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Bioinformatics & Smart Protein Sequence Analysis – Engineering Assignment Help

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Bioinformatics

1. Protein BLAST – protein and homologue identity.

The first step in identifying your protein sequence is to compare it to other known protein sequences using a protein database – here you will use a blastp (protein-protein BLAST) search via the NBCI blastp suite Go to the database link provided above and copy and paste your protein sequence into the sequence query box and press BLAST. You should not need to adjust any of the other settings.

By clicking on the “Accession” numbers in your BLASTp outputs you will be able to see specific information for each sequence result.

Questions: What information can you find out about your protein from the output? What is the identity of your sequence? Has your search identified homologues of your protein in other organisms? Take a note of the first ten rows of your BLASTp – what is the Max Score, Total Score, Query Cover, E value and Ident? Is there an attached reference source?

Now, click on “select all” to de-select all and then select only the top 10 hits – go to download and select download as “FASTA aligned sequences” – copy and paste the sequences into Notebook and save as a .txt file.

2. Multiple Sequence Alignment – comparing sequences (and preparation for phylogenentic analysis) sequences from your notepad file into the box for STEP 1 – Enter your input sequences; then in STEP 2 – Set your Parameters, select the PEARSON/FASTA output format; and then STEP 3 – Submit your job – press Submit. When you get your output alignment, click on Download and then select and copy your alignment. Paste into Notepad and save with an appropriate file name .txt.

You can then run a second sequence alignment using your MUSCLE alignment in UniProt:

This will give you an alignment output image on which you can highlight different features on your alignment that you think might be important and create a figure.

3. SMART protein sequence analysis – looking at protein structure and domains.
Copy and paste your protein sequence into the protein sequence window in SMART Make sure the four boxes underneath the window (Outlier homologues, PFAM, signal peptides and internal repeats) are selected. Then click on Sequence SMART. This should give you a diagram of your protein that you can save as an .svg file and include in your project report, there is also a summary of protein properties that you can click on and note any relevant detail (e.g. what do the domains mean? What is the position of the signal peptides? Etc).

4. Interpro analysis of a protein sequence – what is the protein and what is its function?
Paste your protein sequence into the window in Interpro  And, press search. What you should then see is a diagram showing where the domains (based on homology)
and predicted domains are in the fragments of the gene that you have amplified. You can download the image by clicking the camera icon and then you can save and annotate this as a figure in your report. You will also notice under the Molecular Function title that this protein has carbohydrate binding function. If you click on the link it will tell you all the properties of that carbohydrate binding, make sure you take a detailed account of the output because this is what the protein will be binding to on the surface of bacterial cells. How you present this information is up to you but use diagrams and tables where possible.

5. STRING analysis – exploring the predicted interactions between your protein and other proteins.
On the STRING webpage Protein by Sequence, then paste the same protein sequence you previously used into the window. Click on the Organism box and choose either Ixodes scapularis (for tick sequence) or an appropriate Glossina species (for tsetse sequence) , then click on search. The program will provide a list of homologues, select and take a note of the top one which will explain what the protein is doing and the click continue. You should then see a network of the different proteins that are interacting with your protein. Click on each of these proteins and make a note of what they are and what they do and highlight what is interesting about these. Think about how best to present this information. To download your network as a figure click on Export and it will provide you with options on how to download it.

This analysis could give you integral information about the interactions between your protein and mammalian (including humans) hosts.

6. SWISS MODEL – predicting the tertiary structure of your protein.
Modelling. Then paste in your protein sequence into the Target Sequence(s) box and click on Build Model. You should then see a page of output showing you the predicted protein structure, which you should be able to download – you can click on the image and rotate it and then capture this from different viewpoints using the camera icon (remember to click on high resolution) to create a set of figures. Take a note of any of the other information provided that you think is relevant. The QM value is important and should be above -4 (scores of -4 or below indicate that the model is of poor quality, if the QM has a thumbs up and a score higher than -4 then it suggests a good quality model. If your model does not look like it is good quality, you should still use and discuss why this might be the case). You could include a screenshot(s) of the full output in your appendices and refer to this but make sure the main results are presented in your results section.

I-TASSER is another online platform that can be used for protein structure and function predictions. However, this programme can take a long time to run and so we are not recommending you use it for your project analysis. You only need to run the SWISS-MODEL analysis but if you want to also run an I- TASSER model for comparison you can.

7. Using a program called DALI you can do a pariwise comparison (under the pairwise tab) of your 3D protein model with another 3D protein model for one of the homologues (from a different species or the same species but a different geographical location, etc.) you identified from your Blastp search. You could also repeat this again to compare to another homologue model. For this analysis you will need two model pdb files, the pdb for your protein model and the pdb file for the second protein. You will need to get the pdb files by running the Swiss Model analysis for your protein and then your chosen other sequence. To download the pdf files you can click on the model number tab (on the model output page) and then download the pdb format. Then in DALI you will need to add in the first file (step 1) and then click on the + sign to add the next (step 2) and then run the analysis (final step).


Remember to look at examples in published papers to help you with presentation, etc. Guidance on interpreting your DALI pairwise comparison results (use the tutorial document to help you also – page 3 onwards):

Look at the Summary – what is the Z-score? “Similarities with a Z-score lower than 2 are spurious”
Select the match(es) – you’ll see a box next to where you see the Z-score.
Look at the structural alignment (with/without the Expand Gaps box selected) and within this look at the Stacked Sequence Logos – you may want to produce a figure for these either in the main body of your project thesis or as a supplementary figure(s) – if you right click on the image you can copy it into PowerPoint and then you might need to crop it into sections to make a figure. Look at the tutorial and attached paper (and example papers) to help with interpretation.
3D superimposition – this will show the model of the query sequence superimposed with the other model(s)/selected match(es) (should be in different colours). In the output screen you can make use of the show/hide buttons to show different features.

SANS – interactive homology search against UniProt (does this fit with your original searches?)

PANZ – Table showing estimated biological, molecular, and cellular functions

Pfam – stacked pfam graphics – see description and tutorial for help.

Don’t be afraid to click on things in your outputs and explore. Remember, you may not want to use or show all of these. You need to decide what information you think is important and should go in the main results (whether some should be referred to in the main text but provided in the supplementary material in the appendices and/or not used).


Guidance on interpreting Swiss-Model results:
As demonstrated in the session, once you have your model you can click on the different options to view different properties of your protein model. Again, don’t be afraid to click. If it’s all one colour in the initial output (as for Michaela’s protein) why might this be? Can you see different structures, e.g. alpha helices, beta sheets, etc.?


Guidance on Inter-Pro results:
No molecular function? (Charlotte’s Question). Report that result, a negative/no result is still a result, but is it involved a biological process or cellular function?
Again, don’t be afraid to click on different things, use the tutorials available and look at example papers (these are often shared on the websites of the different programs used). Remember to look at examples in published papers to help you with presentation, etc.


Figures

  • 3D protein model highlighted with different colour showing different characteristics of the protein.
  • Phylogenetic tree representing the relationship between relevant sequences/it is important to identify the protein of interest.
  • Relevant bioinformatic figures.

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