Research output: Contribution to journal › Article › peer-review
Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase. / Popov, Alexander V.; Endutkin, Anton V.; Vorobjev, Yuri N. et al.
In: BMC Structural Biology, Vol. 17, No. 1, 5, 08.05.2017, p. 1-19.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase
AU - Popov, Alexander V.
AU - Endutkin, Anton V.
AU - Vorobjev, Yuri N.
AU - Zharkov, Dmitry O.
N1 - Publisher Copyright: © 2017 The Author(s).
PY - 2017/5/8
Y1 - 2017/5/8
N2 - Background: Formamidopyrimidine-DNA glycosylase (Fpg) removes abundant pre-mutagenic 8-oxoguanine (oxoG) bases from DNA through nucleophilic attack of its N-terminal proline at C1′ of the damaged nucleotide. Since oxoG efficiently pairs with both C and A, Fpg must excise oxoG from pairs with C but not with A, otherwise a mutation occurs. The crystal structures of several Fpg-DNA complexes have been solved, yet no structure with A opposite the lesion is available. Results: Here we use molecular dynamic simulation to model interactions in the pre-catalytic complex of Lactococcus lactis Fpg with DNA containing oxoG opposite C or A, the latter in either syn or anti conformation. The catalytic dyad, Pro1-Glu2, was modeled in all four possible protonation states. Only one transition was observed in the experimental reaction rate pH dependence plots, and Glu2 kept the same set of interactions regardless of its protonation state, suggesting that it does not limit the reaction rate. The adenine base opposite oxoG was highly distorting for the adjacent nucleotides: in the more stable syn models it formed non-canonical bonds with out-of-register nucleotides in both the damaged and the complementary strand, whereas in the anti models the adenine either formed non-canonical bonds or was expelled into the major groove. The side chains of Arg109 and Phe111 that Fpg inserts into DNA to maintain its kinked conformation tended to withdraw from their positions if A was opposite to the lesion. The region showing the largest differences in the dynamics between oxoG:C and oxoG:A substrates was unexpectedly remote from the active site, located near the linker joining the two domains of Fpg. This region was also highly conserved among 124 analyzed Fpg sequences. Three sites trapping water molecules through multiple bonds were identified on the protein-DNA interface, apparently helping to maintain enzyme-induced DNA distortion and participating in oxoG recognition. Conclusion: Overall, the discrimination against A opposite to the lesion seems to be due to incorrect DNA distortion around the lesion-containing base pair and, possibly, to gross movement of protein domains connected by the linker.
AB - Background: Formamidopyrimidine-DNA glycosylase (Fpg) removes abundant pre-mutagenic 8-oxoguanine (oxoG) bases from DNA through nucleophilic attack of its N-terminal proline at C1′ of the damaged nucleotide. Since oxoG efficiently pairs with both C and A, Fpg must excise oxoG from pairs with C but not with A, otherwise a mutation occurs. The crystal structures of several Fpg-DNA complexes have been solved, yet no structure with A opposite the lesion is available. Results: Here we use molecular dynamic simulation to model interactions in the pre-catalytic complex of Lactococcus lactis Fpg with DNA containing oxoG opposite C or A, the latter in either syn or anti conformation. The catalytic dyad, Pro1-Glu2, was modeled in all four possible protonation states. Only one transition was observed in the experimental reaction rate pH dependence plots, and Glu2 kept the same set of interactions regardless of its protonation state, suggesting that it does not limit the reaction rate. The adenine base opposite oxoG was highly distorting for the adjacent nucleotides: in the more stable syn models it formed non-canonical bonds with out-of-register nucleotides in both the damaged and the complementary strand, whereas in the anti models the adenine either formed non-canonical bonds or was expelled into the major groove. The side chains of Arg109 and Phe111 that Fpg inserts into DNA to maintain its kinked conformation tended to withdraw from their positions if A was opposite to the lesion. The region showing the largest differences in the dynamics between oxoG:C and oxoG:A substrates was unexpectedly remote from the active site, located near the linker joining the two domains of Fpg. This region was also highly conserved among 124 analyzed Fpg sequences. Three sites trapping water molecules through multiple bonds were identified on the protein-DNA interface, apparently helping to maintain enzyme-induced DNA distortion and participating in oxoG recognition. Conclusion: Overall, the discrimination against A opposite to the lesion seems to be due to incorrect DNA distortion around the lesion-containing base pair and, possibly, to gross movement of protein domains connected by the linker.
KW - 8-oxoguanine
KW - DNA glycosylase
KW - Fpg
KW - Molecular dynamics
KW - Opposite-base specificity
KW - Reaction mechanism
KW - Catalytic Domain
KW - Molecular Dynamics Simulation
KW - Guanine/analogs & derivatives
KW - DNA-Formamidopyrimidine Glycosylase/chemistry
KW - DNA/chemistry
KW - Base Pairing
KW - Lactococcus lactis/enzymology
KW - ESCHERICHIA-COLI FPG
KW - STRUCTURAL INSIGHTS
KW - OXIDATIVELY DAMAGED DNA
KW - REPAIR ENZYME
KW - CRYSTAL-STRUCTURE
KW - GRAPHICAL USER-INTERFACE
KW - EXCISION-REPAIR
KW - BIOMOLECULAR SIMULATIONS
KW - SUBSTRATE-SPECIFICITY
KW - SEQUENCE ALIGNMENTS
UR - http://www.scopus.com/inward/record.url?scp=85018411806&partnerID=8YFLogxK
U2 - 10.1186/s12900-017-0075-y
DO - 10.1186/s12900-017-0075-y
M3 - Article
C2 - 28482831
AN - SCOPUS:85018411806
VL - 17
SP - 1
EP - 19
JO - BMC Structural Biology
JF - BMC Structural Biology
SN - 1472-6807
IS - 1
M1 - 5
ER -
ID: 8672584