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 4: Case Study - Lysozyme and other
glycosylhydrolases
HTML
version of the Powerpoint lecture slides
Powerpoint
File of lecture
PDF
version of the Powerpoint lecture slides for printing, 2 figs/page:
NO ACTIVE LINKS IN THE PDF VERSION
Structure animations, Pymol scripts, and mechanism animations:
| Structure Animation | Quicktime Movie Links | Pymol script links |
|---|---|---|
| Hen egg white lysozyme: HEW with bound trisaccharide (1at6) | ||
| T4 lysozyme: T4 lysozyme with bound disaccharide (148L) | ||
| HEW lysozyme with bound disaccharide: Zoom in to the active site of wild type HEW with bound disaccharide bound in the active site in ring-flattened form | ||
| Glucoamylase with bound dihydroacarbose: Structure animation of bound disaccharide in the active site highlighting general acid and general base (1gai) | ||
| Human ER alpha-mannosidase I with bound disaccharide: Structure animation of human ERManI with bound thio-disaccharide highlighting putative general acids, the general base, and the Ca2+ ion interaction with the substrate (1x9d) | ||
| T4 lysozyme T26E mutant covalent complex with disaccharide: Zoom in on the covalent intermediate of E26 and the C1 of the disaccharide substrate (148L) | ||
| HexB dimer with bound NAG-thiazoline inhibitor: Structure animation of the HexB dimer with a bound inhibitor in the active site (1np0) | ||
Links to animations and other sites |
||
| Glycosidase Mechanisms | ||
| Glycosylhydrolase classification database | ||
| Database of carbohydrate-active enzymes (CAZy) | ||
| Wild Type and Mutant Lysozyme Mechanisms |