At Telic Thoughts Bradford and some commenters recently exchanged polemics over chemical affinity of codons for their cognate amino acids. The alleged affinity was said to explain the origin of the genetic code. I had that in mind when I came upon a paper in Nature titled Structural insights into amino acid binding and gene control by a lysine riboswitch. It is authored by Alexander Serganov, Lili Huang and Dinshaw J. Patel. The paper notes that amino acid concentration within bacterial cells can be controlled by riboswitches. Of particular interest were lysine-specific riboswitches. The biosynthesis and transport of lysine can be directed by lysine-specific riboswitches.
How is amino acid recognition of riboswitches explained in molecular terms? The riboswitch has an unusual architecture. A five-helical junction connects three-helical and two-helical bundles. Lysine is recognized "through shape-complementarity within the elongated binding pocket and through several direct and K+-mediated hydrogen bonds to its charged ends."1 The authors wrote that:
Our structural and biochemical studies indicate preformation of the riboswitch scaffold and identify conformational changes associated with the formation of a stable lysine-bound state, which prevents alternative folding of the riboswitch and facilitates formation of downstream regulatory elements.2
1. Structural insights into amino acid binding and gene control by a lysine riboswitch by Alexander Serganov, Lili Huang and Dinshaw J. Patel; Nature 455, 1263-1267 (30 October 2008)