Sandbox 46: Difference between revisions
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The <scene name='Sandbox_46/Tryp_secondary_color/2'>secondary structure</scene> of Trypsin consists of two alpha helices (light green) and two beta sheets (peach). | The <scene name='Sandbox_46/Tryp_secondary_color/2'>secondary structure</scene> of Trypsin consists of two alpha helices (light green) and two beta sheets (peach). | ||
Hydrophobic interactions - mainly the hydrophobic collapse - significantly contribute to both secondary and tertiary structure. This <scene name='Sandbox_46/Polar_vs_nonpolar_wire/1'>structure</scene> shows that the majority of the residues are non-polar/hydrophobic (maroon). These residues tend to congregate on the interior of the structure while polar/hydrophilic residues (blue) remain on the exterior. This orientation allows polar molecules to maximize interaction with water and other polar molecules while non-polar molecules minimize such interactions. Adding water molecules to the model, the <scene name='Sandbox_46/Polar_vs_nonpolar/1'>polar/non-polar</scene> interactions can be seen. | Hydrophobic interactions - mainly the hydrophobic collapse - significantly contribute to both secondary and tertiary structure. This <scene name='Sandbox_46/Polar_vs_nonpolar_wire/1'>structure</scene> shows that the majority of the residues are non-polar/hydrophobic (maroon). These residues tend to congregate on the interior of the structure while polar/hydrophilic residues (blue) remain on the exterior. This orientation allows polar molecules to maximize interaction with water and other polar molecules while non-polar molecules minimize such interactions. Adding water molecules to the model, the <scene name='Sandbox_46/Polar_vs_nonpolar/1'>polar/non-polar</scene> interactions can be seen. The color configuration remains with water molecules displayed in green. | ||
===Stability=== | ===Stability=== | ||
<scene name='Sandbox_46/Disulfide_bonds_123/1'> | Many factors contribute to protein stabilization. Disulphide bonds form between the Sulfur atoms of two Cysteine residues and assist in the formation of the tertiary structure. This particular form of trypsin contains three <scene name='Sandbox_46/Disulfide_bonds/3'>disulphide bonds</scene> (yellow). These bonds interact between Cysteine residues at positions 5 and 55, 14 and 38, 30 and 51. Disulphide bond two (residues 14 and 38) interacts with two chiral centers; thus, one Sulfur atom interacts with two Sulfur atoms opposite it. Click <scene name='Sandbox_46/Disulfide_bonds_123/1'>here</scene> to see the labeled disulphide bonds. | ||
In addition to disulphide bonds, Hydrogen bonding plays a large role in stability. As this <scene name='Sandbox_46/Hbonds_backbone/1'>model</scene> suggests, hydrogen bonds are most prominent in alpha helices and beta sheets of the backbone. In alpha helices, hydrogen bonds form between an H-N and a C-O 4 residue away; complementing the specific turn length (3.6 residues). | |||
<scene name='Sandbox_46/Hbonds_backbone/1'>H bonds backbone</scene> | <scene name='Sandbox_46/Hbonds_backbone/1'>H bonds backbone</scene> | ||
Revision as of 20:43, 29 October 2010
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Trypsin
Trypsin, a member of the serine protease family, is produced in the pancreas and found in the digestive tracks of vertebrates. To avoid pancreatic self-degradation, trypsin is synthesized as trypsinogen, a zymogen. Cleavage by enteropeptidase allows tryspin to enter its active form. As a serine protease, trypsin contains a serine residue in its active site.
Structure
The trypsin structure displayed is a mutant form isolated from a bovine pancreas. It contains 58 amino acid residues as well as an altered binding loop. To follow the primary structure (amino acid sequence) of Trypsin, click here. Begin at the N-terminus (blue) and move toward the C-terminus (red).
The secondary structure of Trypsin consists of two alpha helices (light green) and two beta sheets (peach). Hydrophobic interactions - mainly the hydrophobic collapse - significantly contribute to both secondary and tertiary structure. This structure shows that the majority of the residues are non-polar/hydrophobic (maroon). These residues tend to congregate on the interior of the structure while polar/hydrophilic residues (blue) remain on the exterior. This orientation allows polar molecules to maximize interaction with water and other polar molecules while non-polar molecules minimize such interactions. Adding water molecules to the model, the polar/non-polar interactions can be seen. The color configuration remains with water molecules displayed in green.
Stability
Many factors contribute to protein stabilization. Disulphide bonds form between the Sulfur atoms of two Cysteine residues and assist in the formation of the tertiary structure. This particular form of trypsin contains three disulphide bonds (yellow). These bonds interact between Cysteine residues at positions 5 and 55, 14 and 38, 30 and 51. Disulphide bond two (residues 14 and 38) interacts with two chiral centers; thus, one Sulfur atom interacts with two Sulfur atoms opposite it. Click here to see the labeled disulphide bonds. In addition to disulphide bonds, Hydrogen bonding plays a large role in stability. As this model suggests, hydrogen bonds are most prominent in alpha helices and beta sheets of the backbone. In alpha helices, hydrogen bonds form between an H-N and a C-O 4 residue away; complementing the specific turn length (3.6 residues).
The yellow and red molecules represent SO4 (2-) moieties which are not part of the traditional trypsin structure; they were added during crystallization to freeze Trypsin in a specific conformation. Fix THIS. they bind at active site
Function
The reaction catalysed by Enteropeptidase:
trypsinogen → trypsin + hexapeptide
Val--(Asp)4--Lys--Ile--Val~ (trypsinogen) → Val--(Asp)4--Lys (hexapeptide) + Ile--Val~ (trypsin)
Enteropeptidase cleaves after Lysine if the Lys is preceded by four Asp and not followed by a Pro. Source ^ "Enterokinase, light chain (P8070), Proteases, NEB". https://www.neb.com/nebecomm/products/productP8070.asp. Retrieved 2007-10-04.
All active sites Shared active site
