Sandbox 30: Difference between revisions

= Trypsin =  

(Specifically PDB: 1QLQ)

==Overview and Quick Links==

Trypsin was first isolated by Wilhelm Kühne in 1867<ref>[https://www.doria.fi/bitstream/handle/10024/2142/trypsinr.pdf?sequence=1 ISBN 952-10-1863-1]</ref>. 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<ref> [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TGT-49S6WV8-1&_user=4187488&_coverDate=12/31/2003&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000062504&_version=1&_urlVersion=0&_userid=4187488&md5=a7d7e1b154a43b709d5228c4852e5d10&searchtype=a doi:10.1016/j.theochem.2003.08.072]</ref>. Trypsin cleaves on the C-terminus side of lysine and arginine<ref>[http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb46_1.html  Protein Data Bank</ref>.

==Structure==

Trypsin's primary amino acid sequence (RPDFCLEPPYAGACRARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCLRTCGGA) <ref>[http://bip.weizmann.ac.il/oca-bin/send-seq?1qlq_A 1qlq]</ref> forms the <scene name='Sandbox_30/Backbone/1'>backbone</scene> of the protein, which then folds into secondary structures, consisting of two <scene name='Sandbox_30/Helixs_maroon/3'>α helices</scene> and two <scene name='Sandbox_30/Sheets_green/4'>β sheets</scene>.  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 <scene name='Sandbox_30/Trypsin_cartoon_rainbow/2'>rainbow coloration</scene> 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==

Another way to show this principle is by looking at the location of the <scene name='Sandbox_30/Hydrophobic_red/1'>hydrophobic sections</scene> of Trypsin (red).  Alternatively, for a more in depth analysis of trypsin, you can view   

<scene name='Sandbox_30/Space_fill_charge_and_polar/1'>charged (Blue +)(Red -), uncharged polar (purple), and hydrophobic (gray) space filling rendering</scene> which can be even more informing. 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 <scene name='Sandbox_30/Ball_and_stick_with_water/1'>rendering with water</scene> (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<ref> 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 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45F4TXM-2W&_user=4187488&_coverDate=02/04/2000&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000062504&_version=1&_urlVersion=0&_userid=4187488&md5=221a9d3b8b66f6f908a8d93c6b10f18f&searchtype=a#secx12 doi:10.1006/jmbi.1999.3445] </ref>.

==Intramolecular and Intermolecular Forces==

<scene name='Sandbox_30/A_helix_hydrophobic/1'>hydrophobic residues</scene> 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 <scene name='Sandbox_30/A_helix_hydrogen_bonds/1'>intramolecular hydrogen bonding,</scene> as well as  

<scene name='Sandbox_30/A_helix_hydrogen_bonds/2'>the addition of hydrogen bonding to water molecules</scene> (water is dark blue).

====Ligands====