Proteins and Enzymes Coursework

Proteins and Enzymes Coursework

Part 1: Protein bioinformatics

The section contains a series of question that test you understanding of protein bioinformatics and the ability to use a variety of protein bioinformatics tools.

ANSWER THE QUESTIONS FOR PART 1 IN THE SPACE PROVIDED AND THEN COPY THIS INTO A SINGLE DOCUMENT THAT COMBINES YOUR ANSWERS TO THIS PART OF THE COURSEWORK (I.E. PART 1) WITH YOU ANSWER TO PART 2 (I.E. PRIMER DESIGN).

i) Using an appropriate online tool give the amino acid sequence encoded by the following DNA sequence:

atgtccaaaaaaatcagtggcggttctgtggtagagatgcaaggagatgaaatgacacgaatcatttgggaattgattaaagagaaactcatttttccctacgtggaattggatctacatagctatgatttaggcatagagaatcgtgatgccaccaacgaccaagtcaccaaggatgctgcagaagctataaagaagcataatgttggcgtcaaatgtgccactatcactcctgatgagaagagggttgaggagttcaagttgaaacaaatgtggaaatcaccaaatggcaccatacgaaatattctgggtggcacggtcttcagagaagccattatctgcaaaaatatcccccggcttgtgagtggatgggtaaaacctatcatcataggtcgtcatgcttatggggatcaatacagagcaactgattttgttgttcctgggcctggaaaagtagagataacctacacaccaagtgacggaacccaaaaggtgacatacctggtacataactttgaagaaggtggtggtgttgccatggggatgtataatcaagataagtcaattgaagattttgcacacagttccttccaaatggctctgtctaagggttggcctttgtatctgagcaccaaaaacactattctgaagaaatatgatgggcgtttta aagacatctttcaggagatatatgacaagcagtacaagtcccagtttgaagctcaaaagatctggtatgagcataggctcatcgacgacatggtggcccaagctatgaaatcagagggaggcttcatctgggcctgtaaaaactatgatggtgacgtgcagtcggactctgtggcccaagggtatggctctctcggcatgatgaccagcgtgctggtttgtccagatggcaagacagtagaagcagaggctgcccacgggactgtaacccgtcactaccgcatgtaccagaaaggacaggagacgtccaccaatcccattgcttccatttttgcctggaccagagggttagcccacagagcaaagcttgataacaataaagagcttgccttctttgcaaatgctttggaagaagtctctattgagacaattgaggctggcttcatgaccaaggacttggctgcttgcattaaaggtttacccaatgtgcaacgttctgactacttgaatacatttgagttcatggataaacttggagaaaacttgaagatcaaactagctcaggccaaactt

4 marks

ii) Give the full names, the single letter and the three code for the N and C terminal amino acids for the translated sequence.

Answer:

N-terminal amino acid name, single letter and three letter code:

C-terminal amino acid name, single and three and three letter code:

6 marks

Use Protein BLAST to find the name of the organism from which the sequence was derived?

Answer:

2 mark

Use the Pfam protein family database to determine the number(s) and types of domain(s) in the protein sequence. Explain how confident you are with the predicted function for the protein based on the Pfam prediction (Hint: look at the E-value(s)).

Answer:

Number of domains?

Domain type?

Comment(s) on reported E-value(s):

4 marks

Give the PDB identifiers of the four best matches to your protein sequence in the PDB. You will need to repeat your Protein Blast but select the PDB as
the searched database.

Answer:

PDB ID:

PDB ID:

PDB ID:

PDB ID:

4 marks 20 marks

Question 2

The multiple sequence alignment below shows the alignment between three members of an enzyme family:

What is the name of the enzyme family shown is this alignment? Give a balance equation for the reaction catalysed by this enzyme family.

Answer:

Name of enzyme family:

Balanced equation for reaction catalysed by enzyme family:

4 marks

i) Using Enz_1 as a guide (Hint: check the Uniprot entry for this protein), clearly highlight in the alignment below the four conserved key amino acid residues in this enzyme family that are involved in metal binding.

ii) What is the function of the bound metal ion in the functioning of this enzyme family.

Answer:

i) Clearly highlight the metal binding residues in the above alignment.

ii) Function of bound metal ion in this enzyme family?

6 marks 10 marks
Question 3

i) Summarise the multiple sequence alignment shown below in the form of a Prosite signature sequence (e.g. [FY]-[LIV]-[GV]-[DE]-E-[ARV]-[QLAH]-x).

Your motif should be no longer than 12 amino acids long:

             1   5   10
     Seq_1   LSEKIEYYFPLS
     Seq_2   IYDKIESHWRIS
     Seq_3   MADKVESAFSIS
     Seq_4   VHQKLEYMFALS
     Seq_5   INNKIESDYDVT
     Seq_6   IVNKLETLYGVS
     Seq_7   AFEKIETIFWLT
     Seq_8   ILEKVESWFHVS

ii) For position 7 and position 10 in your motif clearly explain the basis for your choice of amino acid(s) at those positions.

Answer:

i) Type your Prosite signature sequence below:

ii)

Rationale for your choice of amino acid(s) at Position 7?

Rationale for your choice of amino acid(s) at Position 10?

20 marks

Online resources:

1. DNA translate tool: http://web.expasy.org/translate/
2. Protein BLAST homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins
3. Pfam homepage: https://pfam.xfam.org/
4. PDB homepage: www.rcsb.org
5. Uniprot homepage: www.uniprot.org