Journal
NUCLEIC ACIDS RESEARCH
Volume 44, Issue 2, Pages 683-694Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkv1092
Keywords
-
Categories
Funding
- National Cancer Institute [CA017395-33]
- National Science Foundation [0549370]
- Russian Science Foundation [14-24-00093]
- Russian Foundation for Basic Research [14-04-01879-a]
- NSF PetascaleComputational Resource (PRAC) Award from the National Science Foundation [OCI-1036208]
- Novosibirsk State University
- Russian Federation
- Direct For Education and Human Resources
- Division Of Graduate Education [0549370] Funding Source: National Science Foundation
- Russian Science Foundation [14-24-00093] Funding Source: Russian Science Foundation
Ask authors/readers for more resources
In contrast to proteins recognizing small-molecule ligands, DNA-dependent enzymes cannot rely solely on interactions in the substrate-binding centre to achieve their exquisite specificity. It is widely believed that substrate recognition by such enzymes involves a series of conformational changes in the enzyme-DNA complex with sequential gates favoring cognate DNA and rejecting nonsubstrates. However, direct evidence for such mechanism is limited to a few systems. We report that discrimination between the oxidative DNA lesion, 8-oxoguanine (oxoG) and its normal counterpart, guanine, by the repair enzyme, formamidopyrimidine-DNA glycosylase (Fpg), likely involves multiple gates. Fpg uses an aromatic wedge to open the Watson-Crick base pair and everts the lesion into its active site. We used molecular dynamics simulations to explore the eversion free energy landscapes of oxoG and G by Fpg, focusing on structural and energetic details of oxoG recognition. The resulting energy profiles, supported by biochemical analysis of site-directed mutants disturbing the interactions along the proposed path, show that Fpg selectively facilitates eversion of oxoG by stabilizing several intermediate states, helping the rapidly sliding enzyme avoid full extrusion of every encountered base for interrogation. Lesion recognition through multiple gating intermediates may be a common theme in DNA repair enzymes.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available