Sandbox 50

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. spinqualitylabelsall models Insert caption here Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image TrypsinTrypsin Trypsin is a medium sized, globular, digestive serine protease that is synthesized by the pancreas and secreted into the duodenum of the small intestine. Trypsin hydrolyzes peptide bonds based on side chain specificities of the amino acids surrounding the bond to be cleaved. Trypsin's specificity is for the positively charged side chains of lysine and arginine. StructureStructure Trypsin's primary structure is a polypeptide chain of 237 amino acids. These amino acids interact with each other mostly through hydrogen bonding to form trypsin's secondary structural units. Trypsin has many important , including two alpha helices (blue), an anti-parallel beta sheet (green), and random coils (gray). The arrows on these elements point toward the carboxy terminus of the protein. These secondary structures interact together to form the fully folded, native trypsin. Polar and Nonpolar ResiduesPolar and Nonpolar Residues Trypsin's distribution of follow the rules of the hydrophobic effect. The nonpolar (gray) residues are located on the interior of the protein so they can be shielded from water, while the polar (purple) residues are distributed on the exterior of the protein because they can interact with water. This model shows the distribution of the hydrophilic and hydrophobic residues and the actual space they occupy. Again the hydrophobic, nonpolar residues are shown in gray, and the hydrophilic, polar residues are purple. This type of residue distribution in trypsin is entropically favorable becuase the water surrounding the protein does not become ordered. In this figure the can be seen. The puprle polar residues are the residues that are interacting with the red water molecules. Attractions Between Structural Components and the Remainder of the ProteinAttractions Between Structural Components and the Remainder of the Protein Disulfide BondsDisulfide Bonds Trypsin contains three involving six cysteine residues. These disulfide bonds are intramolecular forces that stabalize the tertiary structure of Trypsin. The figure shows the yellow disulfide bonds between the cysteine residues connecting two random coils, connecting one of the alpha helices to the beta sheet, and the other disulfide connecting the two alpha helices. Residue ChargeResidue Charge This shows the different charges of the amino acid residues that make up Trypsin. The blue residues have cationic side chains, the red residues have anionic side chains, the light purple are the polar, uncharged residues, and the gray residues are hydrophobic. When compared to the spacefilled figure above, the direct correlation between polarity of the side chain and charge of the side chain can be seen. Those residues with charged (blue and red) side chains as well as the polar, uncharged residues are the residues on the exterior of the protein, while the hydrophobic residues remain at the protein's core. Those residues that are cationic and anionic are able to participate in salt bridges. Ion ContactsIon Contacts Trypsin interacts with four . The red and yellow atoms are the ions. The yellow atoms are sulfur and the red atoms are oxygen. Catalytic MechanismCatalytic Mechanism Active SiteActive Site Trypsin's active site is composed of its catalytic triad, three amino acid residues that are crucial to the enzymes proteolytic function. The catalytic triad consists of Asp 102, His 57, and Ser 195. Serine is the major player in the cleaveage of the peptide bond, thus the name serine protease. His 57 and Asp 102 are aid in the cleavage by hydrogen bonding and electrostatically stabalizing the substrate. Ser 195 performs a nucleophilic attack on the substrate's peptide carbonyl. This causes the oxyanion hole to form. The nucleophilic attack by the oxygen of Ser 195 also forms a tetrahedral intermediate. By reconstruction of the carbonyl double bound, the amino portion of the peptide leaves as a product, and an acyl-enzyme intermediate is left in the active site. Now the active site needs to be regenerated. To do this a water molecule nucleophillically attacks the carbonyl carbon, forming another tetrahedral intermediate and reforming the oxyanion hole. The nitrogen of the His 57 ring makes the oxygen of the water more nucleophilic by hydrogen bonding to one of water's oxygens. By reforming the double bond of the carbonyl carbon, the carboxy end of the original substrate's peptide bond is released, and the active site has been regenerated. The picture in the thumbnail to the left shows the entire catalytic mechanism for a serine protease. A figure of the oxyanion whole can be seen in greater detail in the thumbnail on the right.