venew Online bioinformatics tools make hydropathy analysis easy if you know the amino acid sequence of a protein At the Protein

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venew Online bioinformatics tools make hydropathy analysis easy if you know the amino acid sequence of a protein At the Protein Data Bank 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 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 Knowledgebase ID For glycophorin A the UniProtKB ID is P02724 For myoglobin the UniProtKB ID is P02185 For aquaporin the UniProtKB ID is Q6J819 Go to the ExPASy portal http web expasy org protscale and select the Kyte Doolittle hydropathy analysis option with a window of 7 amino acids Enter the UniProtKB ID for aquaporin Q6J819 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 15 residue window 7 residue window 15 residue window Under what circumstances would it be important to use a narrower window Smaller window ranges identify hydrophilic regions of the protein that are likely surface exposed Narrow windows permit identification of membrane spanning regions at either end of the protein Smaller range windows alter the sensitivity of the analysis increasing the signal to noise ratio

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