Predicting Membrane Protein Topology I Online bainformatics tools make
hydropathy analysis easy if you know the amino acid sequence of a protein. At
the Protein Data Bank (www?rosharg), the Protein Feature View displays
additional information about a protein gleaned from other databases, such as
Uniprot and SCOP2. A simple graphical view of a hydropathy plot created using
a window of 15 residues shows hydrophobic regions in red and hydrophilic
regions in blue.
a. Looking only at the displayed hydropathy plots in the Protein Feature View,
what predictions would you make about the membrane topology of these proteins:
glycophorin A (PDB ID 1AFO), myoglobin (PDB ID \(1 \mathrm{MBO}\), and aquaporin
(PDB ID 2B6O)?
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b. Now, refine your information using the ProtScale tools at the ExpASy
bioinformatics resource portal. Each of the PDB Protein Feature Views was
created with a UniProt Knowledgebsese ID. For glycophorin \(A\), the UniProtKB
ID is P02724; for myoglobin, P02185; and for aquaporin, Q6J819. Go to the
ExPASy portal (http://web.expasy orgLprotscale) and select the Kyte \&
Doolittle hydropathy analysis option, with a window of 7 amino acids. Enter
the UniProtKB ID for aquaporin (Q6JS19, which you can also get from the PDB's
Protein Feature View page), then select the option to analyze the complete
chain (residues 1 to 263). Use the default values for the other options and
click Submit to get a hydropathy plot. Save a GIF image of this plot. Now
repeat the analysis using a window of 15 amino acids. Compare the results for
the 7 -residue and 15-residue window analyses. Which window size gives you a
better signal-to-noise ratio? c Under what circumstances would it be important
to use a narrower window?