BCMB 8010 Advanced Biochemistry and Molecular Biology
PLEASE NOTE: The lecture notes below are available as HTML versions of the Powerpoint slides or as a direct download of the Powerpoint file. Note, the Powerpoint files can be large and may take some time to download. The lecture notes are also available as PDF files as 2- or 3-figures per page for direct printing. Animations that are used in each of the lectures were generated with Pymol and are available as Quicktime files or as Pymol scripts. Quicktime movies can be viewed as stand-alone movies using the free QUICKTIME VIEWER available for Mac or Windows computers. Pymol scripts can be used to directly view the animations by downloading the script to your hard drive and opening the file within Pymol (download PYMOL here) by using the pull-down menu option of File-> Run... Navigate to the script file name and select Open. The script should launch, download the PDB file, and start the animation script. PLEASE NOTE: the computer must have an active internet connection to download the PDB file. The first time that the script is launched the animation may take extra time because the PDB file must download before the animation can start.
Lecture 5: Case Study - Serine proteases
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version of the Powerpoint lecture slides
Powerpoint
File of lecture
PDF
version of the Powerpoint lecture slides for printing, 2 figs/page:
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Structure animations, Pymol scripts, and mechanism animations:
| Structure Animation | Quicktime Movie Links | Pymol script links |
|---|---|---|
| Chymotrypsin: Structure of bovine gamma-chymotrypsin with bound D-Leucyl-L-Phenylalinyl-P-Fluorobenzylamide (1afq) | ||
| Trypsin: Bovine trypsin with bound 4-Fluorobenzymamine (1tnh) | ||
| Elastase: Porcine elastase with bound 1-Benzyl-1-Methyl-1-(2-Acetyl)Hydrazinium ion (and bound Ca2+) | ||
| Trypsin - bovine trypsin inhibitor complex: Structure of bovine trypsin and bovine pancreatic trypsin inhibitor highlighting the catalytic trial and side chain in the specificity pocket (2ptc) | ||
| Serpin mechanism #1 - complex of trypsin-serpin prior to cleavage: Structure of rat trypsin II in complex with tobacco hornworm serpin 1 (Alaserpin) (1k9o) | ||
| Serpin mechanism #2 - complex of trypsin-serpin after cleavage and conformational change: Structure of human trypsin in complex with human alpha-1-antitrypsin(1ezx) | ||
| Oxyanion hole of serine protease: Zoom in structure of trypsin in complex with bovine trypsin inhibitor highlighting the amide nitrogen residues of the oxyanion hole (2ptc) | ||
| Subtilisin: Subtilisin with bound N-(Tert-Butoxycarbonyl-alanyl-prolyl-phenylalanyl) O- benzoyl hydroxylamine (1scn) | ||
| Carboxypeptidase II: Wheat serine carboxypeptidase II in comples with L-Benzylsuccinic acid (1wht) | ||
| Carboxypeptidase A: Bovine pancreatic carboxypeptidase A with no substrate analog, but with bound Zn2+ (1yme) | ||
| Carboxypeptidase A: Bovine pancreatic carboxypeptidase A with with bound substrate analog (Glycyl-L-Tyrosine) and bound Zn2+ (3cpa) | ||
| Chymotrypsinogen: Bovine chymotrypsinogen A highlighting the catalytic triad, oxyanion hole, and position of cleavage to form chymotrypsin (1chg) | ||
| alpha-Chymotrypsin: Bovine gamma-chymotrypsin highlighting the position of the catalytic triad, oxyanion hole, and the position of cleavage fron chymotrypsinogen (1afq) | ||
Links to animations and other sites |
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| Serine Protease Mechanism Animation | ||
| Metalloproteinase Animation | ||
| Comparison of hydrolase mechanisms |