Annotation and analysis of the secondary structure elements in the Cytochrome P450 protein family

<p>We collected all currently available structures for proteins in the Cytochrome P450 family and annotated their secondary structure elements using SecStrAnnotator software&nbsp;(https://webchem.ncbr.muni.cz/Wiki/SecStrAnnotator).&nbsp;We used 2nnjA as&nbsp;the template domain for the annotation. Based on these annotations, we analysed the occurrence, length distribution,&nbsp;amino acid sequence, and presence&nbsp;of structural irregularities (&beta;-bulges, 3₁₀-helices, &pi;-helices)&nbsp;of each secondary structure element class. We also statistically compared the bacterial vs eukaryotic structures. For the&nbsp;secondary structure element classes with sufficient sequence&nbsp;conservation, the most conserved residue is annotated&nbsp;as the reference residue.</p> <p>Main files:</p> <ul> <li><strong>set_ALL.json</strong> - Set-ALL: list of 1012 protein domains belonging to the Cytochrome P450 family (CATH accession 1.10.630.10 + Pfam accession PF00067, accessed&nbsp;on 7&nbsp;July 2020, one domain&nbsp;per PDB entry)</li> <li><strong>set_NR.json</strong> - Set-NR: non-redundant list of 183&nbsp;domains (one domain per UniProt ID)</li> <li><strong>domain_lists_table.tsv</strong> - Overview of Set-ALL and Set-NR and separation into subsets Set-NR-Bact (bacterial),&nbsp;Set-NR-Euka&nbsp;(eukaryotic),&nbsp;Set-NR-Arch&nbsp;(archaeal),&nbsp;Set-NR-Viru (viral)</li> <li><strong>structures/template_2NNJ-template.sses.json</strong> - Manually prepared annotation template (domain 2nnjA)</li> <li><strong>structures/template_2NNJ.cif</strong>&nbsp;- Structure of the template domain (2nnjA)</li> <li><strong>annotations_with_reference_residues_ALL.json, annotations_with_reference_residues_ALL.tsv</strong> - Annotation of secondary structure elements for Set-ALL</li> <li><strong>annotations_with_reference_residues_NR.json, annotations_with_reference_residues_NR.tsv</strong> - Annotation of secondary structure elements for Set-NR</li> <li><strong>aligments_NR</strong>&nbsp;- Multiple sequence alignments for each SSE class (Set-NR)</li> <li><strong>logos_NR</strong>&nbsp;- Sequence logos for each SSE class (Set-NR)</li> <li><strong>plots</strong> - Plots of SSE occurrence, length distribution, contained helix types and beta-bulge occurrence (Set-NR), some plots show the comparison between Set-NR-Bact and Set-NR-Euka</li> <li><strong>statistical_tests.ods</strong>&nbsp;- Comparison of SSE occurrence between Set-NR-Bact and Set-NR-Euka by the test of equal proportions and the Fisher test, comparision of the SSE length by the Kolmogorov-Smirnov test and the two-sample Wilcoxon test</li> </ul>