Insights into the DNA repair process by the formamidopyrimidine-DNA glycosylase investigated by molecular dynamics

Abstract

Formamidopyrimidine-DNA glycosylase (Fpg) identifies and removes 8-oxoguanine from DNA. All of the X-ray structures of Fpg complexed to an abasic site containing DNA exhibit a common disordered region present in the C-terminal domain of the enzyme. However, this region is believed to be involved in the damaged base binding site when the initial protein/DNA complex is formed. The dynamic behavior of the disordered polypeptide (named Loop) in relation to the supposed scenario for the DNA repair mechanism was investigated by molecular dynamics on different models, derived from the X-ray structure of Lactococcus lactis Fpg bound to an abasic site analog-containing DNA and of Bacillus stearothermophilus Fpg bound to 8-oxoG. This study shows that the presence of the damaged base influences the dynamics of the whole enzyme and that the Loop location is dependent on the presence and on the conformation of the 8-oxoG in its binding site. In addition, from our results, the conformation of the 8-oxoG seems to be favored in syn in the L. lactis models, in agreement with the available X-ray structure from B. stearothermophilus Fpg and with a possible catalytic role of the flexibility of the Loop region.

Figure 1.

Hydrogen bond network between the protein residues and the 8-oxoG in (A) the oxosynin model, (B) the oxoantiin model, and (C) the bsoxo model. The mean distances over the last nanosecond dynamics are indicated, with an asterisk when the standard deviation is larger than 0.5 Å. Distances in square brackets refer to values in the corresponding crystal structures; distances in parentheses refer to the distances in the starting models. All distances are given in Angstroms.

Figure 1.

Hydrogen bond network between the protein residues and the 8-oxoG in (A) the oxosynin model, (B) the oxoantiin model, and (C) the bsoxo model. The mean distances over the last nanosecond dynamics are indicated, with an asterisk when the standard deviation is larger than 0.5 Å. Distances in square brackets refer to values in the corresponding crystal structures; distances in parentheses refer to the distances in the starting models. All distances are given in Angstroms.

Figure 2.

Distance between the nitrogen atom of Pro 2_bs and the C₁′ atom of the 8-oxoG in bsoxo and the corresponding distance between the nitrogen atom of Gly 1 and the C₁′ atom of the 8-oxoG in oxosynin, oxosynout, and oxoantiin during the last nanosecond dynamics. The distance and the time are given in Angstroms and in nanoseconds, respectively.

Figure 3.

Rmsd of the backbone atoms within the Loop for all models, calculated along the whole trajectory with respect to the starting X-ray model structure for L. lactis-derived models (oxosynin in cyan, oxosynout in yellow, oxoantiin in red, freein in purple, and freeout in magenta) and bsoxo (in green). The rmsd and the time are given in Angstroms and in nanoseconds, respectively.

Figure 4.

Covariance matrices for the fluctuations of the C_α atoms in the models bsoxo, oxosynout, freeout, oxosynin, freein, and oxoantiin. For clarity, the oxo-correlated values with the rest of the protein are amplified and shown in region 273–283 for bsoxo and 271–281 for oxosynout, oxosynin, and oxoantiin. The correlation goes from −1 to 1 from blue to red.

Figure 5.

Covariance for the 8-oxoG with the protein residues for models bsoxo, oxosynout, and oxoantiin.

Figure 6.

Superposition of the averaged structures over the last nanosecond dynamics for bsoxo (in green), oxoantiin (in red), oxosynin (in cyan), and oxosynout (in yellow).