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13.9

Exercises for Chap. 13

In addition to this part, please work on the exercises in Chaps. 10 and 11.

Task 13.1

Give examples of domain databases and find them on the web.

Task 13.2

Where do I find protein structures? Which database do I use? Get an overview of the

wealth of forms. Also find out about SCOP and CATH.

Task 13.3

Protein design: locate artificial folds in the PDB database.

Task 13.4

Can you show the Tissue Plasminogen Activator and the engineering of the loop structure

with RasMol to understand the design?

Task 13.5

How does the inhibition of the HIV protease actually work? Please refer to the following

figure: https://www.hiv.lanl.gov/content/sequence/STRUCTURE/PROTEASE.HTML

1A30: Biochemistry. 1998 Feb 24;37(8):2105–2110.

HIV-1 protease complexed with tripeptide inhibitor from HIV-1 trans-frame region.

Now describe exactly what you see, that is, how inhibition works.

Task 13.6

Protein helix permutations: Might there be general design principles for proteins? Search

for relevant papers by David Baker in Nature or Science in PubMed.

Task 13.7

1. Use the GoSynthetic database. How would one find the GoSynthetic database on

the net?

2. Oncolytic virus

Oncolytic viruses are a fine example of successful synthetic biology. The idea is that the

cancer-dissolving virus multiplies preferentially in cancer cells, dissolving them (“oncoly­

sis”) while leaving the healthy cells largely alone. The immune system then removes these

viruses from the recovered body.

Thus, in order to convert a normal virus into such an oncolytic virus, the natural virus

must be modified in such a way that it preferentially replicates in cancer cells.

Find more information about this.

13  Life Invents Ever New Levels of Language