1) Display the structures with VMD or Pymol and save informative snapshots.
2) Evaluate the model(s) from the parameters provided in the output of Swiss Modeller.
3) Evaluate the model(s) and template structures with Molprobity.
4) Using public repositories and servers comment on possible functions for the gene corresponding to the selected sequence.
5) Perform a TreeFam analysis. Discuss the domain architecture and the evolutionary relationships with homologous ones.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).
Practical exercise
Main steps of the exercise:
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
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.
Essay
Describe your observations during the main steps of the construction of the model in an essay-like document of 3000 words including figure legends and references.
The essay should include:
Introduction to the protein, analysis of the results, critical evaluation of the model and of the alignments. Discuss a possible function for the protein. Add essential plots, figures and analysis results in the essay, but they have to be INCLUDED within the total 3000 words limit.
You may add the alignments as an Appendix.
Suggestions
The essay should be written in your own words. Beware of Plagiarism. A charge of plagiarism results in the student getting zero for his or her poster and also potentially being disciplined by the College.
If you are unsure about what is plagiarism you must ask the module coordinator. Sources
The source material for your essay should be textbooks and scientific articles, and your own analysis of the results.
Use the library and/or literature searches (Medline, Pubmed, Google). The web can be useful for figures and diagrams. However material available on the web may not be of an appropriate standard and the accuracy cannot be easily checked. In addition the content of websites is continually changing, therefore a web-site address is not an adequate reference for the material used. You will be marked down if you only use websites.
You must list the sources of information (references) that you have used to generate your essay. You should be particularly aware of cutting and pasting the contents of a website into your essay. This is Plagiarism. If this is detected you will be given a zero mark.
Attachment:- Assignment.pdf