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Case Study 2 – THE SWEATY PALMS MISHAP

You have just begun a new job in a toxins laboratory developing antidotes against a range of protein toxins from various sources. On your first day, you are given a rack of 3 tubes containing toxins of one sort or another. You are asked to determine some of the chemical and functional properties of the molecules so antidotes may be designed accordingly. As you look curiously at the contents of each tube, you suddenly realise your sweaty palms have rubbed off the labels!

Luckily for you, the boss is away for 3 days, which gives you enough time to determine the identity of the proteins by using a combination of protein identification techniques and bioinformatics. To begin, you subject the samples to Edman degradation and acquire the following sequences.

Protein1:

LysAspThrLysLeuGlyAsnTyrAspAsnValArgValGluPheLysAsnLysAspLeuAlaAsp

LysTyrLysAspLysTyrValAsp

Protein2:

ValIleThrLeuGluAsnSerTrpGlyArgLeuSerThrAlaIleGlnGluSerAsnGlnGlyAlaPheAlaSerProIleGlnLeuGlnArgArgAsnGlySerLysPhe

Protein3:

AspTyrThrAspTyrGlyCysTyrCysGlyLysGlyGlyArgGlyThrProValAspAspLeuAsp

ArgCysCysGlnValHisAspGluCysTyrGlyGluAlaGluLysArgLeuGlyCysSerProPhe

ValThrLeuTyrSerTrpLysCysTyrGlyLysAlaProSerCysAsn

 

You can now use this sequence information to determine the likely identity of the protein.  Using the bioinformatics tools that you have learnt so far, you proceed to find the relevant biological information for each protein. Using this information, prepare a information sheet for each protein. Keep your report to 3 pages not including references.

 

The following information must be in your report:

1. Protein Identity

Provide your best guess for the identities of the proteins you had in each tube, including the biological source. What bioinformatics tool did you use for this purpose? How did you determine the identity of your protein? What factors did you consider? For each protein, indicate how confident you are of your identification.

2. Functional Properties

What are the predicted subcellular localization, molecular weight and significant domains (if any) of each protein? Can you then find articles or textbooks to verify or contradict these predictions? Look for information on domain maps, function and size. Even if no known information exists for any of the proteins, state this.

3. Structural Characteristics

What is the structure of each protein (if available)? If not, has a crystal structure of a similar molecule been discovered? What method was used to determine the structure? Include the structures, where possible, in your report in a neat, presentable and labeled format.

4. Antidote design

Based on the information you have acquired on each protein, suggest a mechanism by which the protein action can be inhibited.