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The lab reports are a training to write scientific texts and an important part of the course. To pass you need to provide a final version of the lab report within 7 days after the lab. You have one chance to submit a preliminary version and receive feedback on it (not mandatory). The preliminary version needs to be submitted within 72 hours of the lab and feedback will be provided at the latest 24 hours before the deadline of the assignment. If the final report it not submitted in time or it contains an error you will get an Fx on the lab course.  This means that you have to submit an updated lab report within 7 days after the exam and that the highest grade you can get is an E on the entire course. If this does not occur you will have to re-register for the course next time it is given (normally next year) and complete the missing parts that year and you can still not receive a grade higher than E.  So in short this is the rules for the lab reports.

A. 0-0 Lab

B. 0-3 days after the lab – Preliminary version

C. 3-6 days after the lab – Feedback

D. 7 days after the lab – Final version

The lab report must be complete upon submission, i.e. you have to provide an answer to each question. The assistant has the right to return / not approve the submission if it is not complete. Linguistic accuracy is a must.

Returns should get back to s within a week after you have received it. The submission of returns must be a version where all comments appear. All comments should be considered carefully or else it does not count as a return. A maximum of 1 return is allowed. The second return means that you have to re-register for the course next time it is given (normally next year) and complete the lab then.

Complete reports in time for all bioinformatics and programming labs are compulsory.

Secondary structure prediction

1. What are the differences between secondary and tertiary structure?

2. Why do researchers want to predict  protein secondary structures from sequences?

Use your sequence retrieval skills to get the full protein sequence of myoglobin in humans in Swissprot. Use the server PREDATOR to predict the secondary structure of the protein sequence.

 3. What is the Swissprot accession number of the sequence?

4. How many helices longer than five residues are predicted by the method?

Myoglobin was the first protein structure that was determined. This was done by John Kendrew and coworkers in 1957. Later he won the Nobel prize together with Max Perutz for this discovery.

5. Find the myoglobin (human) protein structure in pdb. How many alpha helices does it have? (Hint: look for the word HELIX in the .pdb file)

6. Submit the sequence of chicken c-fos to MARCOIL and COILS. Compare the predictions and describe the results you get?

For MARCOIL use:

https://toolkit.tuebingen.mpg.de/#/tools/marcoil

Membrane protein topology prediction

1. Pick your favorite transmembrane helical protein and describe based on it the typical features of transmembrane helices.

2. What does membrane protein topology mean?

Use the TMHMM and the Topcons servers to predict the topology of the protein available in the attached file (1j4n.fa).

3. How many transmembrane helices were predicted by the two methods for 1j4n.fa? Include screenshots of the predictions.

4. Are the N- and C-termini of the sequence predicted to be inside or outside of the cell membrane?

Use the server PREDATOR to predict the secondary structure of the protein sequence.

5. How many helices with at least 5 residues were predicted using the method?

6. Explain the difference between predicting secondary structure and predicting the membrane protein topology.

7. Go to pdb and find the experimentally determined structure of the protein. What is the name of the protein?

Download the structure file from pdb, save it for example under a directory called “lab7”.
In the terminal type:

pymol [STRUCTURE]

where [STRUCTURE] is the name + path of the downloaded file. Now study the three-dimensional structure in the viewer program by typing

show cartoon
hide lines

8. How many helices do you think the protein has? Include a screenshot of the image.

9. How many transmembrane helices do you think the protein has? Motivate your answer.

Go back to pdb and the structure you found. Go to the sequence tab. There you can find the contents of secondary structures in the experimentally determined structure derived from two programs called DSSP and STRIDE. These programs automatically assign the secondary structure states for each amino acid residue based on the true three-dimensional structure.

10. How many helices do the determined structure contain according to DSSP and STRIDE? Does this result agree with your predictions and your visual inspection? Why / Why not?