3D structural alignment of bacterial and mitochondrial SSU rRNA structures with conservation and Solvent Accessible Surface Areas (SASA) data
This database includes the 3D alignment of the nts from bacteria SSU rRNA - E. coli (PDB file 4YBB) and mammalian mitochondria - Porcine ( PDB file 5AJ3), base conservation data, and the Surface area solvent accessibility data (SASA) 3D structural alignment of bacterial and mitochondrial SSU rRNA structures: The 3D structures of the E.coli SSU rRNA (PDB entry: 4YBB) and mmt SSU rRNA (PDB entry: 5AJ3) were aligned manually using SwissPDBViewer. We call positions with equivalent nts in the mmt and bacterial 3D structures “Core positions” Base composition at each position in the bacterial and mmt SSU rRNA alignments: 1533 positions in the bacterial alignment that correspond to the E. coli SSU sequence “>000736::E.coli.01 – Escherichia coli” and 961 positions in the mmt alignment that correspond to the S.sc. sequence (SeqID “>00307::AF486866 – Sus scrofa”) were selected ( the only columns of the alignments that we worked with). For each position in the alignment, the total count of each type of base was divided by the total count of bases in that position to calculate the base composition in each position. We refer to these compositions as %A, %C, %G, %U. Analysis of Solvent Accessible Surface Areas (SASA): SASA for the 12S and 16S rRNA from E.coli SSU (PDB entry: 4YBB, chain AA) and mmt-SSU (PDB entry: 5AJ3) were calculated for each atom in the presence and absence of the associated rProteins, using Gerstein’s accessible surface algorithm (Gerstein, 1992) available at the High-Performance Computing server at NIH (https://hpcwebapps.cit.nih.gov/structbio/basic.html). Probe radius used for solvent accessibility calculations was 1.4 Å, typical for water molecule. Estimated SASA of isolated nucleobases: In order to estimate the SASA of the base atoms of an isolated nt of each type (without any other nt or protein nearby), 30 nts of each type of nucleobases (A, U, G or C) were randomly selected and each full nt was saved individually as a PDB file using SwissPDBViewer. Using the PDB files of the single nts as an input for the SASA calculation server, a text file containing calculated SASA of each atom was obtained. A Python program was written to sum the SASA contributions of the base atoms. The average SASA of 30 selected isolated nts of each type of base was calculated. The numbers were G: 210.4, A:195.2, C:168.0, U:161.7 Å^2. Normalized SASA (N-SASA) of nucleobases in each position of bacterial and mmt structures: The absolute SASA for each nt in the reference bacterial and mmt 3D structures was divided by the estimated SASA for an isolated base to determine a normalized SASA (N-SASA) which is more robust to the varying sizes of the bases.