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 2: Domain Structures
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version of the Powerpoint lecture slides
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File of lecture
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version of the Powerpoint lecture slides for printing, 2 figs/page:
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Structure animations and Pymol scripts:
| Structure Animation | Quicktime Movie Links | Pymol script links |
|---|---|---|
| Alpha domain examples: Two hemaglobin S tetramers (1hbs) | ||
| Alpha domain examples: Interaction between two HbS molecules at the interface between a beta2 subunit in one tetramer with beta1 subunit in another tetramer (1hbs) | ||
| Alpha domain examples: cytochrome c6 from Monoraphidium braunii (1ctj) | ||
| Alpha domain examples: chicken citrate synthase (1csh) with acetylCoA derivative and oxaloacetate | ||
| Alpha domain examples: chicken prenyl transferase (1fps) | ||
| Alpha domain examples: bovine cytochrome c oxidase (1occ) | ||
| Alpha domain examples: bacterial GroEL/GroES complex (1aon) | ||
| Alpha/beta domain examples: TIM with 2-phosphoglycocolic acid, a substrate analog (2ypt) | ||
| Alpha/beta domain examples: pyruvate kinase, a three domain enzyme with a central TIM barrel (1aqf) | ||
| Alpha/beta domain examples: PRA-IGP synthetase, a 2 TIM barrel protein (1pii) | ||
| Alpha/beta domain examples: flavodoxin from Chondrus crispus (2fcr) | ||
| Alpha/beta domain examples: adenylate kinase from Bacillis stearothermophilus (1zin) | ||
| Alpha/beta domain examples: Tyr tRNA synthetase from Bacillis stearothermophilus (3ts1) | ||
| Alpha/beta domain examples: bovine carboxypeptidase A (1yme) | ||
| Alpha/beta domain examples: E. coli arabinose binding protein (1abe), a two domain open twisted sheet protein | ||
| Beta domain examples: E. coli superoxide dismutase (1eso) with bound Zn2+ and Cu2+ | ||
| Beta domain examples: bovine retinol binding protein (1erb) with bound retinol | ||
| Beta domain examples: galectin-1 (1slc) with bound carbohydrate ligand | ||
| Beta domain examples: E. coli porin (1omf) | ||
| Beta domain examples: E. coli maltoporin (1af6) with bound maltose | ||
| Beta domain examples: viral neuramindase (1nsc), an antiparallel superbarrel with bound sialic acid | ||
| Beta domain examples: viral hemagglutinin (1hgh) trimer structure showing the jellyroll binding site at one end containing bound sialic acid | ||
| Beta domain examples: jellyroll domain of viral hemagglutinin containing bound sialig acid |