From Proteopedia

Trypsin

(Specifically 1QLQ)

Overview and Function

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 forms 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 polar residues are shielded by they nonpolar 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^[1].

Ligand Interactions

References

1. ↑ 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