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Supplemental Information

Phylogenetic reconstruction of Trypanosoma brucei brucei DdRPII RPB1 model DdRpII RPB1 protein sequences.

The tree was generated using the DdRpII family dataset (36 foul length protein sequences samples) and the Jalview software. Tree was constructed using the average distance statistical method with PAM 250. In the tree representation there are clearly shown the two RNA polymerases II subunits RPB1 and RPB2 as two main monophyletic sub-trees. Trypanosoma brucei DdRpII RPB1 protein sequence was correctly classified in the monophyletic sub-tree of the RPB1 group.

DOI: 10.7287/peerj.preprints.2775v1/supp-1

Multiple sequence alignment

The alignment was performed using the Trypanosoma brucei brucei DdRPII RPB1, the Trypanosoma brucei gambiense DdRpII RPB1, the crystal structure of Schizosaccharomyces pombe DdRpII RPB, the crystal structure of Saccharomyces cerevisiae DdRpII RPB1 and the electron microscopy structure of Human DdRpII DdRpII RPB1. (A) All nine suggested conserved motifs and major domains of DdRpII RPB1 have been marked (Motifs 1a, 1b, 2, 3a, 3b, 3c, 4a, 4b, 4c). Additionally, in the multiple sequence alignment were presented the major differences. (B) Domains and domainlike regions of the DdRpII subunit Rpb1. The amino acid residue numbers at the domain boundaries are indicated.

DOI: 10.7287/peerj.preprints.2775v1/supp-2

Multiple sequence alignment

The alignment was performed using the Trypanosoma brucei brucei DdRPII RPB1, the crystal structure of Schizosaccharomyces pombe DdRpII RPB and the electron microscopy structure of Bos taurus DdRpII RPB1. All five sub-domains (A-E) as referred in Pfam database have been marked with different colours.

DOI: 10.7287/peerj.preprints.2775v1/supp-3

Molecular dynamicssimulation charts of the root mean square deviation (RMSD) for the Trypanosoma brucei brucei DdRpII RPB1 sub domainsof the model A.

The energy (Kcal/mol) vs time (ns) plot of the 100ns simulation trajectory of the TBB DdRpII RPBI model A. Sub-domain regions of the Trypanosoma brucei brucei DdRPII RPB1 have been separated according to conventions of Supplementary Figure 3. (A) Domain A RMSD. (B) Domain B RMSD. (C) Domain C RMSD. (D) Domain D RMSD. (E) Domain E RMSD.

DOI: 10.7287/peerj.preprints.2775v1/supp-4

Molecular dynamics simulationcharts of the root mean square fluctuation (RMSF) for the Trypanosoma brucei brucei DdRpII RPB1 sub domains of the model A.

Sub-domain regions of the Trypanosoma brucei brucei DdRPII RPB1 have been separated according to conventions of Supplementary Figure 3. (A) Domain A RMSF. (B) Domain B RMSF. (C) Domain C RMSF. (D) Domain D RMSF. (E) Domain E RMSF.

DOI: 10.7287/peerj.preprints.2775v1/supp-5

Molecular dynamics simulationcharts of the root mean square deviation (RMSD) for the Trypanosoma brucei brucei DdRpII RPB1 sub domainsof the model B.

The energy (Kcal/mol) vs time (ns) plot of the 100ns simulation trajectory of the TBB DdRpII RPBI model B. Sub-domain regions of the Trypanosoma brucei brucei DdRPII RPB1 have been separated according to conventions of Supplementary Figure 3. (A) Domain A RMSD. (B) Domain B RMSD. (C) Domain C RMSD. (D) Domain D RMSD. (E) Domain E RMSD.

DOI: 10.7287/peerj.preprints.2775v1/supp-6

Molecular dynamics simulationcharts of the root mean square fluctuation (RMSF) for the Trypanosoma brucei brucei DdRpII RPB1 sub domains of the model B.

Sub-domain regions of the Trypanosoma brucei brucei DdRPII RPB1 have been separated according to conventions of Supplementary Figure 3. (A) Domain A RMSF. (B) Domain B RMSF. (C) Domain C RMSF. (D) Domain D RMSF. (E) Domain E RMSF.

DOI: 10.7287/peerj.preprints.2775v1/supp-7

DdRPII related proteins dataset

DOI: 10.7287/peerj.preprints.2775v1/supp-8

MEGA software phylogenetic tree in newick format

The tree was constructed the Neighbour – Joining statistical method for 100 bootstrap replicates and the 36 extracted samples of the DpRpII.

DOI: 10.7287/peerj.preprints.2775v1/supp-9

Supplementary Data 3: Jalview software phylogenetic tree in newick format

The tree was constructed using the average distances statistical method and the 36 extracted samples of the DpRpII.

DOI: 10.7287/peerj.preprints.2775v1/supp-10

Trypanosoma brucei brucei DdRPII RPB1 model A in .pdb format.

DOI: 10.7287/peerj.preprints.2775v1/supp-11

Trypanosoma brucei brucei DdRPII RPB1 model B in .pdb format.

DOI: 10.7287/peerj.preprints.2775v1/supp-12

Protein structure report of the template

DOI: 10.7287/peerj.preprints.2775v1/supp-13

Protein structure report of the model.

DOI: 10.7287/peerj.preprints.2775v1/supp-14

Protein structure report of the superposed models and templates

DOI: 10.7287/peerj.preprints.2775v1/supp-15

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Louis Papageorgiou conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables.

Vasileios Megalooikonomou analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Dimitrios Vlachakis conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

The raw data has been supplied as supplementary files.

Funding

The authors received no funding for this work.


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