Commit 50ca25de authored by Vladimir Reinharz's avatar Vladimir Reinharz
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started dataset

parent 0b62a3eb
......@@ -389,17 +389,28 @@ The whole implementation is freely available at:
\subsection{Dataset}
To evaluate the efficiency of our method, data with the desired properties was available for three RNAs~\cite{Cordero:2012aa}. These required properties are a mutate-and-map experiment data set, a determined three-dimensional structures interacting with other chain(s) and and \rfam alignment. Those three RNAs are the 5S ribosomal RNA, the c-di-GMP riboswitch and the glycine riboswitch. The latest only had one determined structure with only one position close to another molecule. Due to the poor quality of the data and thus the uncertainty in the results, it was omitted in the present analysis. The results are shown in supplementary material (Fig.~S7).
To evaluate the efficiency of our method, data with the desired properties was available for {\color{red}seven} RNAs~\cite{Cordero:2012aa}. These required properties are a mutate-and-map experiment data set, a determined three-dimensional structures interacting with other chain(s) and and \rfam alignment. Those seven RNAs are the 5S ribosomal RNA, {\color{red}the phenylalanine tRNA, the c-di-GMP riboswitch, the cobalamin riboswitch (Puzzle 6), the adenine riboswitch and the glycine riboswitch }.
{\color{red}The latest gave poor results, potentially due to an artificial hairpin, introduced in the sequence, binding to a small protein to help the crystalisation. The protein was missing in the MaM experiments. It was thus omitted in the present analysis. The results are shown in supplementary material (Fig.~S7).}
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}. We present in Fig.~\ref{fig:shape}a, for every position $i$, the value of $\Delta(S, S_i)$, with the aligned \rfam consensus secondary structure below. Those four determined structures have almost the same sequence with slight differences in the length on their $5'$ and $3'$ extremities.
{\color{red}
The phenylalanine tRNA RF00005 we have binding to MG and MN
}
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}. We similarly present in Fig.~\ref{fig:shape}b the values of $\Delta(S, S_i)$, with the aligned \rfam consensus secondary structure below.
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}. 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. Here, we included these positions in the set of interacting positions. Nonetheless, for completeness, we also show in the supplementary material the results obtained without these positions, hence with the c-di-gmp binding interface only.
{\color{red}
The cobalamin riboswitch RF00174
}
{\color{red}
The adenine riboswitch RF00167
}
\begin{figure}[ht!]
\centering
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