Journal:

Article Title: Structural insights by molecular dynamics simulations into differential repair efficiency for ethano-A versus etheno-A adducts by the human alkylpurine-DNA N -glycosylase

doi:

Figure Lengend Snippet: (A) Chemical structures of the εA and ΕA adducts. (B) The APNG active site structure showing the stacking between εA and aromatic side chains of Tyr127, His136 and Tyr157. The black dashed lines show hydrogen bonds between εA N9 and His136 N, Tyr157 O4 and His136 Nπ and εA OP1 and His136 Nτ. The picture was generated using the atomic coordinates of the crystallized εA-DNA/APNG complex [PDB ID code 1f4r (11)].

Article Snippet: To generate the ΕA-DNA/APNG complex, εA was replaced by the geometry optimized ΕA adduct, using Insight II (Biosym/MSI, San Diego, CA).

Techniques: Generated

Journal:

Article Title: Structural insights by molecular dynamics simulations into differential repair efficiency for ethano-A versus etheno-A adducts by the human alkylpurine-DNA N -glycosylase

doi:

Figure Lengend Snippet: (Left) Protein-dependent cleavage of a 25mer oligonucleotide containing either ΕA or εA by human APNG protein. Increasing amounts of APNG protein (0.3–4.8 ng for ΕA and 0.01–0.15 ng for εA) were incubated with 2 nM 32P-end-labeled oligomer substrates for 30 min at 37°C. The AP site produced by DNA glycosylase action was further cleaved by adding HAP1 (5 ng), a 5′ AP endonuclease, to the reaction mixture. Note that the use of HAP1 alone had no detectable effect on either ΕA- or εA-containing templates. (Right) Time-dependent cleavage of a 25mer oligonucleotide containing either ΕA or εA. Oligomer duplexes were reacted with 3 (for EA) or 0.15 ng (for εA) APNG protein for varying times at 37°C. The scanning data were normalized as nM oligomer substrate cleaved per ng APNG protein. (Inset) Detailed time-dependent response of EA excision by APNG.

Article Snippet: To generate the ΕA-DNA/APNG complex, εA was replaced by the geometry optimized ΕA adduct, using Insight II (Biosym/MSI, San Diego, CA).

Techniques: Incubation, Labeling, Produced

Journal:

Article Title: Structural insights by molecular dynamics simulations into differential repair efficiency for ethano-A versus etheno-A adducts by the human alkylpurine-DNA N -glycosylase

doi:

Figure Lengend Snippet: Time dependence of RMS deviations (RMSD) of the εA-DNA/APNG (A) and ΕA-DNA/APNG complexes (B). Black, complex (DNA + enzyme); blue, enzyme alone; green, DNA alone; red, active site. The conformational families produced by molecular dynamics simulation for the εA-DNA/APNG and ΕA-DNA/APNG complexes deviate minimally from the crystal coordinates. High RMSD fluctuations for the DNA duplex (green traces) can be explained by the contribution of the more flexible ends. (C) The RMSD values for the εA (blue) and ΕA (gray) adducts.

Article Snippet: To generate the ΕA-DNA/APNG complex, εA was replaced by the geometry optimized ΕA adduct, using Insight II (Biosym/MSI, San Diego, CA).

Techniques: Produced

Journal:

Article Title: Structural insights by molecular dynamics simulations into differential repair efficiency for ethano-A versus etheno-A adducts by the human alkylpurine-DNA N -glycosylase

doi:

Figure Lengend Snippet: Superimposition of the εA-DNA/APNG active site from the crystal structure (green) (PDB code 1b4r) over the εA-DNA/APNG active site produced by 2 ns molecular dynamics simulation (red). The RMSD between active site conformations is <0.91 Å. The yellow dashed lines indicate the key hydrogen bond between the εA adduct and main chain amide of His136 and two hydrogen bonds which stabilize the position of the His136 side chain. All three hydrogen bonds remained intact during molecular dynamics simulation.

Article Snippet: To generate the ΕA-DNA/APNG complex, εA was replaced by the geometry optimized ΕA adduct, using Insight II (Biosym/MSI, San Diego, CA).

Techniques: Produced

Journal:

Article Title: Structural insights by molecular dynamics simulations into differential repair efficiency for ethano-A versus etheno-A adducts by the human alkylpurine-DNA N -glycosylase

doi:

Figure Lengend Snippet: APNG active site structure for the εA-DNA/APNG (blue) and ΕA-DNA/APNG (yellow) complexes produced by molecular dynamics simulations. The green dashed lines indicate hydrogen bonds between εA N9 and His136 NH in the APNG/εA-DNA complex and ΕA N9 and His136 NH in the APNG/ΕA complex. The steric clash between the ΕA exocyclic ring and His136 side chain (indicated by red arrow) resulted in reduced stacking interactions (edge-to-edge packing between ΕA and His136) and destabilized the position of the ethano adduct in the enzyme active site.

Article Snippet: To generate the ΕA-DNA/APNG complex, εA was replaced by the geometry optimized ΕA adduct, using Insight II (Biosym/MSI, San Diego, CA).

Techniques: Produced

Journal:

Article Title: Structural insights by molecular dynamics simulations into differential repair efficiency for ethano-A versus etheno-A adducts by the human alkylpurine-DNA N -glycosylase

doi:

Figure Lengend Snippet: Evolution over time of the three hydrogen bond distances in the APNG binding pocket for the εA- (green) and ΕA-containing (blue) DNA/APNG complexes. The εA N9–His136 NH and ΕA N9–His136 NH hydrogen bonds remained intact during the entire simulation.

Article Snippet: To generate the ΕA-DNA/APNG complex, εA was replaced by the geometry optimized ΕA adduct, using Insight II (Biosym/MSI, San Diego, CA).

Techniques: Binding Assay

Journal: BMC Bioinformatics

Article Title: Investigating heterogeneous protein annotations toward cross-corpora utilization

doi: 10.1186/1471-2105-10-403

Figure Lengend Snippet: Experimental results of the GENIA subcategory annotations plus AIMed and GENETAG, respectively

Article Snippet: 4 , GENETAG+ DNA , Exact , 69.82 , 36.44 , 47.89.

Techniques: