Commit 467218b1 authored by Vladimir Reinharz's avatar Vladimir Reinharz
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update description data

parent 59a57f61
......@@ -750,3 +750,25 @@
year={2005},
publisher={BioMed Central Ltd}
}
@article{becker1997yeast,
title={The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of $\Psi$55 in both mitochondrial and cytoplasmic tRNAs},
author={Becker, HF and Motorin, Y and Planta, RJ and Grosjean, H},
journal={Nucleic acids research},
volume={25},
number={22},
pages={4493--4499},
year={1997},
publisher={Oxford Univ Press}
}
@article{will2007inferring,
title={Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering},
author={Will, Sebastian and Reiche, Kristin and Hofacker, Ivo L and Stadler, Peter F and Backofen, Rolf},
journal={PLoS Comput Biol},
volume={3},
number={4},
pages={e65},
year={2007},
publisher={Public Library of Science}
}
......@@ -117,6 +117,7 @@
\newcommand{\rnasnp}{\texttt{RNAsnp}\xspace}
\addtolength{\textheight}{-2em}
\mathchardef\mhyphen="2D %math hyphen
\begin{document}
%\firstpage{1}
......@@ -420,7 +421,7 @@ To evaluate the efficiency of our method, data with the desired properties was a
The 5S ribosomal RNA is the family \texttt{RF00001} on \rfam. Its seed alignment consist of $713$ sequences. The family also provides the consensus structure. The mutate-and-map protocol was applied to the consensus sequence of $4$ structures which have as PDB identifiers \texttt{2WWQ}~\cite{2WWQ}, \texttt{3OAS} and \texttt{3OFC}~\cite{3OAS_3OFC}, and \texttt{3ORB}~\cite{3ORB}. Those four determined structures have almost the same sequence with slight differences in the length on their $5'$ and $3'$ extremities.
The c-di-GMP riboswitch is present in family \texttt{RF01051} in \rfam, which contains $156$ sequences in its seed alignment, and a consensus structure. The consensus sequence was also built from $4$ structures, with PDB identifiers \texttt{3IWN}~\cite{3IWN} and \texttt{3MXH}, \texttt{3MUV}, \texttt{3MUT}~\cite{3MXH_3MUV_3MUT}.
Importantly, c-di-GMP is known to bind a pocket inside the 3-way junction at positions 11,12,13, 40,41 and 85 of the sequence on which the mutate-and-map experiments were run~\cite{smith2009structural, kulshina2009recognition}, and the MaM experiment was done in presence of its ligand. It is also worth noting that, in order to facilitate the crystallization, the hairpin loop L2 of this molecule has been artificially designed to bind the U1A protein. {\color{red}Here, we included only the positions binding to its ligand. Nonetheless, for completeness, we also show in the supplementary material the results obtained with these positions, hence with the c-di-gmp binding interface only.}
Importantly, c-di-GMP is known to bind a pocket inside the 3-way junction at positions $11\mhyphen 13$, $40\mhyphen 41$ and 85 of the sequence on which the mutate-and-map experiments were run~\cite{smith2009structural, kulshina2009recognition}, and the MaM experiment was done in presence of its ligand. It is also worth noting that, in order to facilitate the crystallization, the hairpin loop L2 of this molecule has been artificially designed to bind the U1A protein. {\color{red}Here, we included only the positions binding to its ligand. Nonetheless, for completeness, we also show in the supplementary material the results obtained with these positions, hence with the c-di-gmp binding interface only.}
{\color{red}
The cobalamin riboswitch is in family \texttt{RF00174} which has $430$ seed sequences. The structure bounded to its ligand is known (PDB identifier \texttt{4GXY}). The MaM experiments
......@@ -428,6 +429,10 @@ were done in the presence of cobalamin ligands.
The yeast phenylalanine tRNA is included in family \texttt{RF00005} which has $960$ seed sequences . Since its known crystal structure (PDB identifier \texttt{1EHZ}) is only
in presence of magnesium and manganese, and there is a lot of variability between species and tRNAs for their binding location, the anticodon site was designated as the binding interface.
Additionally, we located in the two tRNAs in the structure of the yeast 80S ribosome-tRNA complexes (PDB identifier \texttt{3J78}) positions at most at $5$\AA to another chain.
We used \texttt{LocaRNA}\cite{will2007inferring} to align those tRNAs to our yeast phenylalanine tRNA sequence, resulting in the positions 1, 19, $34\mhyphen 36$, $56\mhyphen 57$, $73 \mhyphen76$ (containing the anticodon) as a positive set.
The results for those positions are shown in the Supp. Mat., where we notice extremely good results only at positions $56\mhyphen57$. They are known to follow the extremely conserved pseudouridine at position $55$~\cite{becker1997yeast}.
The adenine riboswitch belongs to family \texttt{RF00167} which has $133$ seed sequences. The structure with the adenine ligand has PDB identifier \texttt {1Y26}. Three different MaM experiments were done on that particular molecule. Experiments \texttt{Adenine\char`_2} and \texttt{Adenine\char`_3} where done in presence of the ligand, and are shown in this paper.
Experiments \texttt{Adenine\char`_4} which was done in absence of the ligand gave poor results, since the MaM experiment was done on the unbounded structure. Those additional results are shown in the Supp. Mat.
......
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