident by the presence of an angle of the hydrogen bonds between the sheets; antiparallel sheets have parallel hydrogen bonding.
Here the residues are pictured in light grey, and in this scene the (charged, polar) residues are pictured in brown. In this representation both the residues are shown in the same colors as previously. It can be seen that there is a cleft in the protein, which is lined with hydrophilic residues. This is most likely the area in which the substrates and/or ligand enter into the active site. It can also be noted that both hydrophobic and hydrophilic residues come in contact with the ligand, which is expected.
Here the , represented by dark grey spheres, is displayed. The placement of the solvent molecules help to confirm the prediction of the location of entry for substrates and ligands, in the cleft. The solvent is mainly on the exterior of the protein; it cannot be found in the "spaces" of the protein. This is because there actually are not any "spaces" the solvent to fit into the protein, as can be seen in this model of adenylate kinase.
In this scene, the interactions between the are represented. Anionic side chains are red, cationic side chains are blue, and histidine residues are light blue. Most of the residues that interact with the ligand are cationic, or positive, which makes sense because the ligand contains many negatively charged phosphate groups. The , pictured in brown, are focused towards the center of the ligand. This also matches the data, as the purpose of adenylate kinase is to transfer a phosphate group from ATP to AMP.