Detailed Data On Ph Influence On Km
6
4
Entering edit mode
14.0 years ago

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).

database • 3.7k views
ADD COMMENT
1
Entering edit mode

Hi Pawel ! Welcome on Biostar :-)

ADD REPLY
0
Entering edit mode

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

ADD REPLY
6
Entering edit mode
14.0 years ago

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
3
Entering edit mode
14.0 years ago
Neilfws 49k

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 :-)

ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Nice. Need to start scraping those HTML tables.

ADD REPLY
2
Entering edit mode
14.0 years ago

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.

ADD COMMENT
2
Entering edit mode
13.9 years ago

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

ADD COMMENT
1
Entering edit mode
14.0 years ago

Perhaps BioNumbers might be a good place to look?

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
14.0 years ago

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.
ADD COMMENT

Login before adding your answer.

Traffic: 952 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6