Protein Structure

Exercises

1. Explore Protein Structures
   
   
   • Goto Brookhaven Protein Data Bank (PDB) and explore the Protein Kinase C Interacting Protein with PDB-ID 1AV5.
     How was the structure obtained?
     Download the file containing the strucure information in pdb-format.
   • Download rasmol and reproduce figures 5 and 6 in the section Different Levels Of Protein Structure.
   • What's the function of the above protein?
     (e.g. find its Swissprot-entry and follow the link to prosite)
   • Search and visualize human hexokinase I (Swissprot entry HXK1_HUMAN, accession number P19367, PDB-id 1HKB).
     Visualize its Glucose Binding domain.
     Which secondary structures does the domain consist of?
     
     
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2. Predict Secondary Structures
   
   
   • There are several websites which offer interfaces for secondary structure prediction.
     For an overview, have a look at the list at the expasy-server.
     Use GOR IV to predict secondary structures of proteins with known structure
     (you may access them at Swissprot or directly at PDB).
     Compare the results to the known structure information..
     Why may the results depend on the proteins you've chosen?
   • Have a look at the PredictProtein server where the PHD-method is implemented.
     Obtain the sequence of the protein with Swissprot-ac Q59007
     and compare secondary structure prediction of PHD-method and GOR IV by means of this protein.
   • Obtain the polypeptide which is referred to in the exercise on comparative modelling (see below)
     and determine its secondary structures.
     Compare to the model obtained by comparative homology modelling.
     
     
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3. Comparative Modelling
   
   
   • Obtain the Genbank entry with the protein id AAF51208 (gi|7295909) from NCBI, save it in Fasta-format.
   • The above polypeptide is a gene product of the Drosophila Genome.
     Find out, if it is possible to apply an automated comparative modelling program by performing a BLAST-search.
     What is the criterion? Which database do you search?
   • Build a model of the protein by means of SWISS-MODEL, an automated comparative protein modelling server.
   • Compare the secondary structure elements of your model to the predicted secondary structures (see exercise 2).
     
     
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