Simulations of DNA pol λ R517 mutants indicate 517's crucial role in ternary complex stability and suggest DNA slippage origin

Meredith C. Foley, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

Unlike some other DNA polymerases, DNA polymerase λ (pol λ) utilizes DNA motion and active-site protein residue rearrangements rather than large-scale protein subdomain changes to transition between its active and inactive states. Pol λ also has an unusual error tendency to generate single-base deletions (also known as frameshift mutations) resulting from DNA template-strand slippage. An understanding of these features requires an atomic-level link between the various structures and motions involved and observed in biochemical functions. Our simulations of pol λ ternary complexes of various 517 mutants (Lys, Glu, His, Met, and Gln) reveal discrete orientations of the 517 residue with respect to the DNA and associated interactions (mainly electrostatic) that explain the wide range (∼3-8 Å) of mutant-dependent DNA motion observed (Figure 2 of manuscript): (wild-type < [R517K ∼ R517H ∼ R517Q] < [R517E ∼ R517A ∼ R517M]). This motion critically impacts stability of the ternary complex and hence drives/hampers the enzyme's catalytic cycle. In addition to pinpointing a trend for interpreting associated frameshift error rates based on template-strand stability, the close connection between DNA movement and active-site protein residue changes suggests that pol λ's unique architecture facilitates frameshift errors because small variations in the active-site environment (e.g., orientation of 517) can have large effects on the dynamics of the ternary pol λ complex.

Original languageEnglish (US)
Pages (from-to)3967-3977
Number of pages11
JournalJournal of the American Chemical Society
Volume130
Issue number12
DOIs
StatePublished - Mar 26 2008

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DNA-Directed DNA Polymerase
DNA
Catalytic Domain
Proteins
Frameshift Mutation
Manuscripts
Coulomb interactions
Static Electricity
Enzymes

ASJC Scopus subject areas

  • Chemistry(all)

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Simulations of DNA pol λ R517 mutants indicate 517's crucial role in ternary complex stability and suggest DNA slippage origin. / Foley, Meredith C.; Schlick, Tamar.

In: Journal of the American Chemical Society, Vol. 130, No. 12, 26.03.2008, p. 3967-3977.

Research output: Contribution to journalArticle

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abstract = "Unlike some other DNA polymerases, DNA polymerase λ (pol λ) utilizes DNA motion and active-site protein residue rearrangements rather than large-scale protein subdomain changes to transition between its active and inactive states. Pol λ also has an unusual error tendency to generate single-base deletions (also known as frameshift mutations) resulting from DNA template-strand slippage. An understanding of these features requires an atomic-level link between the various structures and motions involved and observed in biochemical functions. Our simulations of pol λ ternary complexes of various 517 mutants (Lys, Glu, His, Met, and Gln) reveal discrete orientations of the 517 residue with respect to the DNA and associated interactions (mainly electrostatic) that explain the wide range (∼3-8 {\AA}) of mutant-dependent DNA motion observed (Figure 2 of manuscript): (wild-type < [R517K ∼ R517H ∼ R517Q] < [R517E ∼ R517A ∼ R517M]). This motion critically impacts stability of the ternary complex and hence drives/hampers the enzyme's catalytic cycle. In addition to pinpointing a trend for interpreting associated frameshift error rates based on template-strand stability, the close connection between DNA movement and active-site protein residue changes suggests that pol λ's unique architecture facilitates frameshift errors because small variations in the active-site environment (e.g., orientation of 517) can have large effects on the dynamics of the ternary pol λ complex.",
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