Protein Analysis Subcellular Localization Prediction
Encyclopedia
Protein Analysis Subcellular Localization Prediction is a process (usually through the use of web-based software) of predicting the location or destination of a protein within the cell using only the protein sequence as its inputs.
In the central dogma of molecular biology
, the major copy of the message for protein synthesis is contained in the DNA. The message is transcribed into mRNA and then transported to the cytosol where translation of the copies of mRNA into proteins happens. Several post-translational modification
processes happen before the cell could actually use the modified protein. This protein is then transported to a particular organelle
(intracellular) or outside the cell (extracellular) where the protein is needed. Proteins are then likened to letters with proper address and stamps to deliver it on the proper destination. Likewise, proteins should have proper address to ensure its delivery to the proper localization. The destination of various protein sequences is predicted by these subcellular localization prediction servers.
Protein Localization Prediction is important to predict the possible location or destination of a particular protein. Take note, however, that this is still a prediction. An actual wet-lab procedure is preferred to do actual analysis of the protein's location. Since the prediction servers present possible location of the protein, then it also gives us insights of the possible function of the protein sequence.
One web-based program is the PA Specialized Subcellular Localization Server v2.5 found at Proteome Analyst Research Group, University of Alberta. Several related servers are also available for protein subcellular localization prediction. A list can be found at PSORT.
Oxalate + O2 + 2H+ = 2 CO2 + H2O2.
The hydrogen peroxide, H2O2, produced may play an important role in several aspects of defense mechanisms. In rice, this enzyme has been mapped at chromosome 3.
1. enter an Analysis ID, like, "OxO".
2. Now, copy the FastA sequence below and paste it on the PENCE PA-SUB server opposite the "FastA Sequences" box.
>gi|108710532|gb|ABF98327.1| Oxalate oxidase 2 precursor, putative, expressed [Oryza sativa (japonica cultivar-group)]
MEHSFKTIAAGVVIVVLLLQQAPVLIRATDADPLQDFCVADLDSKVTVNGHACKPASAAGDEFLFSSKIA
TGGDVNANPNGSNVTELDVAEWPGVNTLGVSMNRVDFAPGGTNPPHVHPRATEVGIVLRGELLVGIIGTL
DTGNRYYSKVVRAGETFVIPRGLMHFQFNVGKTEATMVVSFNSQNPGIVFVPLTLFGSNPPIPTPVLVKA
LRVDAGVVELLKSKFTGGY
3. Click the "Plant" radio button on the "Organism Type" table. Click the "Begin Analysis" button. An intermediate page will show up. You may view the file by clicking the appropriate hyperlink or you may download it in *.csv file.
The positive prediction gives as the most probable location of the protein sequence, in this cae, the protein OxO is secreted extracellularly (100%), probably on the cell wall, or transported to vacuole (90.346%).
For references on interpreting the results, click any of the following http://www.cs.ualberta.ca/~bioinfo/PA/Sub/doc/PA_SUB_Output.html
http://pasub.cs.ualberta.ca:8080/pa/dynamicExplain?classifierId=24&userId=2&listId=445439&proteinId=1
http://www.cs.ualberta.ca/~bioinfo/PA/Sub/doc/PA_SUB_Output.html
>gi|476752|gb|AAB02583.1| rubisco large subunit
MSPQTETKASVGFKAGVKDYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVW
TDGLTSLDRYKGRCYHIEPVVGEDNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRI
PPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRACYECLAGGLDFTKDDENVNSQP
FMRWRGRFVFCAEAIYKSQAETGEIKGHYLNATAGTCEEMIKRAVFARELGVPIVMHDYLTGGFTANTSL
AHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRMSGGDHIHAGTVVGKLEGIFFFFFFFFFFFL
RKELYVCVIIQNKHVVQGVAVHACRISSSLWYTYPSKRSKTYETNTQEEES
In the central dogma of molecular biology
Central dogma of molecular biology
The central dogma of molecular biology was first articulated by Francis Crick in 1958 and re-stated in a Nature paper published in 1970:In other words, the process of producing proteins is irreversible: a protein cannot be used to create DNA....
