Hi, I'm asking from the point of view of designing a research plan:
How long (approximately) can it take to determine the transition state structure of an enzyme substrate using kinetic isotope effects and computational tools? (N.B: Enzyme is an octameric protein complex with 2 catalytic subunits. Structures of enzyme's catalytic cycle are known. Natural ligand is PRPP).
Once the transition state structure has been identified, how many transition state analogues are usually designed for screening and how long does the inhibitor design and synthesis take?
Thank you.
Hi Salma,
This is routinely done in our lab. Determining the structure of transition state can be a lengthy process (really depends on your enzyme and whether you have a good assay going).
Even when you know the structure of transition state, there is still a lot that needs to be done to achieve a tight-binding inhibitor. It is very helpful to have the crystal structure of the enzyme in complex with substrate/know inhibitor to use as a guide. It involves a lot of experimentation and collaborative work but the end result is definitely worth it.
Good luck.
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