You are working in a laboratory, trying to identify how the nematode worm C. ele

Question

You are working in a laboratory, trying to identify how the nematode worm C. elegans senses and moves toward specific “attractant” chemicals. You examine an electronic database that compiles mRNA expression profiles of all nematode genes measured by DNA microarray hybridization experiments, and find that an unknown gene is transcribed coordinately with several genes known to be involved in the attractant response. You name this gene Unk1 and set out to learn what it does. (10 points)

A. Without doing a single experiment at the lab bench, how can you learn more about what the Unk1 protein might be doing? How might this influence your choice of experiments with Unk1?
B. You decide to look for proteins that bind to Unk1, which may provide important clues to its function. Briefly describe an approach to find binding partners.

Explanation / Answer

A. We can perform bioinformatics tools to predict the structural and possible functional characteristics by comparing the homology with database sequences of different organisms, which are closely similar to Unk1 protein. If Unk1 has structural homology with some other protein of any species, we will look at that particular protein function in that specific organism (if reported) and then we can predict the similar function of Unk1 in C. elegans. Here, you can look deep into its secondary and tertiary structure conformations, domains, coiled-coiled regions, thermodynamical stability prediction upon mutation, and so on. For this study, we will use protein structure prediction tools like ExPASy, I-TASSER, APSSP, SWISS-MODEL, PHYRE2, and etc.

B. The protein-protein interaction can be determined in the laboratory by mass spectrometry, yeast two-hybrid system, phase display, Fluoresce resonance energy transfer (FRET) and immunoprecipitation (IP). Using bioinformatics Softwares like DIP, Suiseki and IE etc. and docking studies give the clues about possible sites or domains on the Unk1 to interact with other proteins.

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