DNA Polymerase λ Active Site Favors a Mutagenic Mispair between the Enol Form of Deoxyguanosine Triphosphate Substrate and the Keto Form of Thymidine Template : A Free Energy Perturbation Study
Maximoff, Sergey N ; Kamerlin, Shina Caroline Lynn LU
and Florián, Jan
(2017)
In The Journal of Physical Chemistry Part B
121(33).
p.7813-7822
- Abstract
Human DNA polymerase λ is an intermediate fidelity member of the X family, which plays a role in DNA repair. Recent X-ray diffraction structures of a ternary complex of a loop-deletion mutant of polymerase λ, a deoxyguanosine triphosphate analogue, and a gapped DNA show that guanine and thymine form a mutagenic mispair with an unexpected Watson-Crick-like geometry rather than a wobble geometry. Hence, there is an intriguing possibility that either thymine in the DNA or guanine in the deoxyguanosine triphosphate analogue may spend a substantial fraction of time in a deprotonated or enol form (both are minor species in aqueous solution) in the active site of the polymerase λ mutant. The experiments do not determine particular forms of the... (More)
Human DNA polymerase λ is an intermediate fidelity member of the X family, which plays a role in DNA repair. Recent X-ray diffraction structures of a ternary complex of a loop-deletion mutant of polymerase λ, a deoxyguanosine triphosphate analogue, and a gapped DNA show that guanine and thymine form a mutagenic mispair with an unexpected Watson-Crick-like geometry rather than a wobble geometry. Hence, there is an intriguing possibility that either thymine in the DNA or guanine in the deoxyguanosine triphosphate analogue may spend a substantial fraction of time in a deprotonated or enol form (both are minor species in aqueous solution) in the active site of the polymerase λ mutant. The experiments do not determine particular forms of the nucleobases that contribute to this mutagenic mispair. Thus, we investigate the thermodynamics of formation of various mispairs between guanine and thymine in the ternary complex at a neutral pH using classical molecular dynamics simulations and the free energy perturbation method. Our free energy calculations, as well as a comparison of the experimental and computed structures of mispairs, indicate that the Watson-Crick-like mispair between the enol tautomer of guanine and the keto tautomer of thymine is dominant. The wobble mispair between the keto forms of guanine and thymine and the Watson-Crick-like mispair between the keto tautomer of guanine and the enol tautomer of thymine are less prevalent, and mispairs that involve deprotonated guanine or thymine are thermodynamically unlikely. These findings are consistent with the experiment and relevant for understanding mechanisms of spontaneous mutagenesis.
(Less)
- author
- Maximoff, Sergey N
; Kamerlin, Shina Caroline Lynn
LU
and Florián, Jan
- publishing date
- 2017-08-24
- type
- Contribution to journal
- publication status
- published
- keywords
- Catalytic Domain, DNA Polymerase III/chemistry, Deoxyguanine Nucleotides/chemistry, Humans, Hydrogen-Ion Concentration, Molecular Dynamics Simulation, Substrate Specificity, Thermodynamics, Thymidine/chemistry
- in
- The Journal of Physical Chemistry Part B
- volume
- 121
- issue
- 33
- pages
- 10 pages
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- scopus:85028306847
- pmid:28732447
- ISSN
- 1520-5207
- DOI
- 10.1021/acs.jpcb.7b04874
- language
- English
- LU publication?
- no
- id
- 477843d1-5bd0-4047-a23a-a2beb9455843
- date added to LUP
- 2025-01-11 21:23:17
- date last changed
- 2025-01-18 03:18:30
@article{477843d1-5bd0-4047-a23a-a2beb9455843,
abstract = {{<p>Human DNA polymerase λ is an intermediate fidelity member of the X family, which plays a role in DNA repair. Recent X-ray diffraction structures of a ternary complex of a loop-deletion mutant of polymerase λ, a deoxyguanosine triphosphate analogue, and a gapped DNA show that guanine and thymine form a mutagenic mispair with an unexpected Watson-Crick-like geometry rather than a wobble geometry. Hence, there is an intriguing possibility that either thymine in the DNA or guanine in the deoxyguanosine triphosphate analogue may spend a substantial fraction of time in a deprotonated or enol form (both are minor species in aqueous solution) in the active site of the polymerase λ mutant. The experiments do not determine particular forms of the nucleobases that contribute to this mutagenic mispair. Thus, we investigate the thermodynamics of formation of various mispairs between guanine and thymine in the ternary complex at a neutral pH using classical molecular dynamics simulations and the free energy perturbation method. Our free energy calculations, as well as a comparison of the experimental and computed structures of mispairs, indicate that the Watson-Crick-like mispair between the enol tautomer of guanine and the keto tautomer of thymine is dominant. The wobble mispair between the keto forms of guanine and thymine and the Watson-Crick-like mispair between the keto tautomer of guanine and the enol tautomer of thymine are less prevalent, and mispairs that involve deprotonated guanine or thymine are thermodynamically unlikely. These findings are consistent with the experiment and relevant for understanding mechanisms of spontaneous mutagenesis.</p>}},
author = {{Maximoff, Sergey N and Kamerlin, Shina Caroline Lynn and Florián, Jan}},
issn = {{1520-5207}},
keywords = {{Catalytic Domain; DNA Polymerase III/chemistry; Deoxyguanine Nucleotides/chemistry; Humans; Hydrogen-Ion Concentration; Molecular Dynamics Simulation; Substrate Specificity; Thermodynamics; Thymidine/chemistry}},
language = {{eng}},
month = {{08}},
number = {{33}},
pages = {{7813--7822}},
publisher = {{The American Chemical Society (ACS)}},
series = {{The Journal of Physical Chemistry Part B}},
title = {{DNA Polymerase λ Active Site Favors a Mutagenic Mispair between the Enol Form of Deoxyguanosine Triphosphate Substrate and the Keto Form of Thymidine Template : A Free Energy Perturbation Study}},
url = {{http://dx.doi.org/10.1021/acs.jpcb.7b04874}},
doi = {{10.1021/acs.jpcb.7b04874}},
volume = {{121}},
year = {{2017}},
}