Detailed Data On Ph Influence On Km

Question

[Pawel Szczesny]

I'm looking for experimental data showing influence of pH on activity of enzymes (examples, not necessarily systematic analysis). Brenda is a good starting point, as it contains information about pH ranges and links to relevant literature, although I hope there's some comprehensive resource (or a way to extract such data without reading all the papers).

[Pierre Lindenbaum]

Hi Pawel ! Welcome on Biostar :-)

[Pawel Szczesny]

Thanks. I'm late to the party, but at least I know what I've missed ;)

Answer 1

[Khader Shameer]

Have you checked the SABIO.RK ?

SABIO.RK is a literature curated database with reaction kinetics data. You may search using various pH ranges using the search form or via webservices. The manuscript that describe the first version is available here and a recent presentation uploaded to Nature precedings is available here

[Pawel Szczesny]

Great, that's pretty much what I was looking for. Having an API means I don't need to scrape the data manually. Thanks!

Answer 2

[Neilfws]

BRENDA is certainly the most widely-used, comprehensive enzyme database. Unfortunately, as you say, it links out to literature rather than containing any detailed experimental data.

Here's a list from BMC of databases with the keyword "enzyme".

Real experimental databases seem to be scarce. We need to get JC Bradley onto the problem :-)

[Pawel Szczesny]

Thanks Neil, from link to link I have found something containing pretty much the data I'm looking for. It's called Thermodynamics of Enzyme-Catalyzed Reactions and a sample page looks like this: http://xpdb.nist.gov/enzyme_thermodynamics/enzyme_data1.pl?T1=75WYR/GRI_223

[Neilfws]

Nice. Need to start scraping those HTML tables.

Answer 3

[Larry_Parnell]

This is a fantastic question because it points out that trends in biomedical research often get lost - especially as technology moves in other directions. Some 40-60 years ago, enzyme kinetics was very much a standard experimental path researchers took. There are so many data points buried in those old papers - many of which are not so easily found in pdf format - that would be quite useful in building rules and tools to examine and predict pathway fluxes. To this point, I have heard more than a few systems biologists lament the paucity of such data in a common location. If Thermodynamics of Enzyme-Catalyzed Reactions has what you need, then all the power to you!

In a way, this question underscores the need to place the data - data (supplemental included), article, figures - in some type of standard format so that accessibility is widespread and long-lived. Open-access is one option here. Another might be a standardized checklist of genes mentioned in the article and its supplements.

Answer 4

[Casey Bergman]

I stumbled across this today and recalled your post. Maybe The Kinetic Database and associated text mining software is what you are looking for:

This database contains automatically extracted information of kinetic data (KM, Ki, kcat, kcat/KM, Vmax, IC50, S0.5, Kd, Ka, t1/2, pI, nH, specific activity, Vmax/KM together with the enzyme name, EC number, ligand, organism, location, pH and temperature) from PubMed. 16,953,021 abstracts have been screened using textmining.

See also the publication here

Answer 5

[Casey Bergman]

Perhaps BioNumbers might be a good place to look?

[Pawel Szczesny]

Unfortunately BioNumbers contains very little data on enzymes, but I have found interesting pieces concerning cell-wide pH levels. Thanks!

Answer 6

[Pierre Lindenbaum]

This is not an answer, but this is how I would use wikipedia to fill and later retrieve those information:

• create a template for wikipedia to wrap the information, something like
  

  ... the Km is {{km|value=0.005|unit=mM|delta=0.0001|reference=[?]ref>pmid:9999999[?]/ref>}} ...

• call for participation, assign one or more enzyme to each participant and ask them to add the information in wikipedia.

• you can later retrieve the values using the mediawiki API.