Reading (to be completed before class!)
- Section on reading crystallography papers
X-ray structure Article
- Ray et al. Crystal structure of human thimet oligopeptidase provides insight into substrate recognition, regulation, and localization. J Biol Chem (2004) vol. 279 (19) pp. 20480-9
- Prepare to Discuss the paper by reviewing the outline (in the problems) and preparing questions AND answers
In Class Activities
Disussion of paper and reading
- Discussion of the paper
- The intro section, what does it accomplish? Who is the audience?
- Significance of the HEXXH metal binding motif
- Specifically compared TOP and Thermolysin (discussed HEXXH motif, structure in relation to substrate type)
- MEROPS database for classification of peptidases (know how to use the database to find information)
- Discuss the significance of Clans and Families (where is TOP, what is its closest family member)
- Experimental Section
- Compared the information on crystallization and structure determination in the experimental section to that provided the reading in chapter 8
- Crystal growth, space group, phases
- Who is the audience for this section?
- What information is provided related to the quality of the dataset and the model? What is missing that you would like to see?
- Discuss the authors reference to the occupancy of the Zn ion and the thermal (B) factor
- What is the overall fold of the protein?
- Why are some residues missing in the structure?
- What is the significance of the gold region in figure 1A?
- Can you view Fig1 in STEREO?
- What is the evidence provided that TOP and Neurolysin bear strong structural similarity?
- To Be Completed Individually
- The authors discuss regions of flexibility in the enzyme? How could we check this?
- Discuss fig 5 and the differences that the authors suggest influence substrate specificity.
- What is the significance of the the structural elements important in substrate restriction and the modeled "unstructured" peptide substrate
- What are the primary conclusions highlighed by the authors?