Question: Detailed Data On Ph Influence On Km
4
gravatar for Pawel Szczesny
8.3 years ago by
Pawel Szczesny3.2k
Poland
Pawel Szczesny3.2k wrote:

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 • 2.0k views
ADD COMMENTlink written 8.3 years ago by Pawel Szczesny3.2k
1

Hi Pawel ! Welcome on Biostar :-)

ADD REPLYlink written 8.3 years ago by Pierre Lindenbaum116k

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

ADD REPLYlink written 8.3 years ago by Pawel Szczesny3.2k
6
gravatar for Khader Shameer
8.3 years ago by
Manhattan, NY
Khader Shameer17k wrote:

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 COMMENTlink written 8.3 years ago by Khader Shameer17k

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 REPLYlink written 8.3 years ago by Pawel Szczesny3.2k
3
gravatar for Neilfws
8.3 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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 COMMENTlink written 8.3 years ago by Neilfws48k
1

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 REPLYlink written 8.3 years ago by Pawel Szczesny3.2k

Nice. Need to start scraping those HTML tables.

ADD REPLYlink written 8.3 years ago by Neilfws48k
2
gravatar for Larry_Parnell
8.3 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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 COMMENTlink modified 8.3 years ago • written 8.3 years ago by Larry_Parnell16k
2
gravatar for Casey Bergman
8.2 years ago by
Casey Bergman17k
Athens, GA, USA
Casey Bergman17k wrote:

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: http://www.biomedcentral.com/1471-2105/11/375

ADD COMMENTlink written 8.2 years ago by Casey Bergman17k
1
gravatar for Casey Bergman
8.3 years ago by
Casey Bergman17k
Athens, GA, USA
Casey Bergman17k wrote:

Perhaps BioNumbers might be a good place to look?

ADD COMMENTlink written 8.3 years ago by Casey Bergman17k

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

ADD REPLYlink written 8.3 years ago by Pawel Szczesny3.2k
1
gravatar for Pierre Lindenbaum
8.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum116k wrote:

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 COMMENTlink written 8.3 years ago by Pierre Lindenbaum116k
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