Can you help me figure out this from Biochem The sequence of the delta opioid re
ID: 197310 • Letter: C
Question
Can you help me figure out this from Biochem
The sequence of the delta opioid receptor is shown below: I mepapsagae lqpplfanas daypsacpsa ganasgppga rsasslalai aitalysavc 61 avglgnvlv mfgivrytkm ktatniyifn laladalats tlpfqsakyl metwpfgell 121 ckavlsidyy nmftsiftlt mmsvdryiav chpvkaldfr tpakaklini ciwvlasgvg 181 vpimvmavtr prdgavvcml qfpspswywd tvtkicvflf afvwpilit vcyglmlrl 241 rsvrllsgsk ekdrsirrit rmvlvvvgaf vvcwapihif vivwtlvdid rrdplvvaal 30I hlcialgyan ssinpvlyaf Idenfkrcfr qlcrkpcgrp dpssfsrare atarervtac 361 tpsdgpggga aa and can be accessed at http://www.ncbi.nlm.nih.gov/protein/NP of the page) 000902 (scroll to the bottom 12. There are many online tools for predicting structure and function of proteins. Go to http://web.expasy.org/protparam/ (Protein Parameters) and use it to calculate the theoretical pl and molecular weight of the delta opioid receptor: 13. What is the least abundant and most abundant of the 20 normal amino acids in the delta opioid receptor? 14. Go to a secondary structure prediction service like GOR ( http:/Inpsa-pbiljbcp.fricgi- bin/npsa automat.pl?page=npsa gor4.html or google "GOR Secondary Structure" and select the result with "NPS" in the title). Insert the protein sequence and solve for secondary structures (you may have to reformat the sequence). Does it find the same secondary structures as the image on the second page of this worksheet? What does it find? 15. BLAST (basic local alignment search tool) lets us try to find closely related proteins the expasy BLAST tool (http://web.expasy.org/blast/), try to find what proteins are closely related to the delta opioid receptor: Are these results surprising? . UsingExplanation / Answer
1. (Answer to question no. 12) According to the ExPASy tool for protein parameters,
The theoretical pI of the delta opioid receptor is : 9.21.
The molecular weight of the delta opioid receptor is : 40368.79.
2. (Answer to Q. no. 13) Again according to the information provided by the ExPASy protein parameter tool -
The most abundant amino acid in the delta opioid receptor is : Alanine (12.68%)
The least abundant amino acid in the delta opioid receptor is : Histone (0.8%)
3. (Answer to Q. no. 14) According to the NPS@ : GOR4 Protein secondary structure prediction tool, the following secondary structures have been predicted in the delta opioid receptor :
Alpha helix : 28.23% [105 residues]
Extended strand : 28.23% [105 residues]
Random coil : 43.55% [162 residues]
(Any image of the second page of the worksheet has not been provided in the question. Therefore, I am not able to infer whether or not the secondary structure predictions match with the image provided on the second page).
4. (Answer to Q. no. 15) As revealed by the ExPASy BLAST tool :
The proteins with the highest bit score or similarity with the delta opioid receptor are the Opioid receptor delta-1 proteins of gorilla, green monkey, Olive baboon, sheep. mouse, chimpanzee, naked mole rat, rabbit, European domestic ferret, dog, pig, giant panda etc. Observing the BLAST results, it can be stated that the results are not surprising since the delta opioid receptor among different mammalian species has been found to bear similarities in sequence. This is expected, since mammalian genomes are known to be quite similar to each other in terms of sequences.