Saturday, August 9, 2008 - 13:20
Instead of enjoying a sunny summer day today, or partying with SciBlings in New York, I'm staring out my window watching the rain. Inspiration hit! What about searching for August? Folks, meet the HFQ protein from E. coli. I found this lovely molecule by doing a multi-database search at the NCBI with the term 'August'. HFQ is a lovely protein with six identical subunits, that's involved in processing small RNA molecules and is homologous to some eucaryotic proteins that work in RNA splicing (1). Do you see the blue loopy regions in the center of the structure? Those are positively charged. I bet the negatively charged RNA gets clipped apart in that part of the protein. But, that's just speculation. But why did I find this protein when I was searching for August? Ah the vagaries of a database search! Sometimes explaining the results is like playing "Where's Waldo?" Even though I found this protein with 'August,' August isn't mentioned anywhere in the Structure Summary or the title or any place that would link this particular structure to that particular search term. My students would probably conclude that database searching doesn't work or that it sometimes produces random results. Where is "August"? But, I think August is hiding in there somewhere and there's a way to find it. First, I selected "See File" from the Tasks menu on the Structure Summary page. Then, I clicked the Structure View in Cn3D button to see a text version of the structure file. Yeah, I know that's not intuitive, and perhaps even a bit contradictory, but that's what you do. Then I searched the file, from my web browser, with 'August.' And voila!, we've answered the question.
J.T. August was an author an earlier version of the structure, that was published in 1972. Okay, that does seem a little random, but at least now we know why we found this lovely protein during our search for August. Reference: 1. Sauter C, Basquin J, Suck D. Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli. Nucleic Acids Res. 2003 Jul 15;31(14):4091-8.