, the major copy of the message for protein synthesis is contained in the DNA. The message is transcribed into mRNA and then transported to the cytosol where translation of the copies of mRNA into proteins happens. Several post-translational modification
Posttranslational modification
Posttranslational modification is the chemical modification of a protein after its translation. It is one of the later steps in protein biosynthesis, and thus gene expression, for many proteins....
processes happen before the cell could actually use the modified protein. This protein is then transported to a particular organelle
Organelle
In cell biology, an organelle is a specialized subunit within a cell that has a specific function, and is usually separately enclosed within its own lipid bilayer....
(intracellular) or outside the cell (extracellular) where the protein is needed. Proteins are then likened to letters with proper address and stamps to deliver it on the proper destination. Likewise, proteins should have proper address to ensure its delivery to the proper localization. The destination of various protein sequences is predicted by these subcellular localization prediction servers.
Protein Localization Prediction is important to predict the possible location or destination of a particular protein. Take note, however, that this is still a prediction. An actual wet-lab procedure is preferred to do actual analysis of the protein's location. Since the prediction servers present possible location of the protein, then it also gives us insights of the possible function of the protein sequence.
One web-based program is the PA Specialized Subcellular Localization Server v2.5 found at Proteome Analyst Research Group, University of Alberta. Several related servers are also available for protein subcellular localization prediction. A list can be found at PSORT.
Sample run of the tool
For our particular purpose, we will use the PA-Subcellular Localization Prediction server found at the University of Alberta. To do a sample run of the tool, let us consider the Oxalate oxidase (OxO) enzyme from rice (NCBI). To give you an introduction, OxO are involved in plant defence to pathogen infection such as powdery mildew of barley and wheat. It catalyzes the following reaction:Oxalate + O2 + 2H+ = 2 CO2 + H2O2.
The hydrogen peroxide, H2O2, produced may play an important role in several aspects of defense mechanisms. In rice, this enzyme has been mapped at chromosome 3.
1. enter an Analysis ID, like, "OxO".
2. Now, copy the FastA sequence below and paste it on the PENCE PA-SUB server opposite the "FastA Sequences" box.
>gi|108710532|gb|ABF98327.1| Oxalate oxidase 2 precursor, putative, expressed [Oryza sativa (japonica cultivar-group)]
MEHSFKTIAAGVVIVVLLLQQAPVLIRATDADPLQDFCVADLDSKVTVNGHACKPASAAGDEFLFSSKIA
TGGDVNANPNGSNVTELDVAEWPGVNTLGVSMNRVDFAPGGTNPPHVHPRATEVGIVLRGELLVGIIGTL
DTGNRYYSKVVRAGETFVIPRGLMHFQFNVGKTEATMVVSFNSQNPGIVFVPLTLFGSNPPIPTPVLVKA
LRVDAGVVELLKSKFTGGY
3. Click the "Plant" radio button on the "Organism Type" table. Click the "Begin Analysis" button. An intermediate page will show up. You may view the file by clicking the appropriate hyperlink or you may download it in *.csv file.
Result
A screenshot of the result of our sample run is shown at the right pane. It contains statistics on the protein we submitted, along with BLAST results and a Subcellular Prediction.The positive prediction gives as the most probable location of the protein sequence, in this cae, the protein OxO is secreted extracellularly (100%), probably on the cell wall, or transported to vacuole (90.346%).
For references on interpreting the results, click any of the following http://www.cs.ualberta.ca/~bioinfo/PA/Sub/doc/PA_SUB_Output.html
http://pasub.cs.ualberta.ca:8080/pa/dynamicExplain?classifierId=24&userId=2&listId=445439&proteinId=1
http://www.cs.ualberta.ca/~bioinfo/PA/Sub/doc/PA_SUB_Output.html
Try this
Perform the same procedure as above but use the following sequence as an entry. This amino acid sequence is Ribulose bisphosphate carboxylase (RUBISCO) large unit. From this information, we can already predict its possible location.>gi|476752|gb|AAB02583.1| rubisco large subunit
MSPQTETKASVGFKAGVKDYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVW
TDGLTSLDRYKGRCYHIEPVVGEDNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRI
PPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRACYECLAGGLDFTKDDENVNSQP
FMRWRGRFVFCAEAIYKSQAETGEIKGHYLNATAGTCEEMIKRAVFARELGVPIVMHDYLTGGFTANTSL
AHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRMSGGDHIHAGTVVGKLEGIFFFFFFFFFFFL
RKELYVCVIIQNKHVVQGVAVHACRISSSLWYTYPSKRSKTYETNTQEEES