Sandbox 49

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Trypsin is a serine protease that is produced in the pancreas as the inactive proenzyme trypsinogen. It hydrolyses proteins (peptide bonds) and it is found in many vertebrates. Trypsin cleaves peptide chains mainly at the <scene name='Sandbox_49/N_to_c/1'>carboxyl</scene> (red) side of the amino acids lysine or arginine, except when either is followed by proline. The German physiologist Wilhelm Kühne (1837-1900) discovered trypsin in 1876.

 

 

The primary structure of trypsin contains ~240-residue enzymes. The <scene name='Sandbox_49/Secondary/1'>secondary structure</scene> of trypsin contains both <scene name='Sandbox_49/A_helix/1'>alpha helices</scene>, highlighted in blue and <scene name='Sandbox_49/Beta/1'>beta sheets</scene>, highlighted in green. The <scene name='Sandbox_49/Chain/1'>backbone</scene>, also known as the main chain, is the protein and nucleic acid chain that makes up trypsin (blue chain). The amino (N) to carboxy (C) <scene name='Sandbox_49/N_to_c/1'>terminal</scene> can be seen beginning at the blue 5' terminal to the red 3' terminal. Trypsin contains a catalytic triad consisting of the residues histidine, aspartate and serine. Histidine and serine are located in the enzyme-substrate binding site and aspartate is located in a nearby solvent-inaccessible pocket. Serine exists as the nucleopihilic active site due to the charge created by the formation of these residues. Trypsin is referred to as an endopeptidase, as it cleaves within a polypeptide chain rather than at the terminal amino acids at the ends. The reaction mechanism of tryspin can be seen to the right. The transition state is thought to be stabilized by an unusually strong hydrogen bond and is the location of preferential binding.

 

 

The <scene name='Sandbox_49/Hydandpolar/1'>polarity</scene> of trypsin can be seen with purple representing polar areas and gray representing nonpolar areas. It can be seen that mostly hydophilic (purple) residues exist on the outside of the molecule while hydrophobic (gray) residues are located mostly on the inner parts of the molecule. The hydrophobic areas do not favor interaction with an aqueous environment and therefore confine themselves closer to the center of the molecule. The <scene name='Sandbox_49/Side_chains/1'>side chains</scene>, which are the basis for determining the polarity of trypsin, are represented by the green wire frames. They are composed of several different amino acids with a variety of charges.

 

The overall <scene name='Sandbox_49/Charge/1'>charge</scene> of trypsin is observed with red showing the negative charges (anionic) and blue showing the positive charges (cationic), while purple shows the uncharged areas. The charged portions of trypsin can be seen on the outside of the molecule in order to increase attraction forces. Trypsin can be seen interacting with three different <scene name='Sandbox_49/Cpk/1'>elements</scene> including oxygen(red), sodium (blue) and sulfur (yellow). In trypsin (as in all proteins), salt bridges occur between amino acid side chains with opposite positive or negative full-electron charges, namely, (at neutral pH) Glu- or Asp- vs. Arg+ or Lys+. A salt bridge found in trypsin can be seen to the right.

 

 

 

 

 

 

The <scene name='Sandbox_49/Ligands/1'>ligands</scene> found in trypsin are composed of oxygen(red) and sulfur (yellow). Trypsin contains four ligands and these are the areas where intermolecular forces occur, including van der Waals forces, ionic bonds and hydrogen bonds. These forces allow trypsin to bind with other molecules in order to carry out a certain process. Trypsin is active against only the peptide bonds in protein molecules that have carboxyl groups donated by the positively charged amino acids arginine and lysine (seen to the right), which are stabilized and attracted by aspartate, leading to enzyme specificity. <scene name='Sandbox_49/H20/1'>Water</scene> is an example of the van der Waals forces that are occurring with trypsin. Only a small amount of the water binds tightly enough to be seen, whereas there is much more in actuality surrounding trypsin but cannot be seen due to disorder. Trypsin is a hydrolase and cleaves bonds by hydrolysis at the peptide bonds. <scene name='Sandbox_49/Dna/1'>DNA</scene> can interact with the alpha helices and <scene name='Sandbox_49/Dna_sheet/1'>DNA</scene> can also interact with the beta sheets.