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 of3tubes 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 findthe relevant biological information for each protein. Using this information, prepare a one-pageinformation 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? Includethe 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.

Other important information:

• This report is to be done independently and is worth 15% of your mark for the BIO5INF unit.You are free to format your report as you see fit. Going over the specified limit will incur deductions. Any evidence of plagiarism will be dealt with harshly.

• The report is due on Friday 6th October, no later than 5pm. A clearly labelled, Turnitin submission inbox that will be made available on LMS. Late submission penalty of 5% per day after applies after the deadline. A hard-copy submission is not required.

• Ensure that your report is succinct but covers all important points to understand the problem and the solution you have uncovered.

• Remember to include brief figure legends and provide references where necessary.