Additional file 1: Figure S1. of Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase
Creators: name: Popov, Alexander
name: Endutkin, Anton
name: Vorobjev, Yuri
name: Zharkov, Dmitry
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: FOS: Computer and information sciences
subject: Cancer
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Plant Biology
subject: Virology

description: A, R.m.s.d. of the models over time. The traces are color-coded: dark cyan, PRN-GLH-C; light lime, PRN-GLH-Aa; coral, PRN-GLH-As; olive, PRN-GLU-C; dark magenta, PRN-GLU-Aa; light blue, PRN-GLU-As; magenta, PRO-GLH-C; blue, PRO-GLH-Aa; red, PRO-GLH-As; cyan, PRO-GLU-C; yellow, PRO-GLU-Aa; green, PRO-GLU-As. B, Reproducibility of the repeat runs. R.m.s.d. of the initial run (red) and three repeat runs (green, blue, and magenta) of the PRO-GLH-C model are shown together with the cross-run r.m.s.d. between two pairs of the repeat runs (black and green). Repeat runs of other models produced similar within-run and cross-run r.m.s.d. values and are not shown. Figure S2. Circular dichroism spectrum of Fpg at pH 4.0 (black circles) and pH 7.6 (white circles). Figure S3. Conformation of the models around the orphaned nucleotide. A, distance Nε[Arg109]…O2[C(0)] in the C models. B, distance Nη2[Arg109]…N3[C(0)] in the C models. C, distance N6[A(0)]…O2P[A(+1)] in the Aa models. D, distance Nη2[Arg109]…N7[A(0)] in the As models. E, distance N6[A(0)]…O4[T+1] in the As models. F, distance N6[A(0)]…O2P[A(+2)] in the As models. Moving average of a 50-snapshot window is shown in all panels. Figure S4. Occluded area (inaccessible to a 1.4 Å probe) between Phe111 side chain and A(+1) base. The colors of the traces are the same as in Fig. S1. The dashed line indicates the occluded area in the 1XC8 structure. Moving average of a 50-snapshot window is shown. Figure S5. A, Cumulative distribution of the occurrence of hydrogen bonds in the Lla-Fpg–DNA complex. B, Overall reproducibility of hydrogen bonds in replicate PRO-GLH runs. Dots show the coefficient of variation for the occurrence of a particular hydrogen bond calculated over four replicates plotted against the mean occurrence of the bond. The histograms show the distribution of the mean occurrence. The scale in all panels is the same. Numbers above the graphs indicate the percentage of hydrogen bonds with the mean occurrence &gt;90%. Figure S6. Interaction difference maps showing pairs of hydrogen-bond forming amino acids specific (&gt;3σ difference in bond occurrence calculated over all pairs of models) for: A, C models (red) or Aa models (blue); B, C models (red) or As models (cyan); C, As models (cyan) or Aa models (blue); D, PRO models (red) or PRN models (blue); E, GLH models (red) or GLU models (blue). Larger circles correspond to larger deviations from the mean occurrence. Residues 1–271, protein; 272–285, damaged DNA strand; 286–299, complementary DNA strand; 300, Zn2+; 301–307, structural water molecules. The yellow line marks the position of oxoG0, the magenta line, the position of C(0)/A(0). Figure S7. Conservation of Fpg sequence. A, plot of conservation number C n against the residue position. B, view of the PRO-GLH-C model (8 ns) colored according to C n . C, the same model as in B rotated 180° around the vertical axis. The orientation of the molecule in B and C is the same as in Fig. 8. Figure S8. Rank plot of water-mediated bridges (top 100 occurrences) in the Fpg–DNA structures (A–L, the model nature is indicated in the respective panels). Red, pairs; blue, triplets. Dashed lines indicate cutoffs of 2000 snapshots for pairs and 1500 snapshots for triplets. Insets show cumulative distribution frequencies of pairs and triplets. Figure S9. Cladogram of Fpg sequences. The tree was constructed as described in Methods and visualized using TreeDyn [81]. (PDF 3904 kb)