Sandbox 36
From Proteopedia
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==Structure== | ==Structure== | ||
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| + | <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. | 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. | 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. | 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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| - | ===Polar vs Nonpolar Residues=== | ||
===Active Site=== | ===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. | + | 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. | <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== | ==Function== | ||
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==History== | ==History== | ||
| - | + | 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. |
Revision as of 02:07, 29 October 2010
| 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. |
Contents |
Lysozyme
Overview
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. Lysozyme 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.
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.
Secondary Structure
Gallus gallus egg white lysozyme has an alpha+beta fold, consisting of seven alpha helices and a three-stranded antiparallel beta sheet. There is also a large amount of random coils and beta turns. Click 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 for the rainbow color ordered cartoon chain from N to C terminals.
Disulfide and Hydrogen Bonds
Disulfide bonds are formed by the oxidation of two cysteine residues to form a covalent sulphur-sulphur bond [1]. These interactions are not as important for stability, as they are for insuring correct folding patterns. Lysozyme has four disulphide bonds connecting the of the molecule, which are highlighted in yellow. There are also four disulphide bonds in between the , 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[2]. The enzyme has many hydrogen bonds connecting the , these are highlighted red. The hydrogen bonds, in yellow, between the are also numerous.
Active Site
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 and 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 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 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 . The active site residues are highlighted in this polar vs nonpolar dot . 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.
Function
Lysozyme’s main function is to protect from infection. The enzyme is a general non-specific organism defense effective against gram positive bacterial cells. Lysozyme degrades the polysaccharides found in cells 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[3]. 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 [4]. This imposes a strain on the C-O bond on the ring-4 side of the oxygen bridge between rings 4 and 5[5]. The polysaccharide is broken at this point and a molecule of water is inserted between the two hexoses. The reaction mechanism is shown below.
History
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[6]. 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[7]. 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[8]. 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.
References
- ↑ Day, A. (1996). Disulphide bonds. Retrieved from http://www.cryst.bbk.ac.uk/PPS2/projects/day/TDayDiss/DisulphideBonds.html
- ↑ Ophardt, C. (2003). Intermolecular forces: hydrogen bonds. Retrieved from http://www.elmhurst.edu/~chm/vchembook/161Ahydrogenbond.html
- ↑ Lysozyme. (2008). Retrieved from http://lysozyme.co.uk/
- ↑ Voet, D, G., J, & W., C. (2008). Fundamentals of biochemistry: life at the molecular level. John Wiley & Sons Inc
- ↑ Kimball, J. (2010, May 26). Enzymes. Retrieved from http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Enzymes.html#lysozyme
- ↑ Worthington, K. (2010). Lysozyme. Retrieved from http://www.worthington-biochem.com/ly/default.html
- ↑ Goodsell, D. (2000, September). Lysozyme. Retrieved from http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb9_1.html
- ↑ Lysozyme. (2008). Retrieved from http://lysozyme.co.uk/
