Wednesday, February 17, 2010

More RNA Motifs in the Ribosome

RNA (2010), 16:375–381

Matthieu G. Gagnon and Sergey V. Steinberg at the Department of Biochemistry of Montreal University report a "new structural motif" in the ribosome they call it: "A-Wedge Motif".

Every once in a while one can't help but to wonder how an article was accepted to a journal. I am not saying that the research is not unique, or that it's not an important discovery, what I'm saying, in this case, is that the new motif is explained in such an utterly confusing way, that I can't really tell what, or where, or how to find this motif. It almost feels as if one was reading a patent, where the wording is kept ambiguous in order to protect industrial secrets. It also seems unfair when you think about your own work or that of your colleagues which have a hard time being accepted for publication when something like this is published, seemingly, so easily.

Nonetheless my stubbornness has made me produce the following two pictures to try and understand what the A-wedge is.

An additional note to mention a new tool for VMD, it's called VDNA (Bioinformatics, 2009, Vol. 25, Pg. 3187), and it allows you to generate nucleosomal DNA structures automatically, and to produce 3DNA parameter output. Thomas Bishop from Tulane University at New Orleans is the author of this neat tool.