From Proteopedia

Trypsin

(Specifically PDB: 1QLQ)

Overview and Quick Links

Trypsin was first isolated by Wilhelm Kühne in 1867^[1]. Trypsin 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^[2]. Trypsin cleaves on the C-terminus side of lysine and arginine^[3]. An easy way to distinguish between main structural components of the protein is to view it using To see various other specific structures of Trypsin, click on their links.

• - Ball and stick
• - Space filling model

Structure

Trypsin's primary amino acid sequence (RPDFCLEPPYAGACRARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCLRTCGGA) ^[4] forms the of the protein, which then folds into secondary structures, consisting of two and two . 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 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 Residues

Polar 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 (orange). When considering the it may look like the polar (blue) and nonpolar (crimson) residues are not organized in a specific manner, but when you consider the 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 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 (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^[5].

Intramolecular and Intermolecular Forces

The structure of trypsin is stabilized by a variety of intramolecular and intermolecular forces. Trypsin has three 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 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 as well as (water is dark blue).

References

1. ↑ ISBN 952-10-1863-1
2. ↑ doi:10.1016/j.theochem.2003.08.072
3. ↑ [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb46_1.html Protein Data Bank
4. ↑ 1qlq
5. ↑ Czapinska, Honorata et al. "High-resolution structure of bovine pancreatic trypsin inhibitor with altered binding loop sequence." Journal of Molecular Biology. Volume 295, Issue 5, 4 February 2000, Pages 1237-1249 doi:10.1006/jmbi.1999.3445