The invisible data of Isabella Karle

When finding a female scientists' data turns into an archeological treasure hunt.

A few months ago, I decided it would be interesting to celebrate various scientific contributions by making images of chemical / molecular structures in the Molecule World iPad app and posting them on Twitter  (@MoleculeWorld).  Whenever I can, I like to highlight scientific contributions from women on their birthdays.  Tomorrow's post will feature Dr. Isabella Karle, an x-ray crystallographer who worked on the Manhattan project and solved structures of interesting molecules like valinomycin and a South American frog venom (1).

Valinomycin in Molecule World. Valinomycin in Molecule World. The structure was obtained from ChemSpider (2) and converted to a PDB file for viewing. This antibiotic makes a channel in the plasma membrane causing potassium to leak out and triggering apoptosis (3)

 

 

 

 

 

 

 

 

 

 

 

Reading about Dr. Karle's many accomplishments in Wikipedia made me think it should be easy to find and view some of the structures she solved. Indeed, I found 18 papers in PubMed, where she's listed as an author. Most impressively, if this is the same IL Karle, one paper dates from 2012, making her almost 91 at the time of publication!

But in the quest for structures, the results were nil.  Searching the NCBI's Molecular Modeling Database and the PDB structure databases only gave me a few structures –all from her husband. Searching with her maiden name was futile as well.

I went back to scanning her papers.

Titles like "Crystal structure of ..." were so tantalizing. Being involved in genomics for so long, I couldn't imagine how a journal like PNAS could publish a 2004 paper, with a title like "Crystal and molecular structure of a benzo[a]pyrene 7,8-diol 9,10-epoxide N2-deoxyguanosine adduct: absolute configuration and conformation"  without requiring the authors to deposit the structure data in a public database.

Luckily, they did.  But the data weren't in the PDB or the NCBI.  Karle deposited her data in a database I'd never heard of, The Cambridge Crystallographic Data Centre (CCDC).  It still wasn't easy to find her structures, but I could do so if I  looked for an ID in the paper and used it to search.   In the case of valinomycin (above), I only knew about it from Wikipedia, and was able to search for it by name and get it from ChemSpider.

Some additional steps were required to convert structures into a PDB format for viewing, but the structures could be displayed.

It's nice to know that someone so productive left some kind of data behind.

References:

  1. Wikipedia, Isabella Karle,  accessed Dec. 1, 2015.
  2. Valinomycin, downloaded from ChemSpider, Dec. 1, 2015
  3. Valinomycin, PubChem record.  Dec. 1, 2015.

More like this

Something interesting happened in 2014. The total number of databases that Nucleic Acids Research (NAR) tracks dropped by three databases! What happened?  Did people quit making databases?  No.  This year, the "dead" databases (links no longer valid) outnumber the new ones. To celebrate Digital…
We've been fans of the Molecule of the Month series by David Goodsell, for many years. Not only is Dr. Goodsell a talented artist but he writes very clear descriptions of the ways molecules like proteins, RNA, and DNA work together and function inside a cell. To learn about proteins and their…
Sucrose Molecules of sucrose tore apart in their bellies letting glucose course free in their veins. Luckily for us, a system evolved long ago to capture that glucose and minimize it's potential for damage. Removing sugar from the blood and sequestering it in liver, fat, and muscle cells,…
In my last post, I wrote about insulin and interesting features of the insulin structure.  Some of the things I learned were really surprising.  For example, I was surprised to learn how similar pig and human insulin are.  I hadn't considered this before, but this made me wonder about the human…