Science Buddies: "Ask an Expert"

I am interested in catalytically perfect enzymes and would like to do a project on perhaps the structure of an unknown enzyme and/or its' effect and interaction with cell receptors.
Do any specialists in this field have any ideas or suggestions to help me?
Thank you for your time and consideration.

The determination of the structure of an enzyme requires access to several very advanced instruments, and it sometimes involves several researchers over a period of years. You are unlikely to have this access unless you can find a mentor in a university or research company in your locale.

If you had something simpler in mind, please be more specific.

Also, perhaps you should post this message in the Life Sciences forum.

Hi ngrohan17,

I agree with wendellwiggins. Your project would require a university lab, as studying enzyme receptors is something that researchers study all the time.

If possible, you could email many professors (in enzymology) at a nearby university asking them if you could conduct research with them, if you want to go forward your project. If you want to look at signalling and receptors, you could also try some cancer labs, as some of them work with cell signalling.

Hope that helps!

-Sam

Dear wendellwiggins and Sam,

Thank you for the advice and mentioning the constraints on this topic. I understand this and I do have access to researchers at Vanderbilt University and a local medical college.

I have looked up ELISA and MALDI, two possible techniques for identifying structure, in addition the university has a mass spectrometry lab in case nothing else works.

I have two months and would like to do a relatively unexplored and sophisticated topic such as chitinolytic enzymes and their interactions with receptors( binding kinetics)/ morphogenetics/ structure/ effectiveness in different environmental conditions in Trichoderma Reesei, a universal fungus ( in two months time with access to researchers and laboratories). Is this practical/ do you guys have better ideas?

Hi,

I think your original idea dealing with kinetically perfect enzymes is a really neat topic, especially in terms of structural properties. That being said, two months time is way too short, the main reasons being that 1) you need to get a lot of enzyme, and purify it substantially, and 2) that structural explorations vary highly depending on the molecule, ranging from a few months to several years.

In terms of techniques, I might be able to provide you with a little more bearing. ELISA and MALDI aren't really techniques dealing with protein structure; ELISA is for quantifying protein levels by antibodies, and MALDI is an ionization source for mass spectrometry (you don't even get data out of MALDI, it's kind of a setup for mass spec). If you want to deal more with protein-protein interactions, mass spectrometry is perfect (albeit complicated and still time consuming, trust me, I'm in a mass spec lab now). Mass spec (MS) will help you deal more with changes in protein-protein interactions and dynamic proteomics, not so much structure. Another possibility is surface plasmon resonance (SPR) which will tell you about receptor-ligand kinetics (which is something that MS cannot tell you).

If you still want to do some sort of structural analysis, you're looking into the X-ray crystallography and electron microscopy (EM) fields. X-ray crystallography can take several months to years, with the time-limiting step being to crystallize the protein, which turns out to be near impossible depending on the protein. EM is a bit simpler, but will not give you the same complexity and chemical detail, though there have been really nice advances in terms of imaging, especially with immuno-gold-EM and cryo-EM which has really nice resolutions.

With just two months, my advice is to shoot for a bioinformatics project. There is a ton of structural data and functional data out there on public resources -- if you are ok with doing dry work, this can be pretty rewarding.

Hello aelin,
What bioinformatics topic do you recommend? Protein expression analysis?

Hi,

Sorry for the super late reply. Protein expression analysis (protein microarrays) would certainly be one way. Also common are (DNA) microarray analyses, proteomics and genomics analyses, metabolomics -- all sorts of '-omics' are good for bioinformatics. I think the big goal first should be to find a topic of interest and then see what sorts of public data are available for that topic.