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Comparative Modelling and functional investigation of a protein with unknown structure.

This course work involves the analysis of structure and function properties derived from a given protein sequence (the UniProtKB/TrEMBL accession number or the FASTA file with the sequence will be given).

CORE exercise compulsory

1) Identification of the protein name and organism; retrieve sequence in FASTA format, or sequence identifier if the FASTA file is given. This is your query sequence: Q6NTF7 >sp|Q6NTF7|ABC3H_HUMAN DNA dC->dU-editing enzyme APOBEC-3H OS=Homo sapiens GN=APOBEC3H PE=1 SV=3

>sp|Q6NTF7|ABC3H_HUMAN DNA dC->dU-editing enzyme APOBEC-3H OS=Homo sapiens GN=APOBEC3H PE=1 SV=3

MALLTAETFRLQFNNKRRLRRPYYPRKALLCYQLTPQNGSTPTRGYFENKKKCHAEICFINEIKSMGLDETQCYQVTCYLTWSPCSSCAWELVDFIKAHDHLNLGIFASRLYYHWCKPQQKGLRLLCGSQVPVEVMGFPKFADCWENFVDHEKPLSFNPYKMLEELDKNSRAIKRRLERIKIPGVRAQGRYMDILCDAEV

2) Perform a Blast search with the target sequence for structure modelling (using PDB database of protein structures).

3) Retrieve Blast sequences.

4) Align the selected sequences with known structure(s) with T-coffee.

5) From the analysis in step 4 select the best template(s) for homology modelling, and justify your selection.

6) Perform automated homology modelling via web server: Swiss Modeller.

7) Download the template(s) used by the server and the model created by the server and e-mailed to you.

8) Compare the template(s) selected by the server and the one you would have selected based n the alignments and other criteria. Compare T-coffee alignments with Swiss Modeller alignments.

9) Perform the alignment mode homology modellling via web server: Swiss Modeller

10) Perform a comparison (structural, 3D superimposition) with the model deposited in the Modbase database (if any) and/or others if you find other deposited models.

11) Display the structures with VMD or Pymol and save informative snapshots.

12) Evaluate the model(s) from the parameters provided in the output of Swiss Modeller.

13) Evaluate the model(s) and template structures with Molprobity.

14) Using public repositories and servers comment on possible functions for the gene corresponding to the selected sequence.

EXTRA exercise

15) Perform a TreeFam analysis. Discuss the domain architecture and the evolutionary relationships

with homologous ones.

Solution image

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