Protein Chemistry

Question: In this semester assignment the task is to analyze two protein sequences from the pathogenic bacterium Pseudomonas aeruginosa. One of the sequences is a characterized protein with a homolog (ortholog) in the human genome and the other is a hypothetical protein (a protein for which the function is not known). The task should use all the relevant methods that you have learned in the protein bioinformatics exercises to learn as much about these proteins as possible and compile this information in a report. The report should contain 1-2 pages of text for each protein sequence.

The protein sequences are from the genome of P. aerugionsa PAO1. The sequence assigned to me is below in the excel file, and also the report template and the report that I have started on.

Protein sequence analysis report

Template for protein sequence analysis report

Question 1. Analyze physical and chemical properties:
o Utilize the various tools you have learned to analyze the physical and chemical properties of your two proteins (e.g., molecular weight, isoelectric point, solubility, extinction coefficient).
o Provide a table that summarizes all predicted parameters.
o Comment on the results and their relevance to experimental work.

Question 2. Sequence homology search:
o Perform a BLAST search to identify homologous sequences across different species.
o Conduct a separate BLAST search to find homologous sequences in humans.
o Select 10-15 relevant sequences for multiple sequence alignment analysis.

Question 3. Multiple sequence alignment (MSA):
o Perform an MSA using the sequences selected in the previous step using one of the programs you have learned.
o Discuss conserved regionsand their potential functional implications.
o Visualize the MSA using ESPript and include a high-quality figure in your report.

Question 4. Phylogenetic tree construction:
o Construct a phylogenetic tree based on the aligned sequences. Discuss evolutionary relationships among the sequences.
o Include the phylogenetic tree as a figurein your report, generated from your analysis.

Question 5. Protein structure prediction:
o Use AlphaFold to predict the 3D structure of your protein. If you suspect that your protein contains multiple subunits and/or one or more cofactors, use Alphafold 3 to predict the structure.
o Evaluate the confidence scores provided by AlphaFold.
o Provide a high-quality figure of the predicted structure using PyMol and highlight key structural features.

Question 6. Gene context and interactions:
o Utilize tools you have learned to infer genomic context and potential interaction networks with other proteins.
o Discuss how genomic context or protein interactions could provide insights into your protein's function.
o Provide a relevant figure if you want to.

Question 7. Final hypothesis:
o Based on your analysis, propose a hypothesis about your protein's function or interaction with other proteins.
o Suggest potential laboratory experiments that could be conducted to test your hypothesis.