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 1: Motifs: Structure and Function
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 and Pymol scripts:
| Structure Animation | Quicktime Movie Links | Pymol script links |
|---|---|---|
| EFhand: Calmodulin extended (3cln) | ||
| EFhand: Calmodulin with skeletal muscle light chain kinase target peptide (2bbm) | ||
| EFhand: Detail of interactions between Calmodulin and skeletal muscle light chain kinase target peptide (2bbm) | ||
| Helix-turn-helix: Cro dimer (5cro) | ||
| Helix-turn-helix: Repressor dimer (1lmb) | ||
| Helix-turn-helix: Repressor dimer (1lmb) bound to DNA target | ||
| Helix-turn-helix: Detail of interactions between Repressor dimer (1lmb) and the DNA target | ||
| Zn-finger proteins: Cys2His2 motif - Xenopus laevis Xfin-31 (1znf). Chemically synthesized protein, structure determined by NMR. | ||
| Zn-finger proteins: Cys2His2 motif - Mouse zif268(1aay) transcription factor coiled in the major groove of the DNA target | ||
| Zn-finger proteins: Cys2His2 motif - Interaction of a mouse zif268(1aay) Zn-finger motif with the major groove of the DNA target | ||
| Zn-finger proteins: Cys3His1 motif - HIV gag protein (2znf) | ||
| Zn-finger proteins: Cys4 motif - Glucocorticoid receptor dimer bound to DNA target (1glu) | ||
| Zn-finger proteins: Cys4 motif - Interaction region between two Glucocorticoid receptor dimers showing the role of the Zn-fingers (1glu) | ||
| Zn-finger proteins: Cys4 motif - Interaction between a Glucocorticoid receptor monomer and the DNA target showing the role of the Zn-fingers (1glu) | ||
| Zn-finger proteins: Binuclear cluster - gal4 transcription factor dimer bound to the DNA target (1d66) | ||
| Zn-finger proteins: Binuclear cluster - Interaction of a gal4 binuclear bound to the DNA target (1d66) |
Jmol morpher: Calmodulin animation