• MRS questions

After doing the MRS part of tools, answer these questions:

Question 9: You have searched for the crambin protein sequence before. Here we will analyze the crambin data a bit further.
What kind of protein is crambin?
Hint 1: Look in the SwissProt file for the function (Hint: look in the comment section).
Hint 2: Use BLAST to find the function of crambin-like proteins (but you can also postpone this untill you have done the introductory exercises on BLAST).

Question 10: To get a idea of the gap between the number of known protein sequences and known protein structures look up how many entries there are in SwissProt and how many in the PDB.

Question 11: Try to find the longest protein that is present in the SwissProt database.
Hint: Look under databases in the 'indices for SwissProt'; perhaps the sequence length has been indexed!

Question 12: Search in the PDB for the structure of TGF-BETA with the FKBP12 inhibitor. (Please remember to put FKBP12 inhibitor together in quotes to avoid that you find all kinds of other inhibitors too). Most likely one of the first hits will be 1IAS. Look at this file. Now what? Which is the problem that we want you to realize?

Lysozyme

The objective of this exercise is to collect as much information about the human lysozyme C protein as you can. The best starting point for this is to first search for human lysozyme sequences in the SwissProt database. That gives you a few hits from which you select the one you need.
Feel free to read the intro page of a very small course on lysozyme to satisfy your scientific curiosity.

Question 13: What is a pre-peptide and what is a pro-peptide? Hint: look up prepeptide in the wiki that you find under Miscellaneous (this entry explains both).

Question 14: Lets look up some things about lysozyme; and we are aware that some of the questions listed below have not yet been discussed. You also have to learn to extend beyond the comfort-zone of the seminars...
1) What are the SwissProt file name and accession number of the human lysozyme C protein?
2) What is the enzyme code (EC) of lysozyme?
Which reaction is catalysed by these enzymes?
Hint: Also browse the course Wiki for information.
3) Find the gene for the human lysozyme. What is the EMBL code of the gene, and what is its accession number? (hint: genbank and the EMBL database are (nearly, 99.99999%) identical, but genbank is easier for us to udate from, so search with MRS in genbank when you need information about a gene, even when the text states that you should search in EMBL...). 4) How many introns does the human lysozyme gene contain?
5) Which repetitive elements are present in the gene, and where are they located?
Do they have an effect on the coding region or not?
6) On which chromosome is the gene located?
7) Are there any hereditary diseases associated which this gene?
For each disease you should find two lysozyme mutations that cause this disease.
Hint: use the (O)MIM database.
8) Search for the pattern describing the lysozyme protein sequence. Which protein pattern appears to be characteristic for lysozyme protein family?
HINT: PROSITE is a database with protein patterns
9) Cysteine bridges
How many disulfide bridges does lysozyme contain?
What are the residue numbers of the bridged cysteines regarding to the SwissProt file?
What are the residue numbers of the bridged cysteines regarding to the PDB file?
Do you understand what causes this difference in residue numbering?

We will look further at lysozyme in the course section on protein structures. Feel free to take a quick look at a very small course just on lysozyme if you are very curious about it.

EU name: ALZEIQ

Alzheimer

Question 15:
1) Search for all entries in SwissProt that have the name Alzheimer in their description field. How many hits do you receive from this query?
2) Search for all entries in SwissProt that have glycoprotein in their description field. How many hits do you get from your query?
3) We want to know if there is any correlation between Alzheimer and the glycoprotein. We therefore want to combine the queries.
4) Another possibility to find out which proteins in the hit list are glycolysated is to search the feature records of the SwissProt files. Use the MRS field-search option to search the feature list (ft) for the feature carbohyd.
How many hits do you get?

Rhodopsin

Question 16: Search for bovine rhodopsin in SwissProt.
1) What is the entry name?
2) How many related entries in EMBL are available?
3) The protein contains transmembrane regions. How many?