Sandbox 36: Difference between revisions

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==Structure==

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.

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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.

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.

~~===Polar vs Nonpolar Residues===~~

===Active Site===

The enzyme is approximately ellipsoidal in shape, with a large cleft in one side forming the active site. The two amino acids that interact with the bound substrate are Asp52 and Glu35. ~~These two amino acids can be viewed on~~ lysozyme as <scene name='Sandbox_36/Lysozyme/4'>cartoon</scene> or <scene name='Sandbox_36/Lysozyme/3'>backbone</scene> ~~representation. The~~ Asp52, in green, and Glu35, in purple, ~~are shown~~ in the ball and stick form. The openness of the secondary representation does not allow cleft identification. The cleft can be viewed from a

The enzyme is approximately ellipsoidal in shape, with a large cleft in one side forming 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

<scene name='Sandbox_36/Lysozyme/5'>surface</scene> view of the enzyme. This view also has the green Asp52 and purple Glu35 visible.

===Polar vs Nonpolar Residues===

Understanding the polar and nonpolar areas of a molecule gives an understanding of where water can and will interact. Lysozyme seems to have an even distribution of polar and nonpolar residues. 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>. 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 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 protonated at neutral pH, because its dissociation is suppressed.

~~<applet load='3IJU'' size='300' frame='true' align='right' caption='Egg White Lysozyme ' />~~

==Function==

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==History==

~~Lysozyme~~ was ~~first discovered~~ by Alexander Fleming ~~during his research for~~ medical antibiotics~~. When searching for any sort of bacterial inhibitor~~, he added a ~~drop of~~ mucus to a live culture. To ~~Fleming’s~~ surprise, it successfully killed the bacteria. The phenomena was carefully analyzed and it was proved 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 used in protein structure and function research because of its unique properties.

Laschtschenko in first described lysozyme from chicken egg in 1909. In 1919 the enzyme was reported in saliva in Bloomfield. 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 added a tested human mucus on a live culture. To his surprise, it successfully killed the bacteria. The phenomena was carefully analyzed and it was proved 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 used in protein structure and function research because of its unique properties.

As mentioned earlier lysosyme can be purified from hen egg-whites and crystallized quite simply. This has made the it the best object for X-Ray analysis for many years. The X-Ray beam diffraction of lysozyme crystals also has a extremely high resolution, reaching 0.94 Angstroms. Lysozyme was the first enzyme to ever have its structure solved. 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>. Today lysozyme is still being used in research and is also commercially valuable enzyme used for many purposes, including the treatment of ulcers and infections, and as a food and drug preservative.

As mentioned earlier lysosyme can be purified from hen egg-whites and crystallized quite simply. This has made the it the best object for X-Ray analysis for many years. The X-Ray beam diffraction of lysozyme crystals also has a extremely high resolution, reaching 0.94 Angstroms. Lysozyme was the first enzyme to ever have its structure solved. 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>. A year later, the mechanism was explained. Today lysozyme is still being used in research and is also 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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@@ Line 9: / Line 9: @@
 ==Structure==
+<applet load='3IJU'' size='300' frame='true' align='right' caption='Egg White Lysozyme ' />
 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.
@@ Line 19: / Line 21: @@
 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.
 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.
-===Polar vs Nonpolar Residues===
 ===Active Site===
-The enzyme is approximately ellipsoidal in shape, with a large cleft in one side forming the active site. The two amino acids that interact with the bound substrate are Asp52 and Glu35. These two amino acids can be viewed on lysozyme as <scene name='Sandbox_36/Lysozyme/4'>cartoon</scene> or <scene name='Sandbox_36/Lysozyme/3'>backbone</scene> representation. The Asp52, in green, and Glu35, in purple, are shown in the ball and stick form. The openness of the secondary representation does not allow cleft identification. The cleft can be viewed from a
+The enzyme is approximately ellipsoidal in shape, with a large cleft in one side forming 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
 <scene name='Sandbox_36/Lysozyme/5'>surface</scene> view of the enzyme. This view also has the green Asp52 and purple Glu35 visible.
+===Polar vs Nonpolar Residues===
+Understanding the polar and nonpolar areas of a molecule gives an understanding of where water can and will interact. Lysozyme seems to have an even distribution of polar and nonpolar residues. 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>. 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 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 protonated at neutral pH, because its dissociation is suppressed.
-<applet load='3IJU'' size='300' frame='true' align='right' caption='Egg White Lysozyme ' />
 ==Function==
@@ Line 35: / Line 36: @@
 ==History==
-Lysozyme was first discovered by Alexander Fleming during his research for medical antibiotics. When searching for any sort of bacterial inhibitor, he added a drop of mucus to a live culture. To Fleming’s surprise, it successfully killed the bacteria. The phenomena was carefully analyzed and it was proved 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 used in protein structure and function research because of its unique properties.
+Laschtschenko in first described lysozyme from chicken egg in 1909. In 1919 the enzyme was reported in saliva in Bloomfield. 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 added a tested human mucus on a live culture. To his surprise, it successfully killed the bacteria. The phenomena was carefully analyzed and it was proved 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 used in protein structure and function research because of its unique properties.
-As mentioned earlier lysosyme can be purified from hen egg-whites and crystallized quite simply. This has made the it the best object for X-Ray analysis for many years. The X-Ray beam diffraction of lysozyme crystals also has a extremely high resolution, reaching 0.94 Angstroms. Lysozyme was the first enzyme to ever have its structure solved.  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>. Today lysozyme is still being used in research and is also commercially valuable enzyme used for many purposes, including the treatment of ulcers and infections, and as a food and drug preservative.
+As mentioned earlier lysosyme can be purified from hen egg-whites and crystallized quite simply. This has made the it the best object for X-Ray analysis for many years. The X-Ray beam diffraction of lysozyme crystals also has a extremely high resolution, reaching 0.94 Angstroms. Lysozyme was the first enzyme to ever have its structure solved.  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>. A year later, the mechanism was explained. Today lysozyme is still being used in research and is also commercially valuable enzyme used for many purposes, including the treatment of ulcers and infections, and as a food and drug preservative.