Sandbox 30
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.
Trypsin(Specifically PDB: 1QLQ)
Overview and Quick LinksTrypsin was first isolated by , Wilhelm Kühnein 1867Trypsin is a serine protease synthesized in the pancreas but is not activated until the zymogen form of trypsin is activated. This presents trypsin from digesting actual body tissue[1]. An easy way to distinguish between main structural components of the protein is to view it using rainbow coloration. To see various other specific structures of Trypsin, click on their links.
StructureTrypsin's primary amino acid sequence (RPDFCLEPPYAGACRARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCLRTCGGA) [2] forms the backbone of the protein, which then folds into secondary structures, consisting of two α helices and two β sheets. Both of the α helices are right handed and the β sheets are anti-parallel. The order of the secondary structures is easily visible when using the rainbow coloration scheme to identify secondary structures. The N-terminus (blue) is the beginning of trypsin and the C-terminus (agua-green) is the end.
Polar and Nonpolar ResiduesPolar residues are typically hydrophobic, and seek to be sheltered from the aqueous environments that proteins typically inhibit. The polarity of an amino acid is determined by its side chain (orange). When considering the ball and stick model it may look like the polar (blue) and nonpolar (crimson) residues are not organized in a specific manner, but when you consider the space filling model, it is evident that the majority of the nonpolar residues are shielded by the polar residues. Another way to show this principle is by looking at the location of the hydrophobic sections of Trypsin (red). The hydrophobic portions desire to be shielded from the water in the smallest area possible in order to minimize its interaction with water, thereby maximizing the entropy of the water. It is evident that basically all water molecules are kept outside the protein when viewing a rendering with water (water-blue, trypsin-orange). This form of trypsin (PDB 1QLQ), has been modified to help enable its crystalization, and thus has four water molecules inside of it instead of the normal three which is present in the wild-type trpsin[3]. Intramolecular and Intermolecular ForcesThe structure of trypsin is stabilized by a variety of intramolecular and intermolecular forces. Trypsin has three disulfide bonds, which form between cysteine amino acids. Disulfide bonds are especially important for structural stability in extracellular environments, where conditions are more prone to fluctuation. Secondary structures are stabilized via interactions that compliment their specific side chains. For example, the first α helix in trypsin's structure is stabilized by several other hydrophobic residues in the molecule itself. The ball and stick amino acids marked with an * are part of α helix while the space filling molecules stabilize the α helix. the The α helix is also stabilized by intramolecular hydrogen bonding, as well as the addition of hydrogen bonding to water molecules (water is dark blue).
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