Question

We will refer to the protein as sequence2. It was just 40 amino acids long and had the following amino acid sequence

>sequence2

MSAEALADPAADPLAGNNPDADPEAINLKAIAALAKALLG

Using your knowledge of BLAST searching particularly “Protein BLAST” (http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome), the Expasy (http://www.expasy.org/) and the BLASTP align2seq (http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=align2seq )

Answer the following questions:

a) What is the identity score between the query protein sequence (i.e. sequence2) and the highest scoring (best) aligning sequence from the BLAST search? (1 mark)

b) Using similarity to other species as a guide, what is the likely function of the processed peptide from sequence2 (prepromastoparan)? (2 marks)

(Hint: it would be informative to remove the “prepro-“ prefix from the sequence name and search using the abbreviated name) You can use any search protocols you wish – NCBI databases would be useful.

d) What is the protein sequence of the mature (processed shorter) form of the mason bee prepromastoparan? (Hint: see point 6 of the protein analysis section above) (3marks).

e)What are the molecular weights (in kDa) of mason bee "prepromastoparan (i.e. sequence2)" and mason bee "mastoparan M"? (1 mark)

Answer 1

a) The identity score between the query protein sequence (i.e. sequence2) and the highest scoring (best) aligning sequence from the BLAST search is 23.1 with identity percentage of 56.25.

b) The likely function of the processed peptide from sequence2 is a nonspecific secretagogue that act as GTPase-activating protein which itself is involved in cell surface coupling with intracellular mediators.These protein thus display a unique mode of toxicity by directly acting on the plasma membrane associated G proteins which mimmics the role of agonist ligand receptors.

d) the protein sequence of the mature (processed shorter) form of the mason bee prepromastoparan is

MKDTILILFT AFIALLGFFG MSAEALADPL ADPSAGPNAE ADPEAINLKA IAALVKKVLG

e) The molecular weights (in kDa) of mason bee "prepromastoparan (i.e. sequence2)" = 6.157 kDa

and mason bee "mastoparan M" = 6.195 kDa