New technique for identifying atoms in RNA-protein complexes by NMR
In the children’s game ‘Who’s who?’, players ask a series of questions until they finally uncover the identity of their opponent’s character. After playing the game a few times, certain questions emerge as excellent choices to quickly winnow down the list of possibilities. But if you were to play an alternate version, using pictures of dogs instead of people, questions like ‘is it a blonde?’ or ‘does he wear glasses?’ would suddenly become pointless. In the Carlomagno group’s molecular version of this game, Alexander Marchanka at EMBL Heidelberg has had to devise a whole new suite of questions for a similar reason.
“Solid-state NMR is emerging as the technique of choice, for example for membrane proteins,” says Teresa Carlomagno “but we’re one of the first groups using it to look at the RNA part of RNA-protein complexes.”
In nuclear magnetic resonance (NMR), scientists fire sequences of radiofrequency pulses at the molecules they are studying, to deduce where each atom in a molecule is. They can then calculate the distances between atoms and how those atoms are arranged, to build a detailed 3-dimensional picture of the whole molecule or set of molecules. A specific type of NMR called solid-state NMR has the added advantage of being applicable to very large particles, and therefore holds potential for studying RNA-protein complexes – combined sets of RNA and protein molecules, which carry out a variety of tasks inside the cell. The EMBL researchers are keen to exploit this potential. But like the questions in ‘Who’s who?’, the sequences of pulses that elicit relevant ‘answers’ vary according to the type of molecule you’re studying. So Alexander and Teresa devised a new method, featured on the cover of Angewandte Chemie today, specifically for identifying the atoms in an RNA molecule by solid-state NMR.
Now that they have solved the ‘Who’s who’ issue, the scientists plan to move on to developing methods to work out the distances and whereabouts of the different atoms. “This is the first step,” says Alexander. Teresa adds: “if – and hopefully when – Alex solves the structure of an RNA-protein complex by solid-state NMR, it will be a major breakthrough.”
Marchanka, A., Simon, B. and Carlomagno, T. (2013), A Suite of Solid-State NMR Experiments for RNA Intranucleotide Resonance Assignment in a 21 kDa Protein–RNA Complex . Angew. Chem. Int. Ed., 52: 9996–10001. DOI: 10.1002/anie.201304779.