Week 4

Mar 04 - Reading Crystallography Papers

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?


Mar 06 - Structural Bioinformatics

Reading (to be completed before class!)

Berg 5th ed: Chp3: 3.6 The Amino Acid Sequence Determines 3D Structure
Review Voet B. Tertiary Structure, p245 - p256
Voet: Chp8: Sect 3C; Chp9: Sect 3A,B


  • Go to the protein data bank and find a PDB file for Thimet Oligopetidase
  • "Play" with the page. In other words, analyse the information and tools provided.
    For instance, try to view the structure in 3D. Determine CATH and SCOP classification of the enzyme.
    • Your text and Voet have information of SCOP and CATH
  • Find a protein or enzyme of interest to you. Bring a summary of your findings to share in class.


Extra Problem

Voet 3rd ed (note that DALI is now SSM)
Chp8: 10
Chp9: 10, 12

Nomenclature, Sequence and Structure Problems

Web Resources


1) Swiss Institute of Bioinformatics

ExPASy (Expert Protein Analysis System) Tools
(the tools can be accessed by category or by resources A-Z)  

  • Sequence Alignment tools
    - BLAST (BLASTp)
  • ENZYME (repository of information relative to the nomenclature of enzymes)
  • Compute pI/MW and ProtParam (calculate pI, % composition, e280nm, etc)
    - HelixWheel (this is no longer on the ExPASy site, use Helical Wheel)
  • Secondary
    ProtScale - allows you to compute and represent the profile produced by any
    amino acid scale on a selected protein. For instance, you can enter the Accession
    number for a protein and predict the secondary structure content based on the
    amino acid sequence using Chou-Fasman parameters.
    -----Use the following Excel file to assist in the prediction of secondary structure using Chou-Fasman parameters
    ----- Compare the actual secondary structure of Goose Lysozyme to that prediced using Chou-Fasman parameters within ProtScale
  • Tertiary structure analysis tools - http://expasy.org/structural_bioinformatics

2) European Bioinformatics Institute

Tools for Multiple and pairwise protein stuctural comparison and sequence alignment

In Class Activities

Discussion of Structural Informatics Tools


3D Structure of Proteins
- Berg 5th ed: Chp2: 2.3-2.6 Protein 3D Structure
- Cox 5th ed Chp 4.2, 4.3

Mar 09 - Homology Modeling

Reading (to be completed before class!)

Also scan the following tutorials we will be doing in class


Assignment 2, Exercise 4 of the Deepview Tutorial


In Class Activities

Work on Homology Modeling Tutorial

Note!  Before doing the homology model tutorial you will need to create an
account in SwissModel. That is where your results are stored. SwissPDB viewer
communicates with SwissModel to a certain extent. 


Chp9: Sect 3A,B

Make sure you have MASTERED Deepview tutorials 1-8, 10, 11