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


Helpful Definitions

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
  • Results
    • 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?