Optimal and variant metal-ion routes in DNA polymerase β's conformational pathways

Yunlang Li, Bret D. Freudenthal, William A. Beard, Samuel H. Wilson, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

To interpret recent structures of the R283K mutant of human DNA repair enzyme DNA polymerase β (pol β) differing in the number of Mg 2+ ions, we apply transition path sampling (TPS) to assess the effect of differing ion placement on the transition from the open one-metal to the closed two-metal state. We find that the closing pathway depends on the initial ion position, both in terms of the individual transition states and associated energies. The energy barrier of the conformational pathway varies from 25 to 58 kJ/mol, compared to the conformational energy barrier of 42 kJ/mol for the wild-type pol β reported previously. Moreover, we find a preferred ion route located in the center of the enzyme, parallel to the DNA. Within this route, the conformational pathway is similar to that of the overall open to closed transition of pol β, but outside it, especially when the ion starts near active site residues Arg258 and Asp190, the conformational pathway diverges significantly. Our findings should apply generally to pol β, since R283K is relatively far from the active site; further experimental and computational work are required to confirm this. Our studies also underscore the common feature that less active mutants have less stable closed states than their open states, in marked contrast to the wild-type enzyme, where the closed state is significantly more stable than the open form.

Original languageEnglish (US)
Pages (from-to)3630-3639
Number of pages10
JournalJournal of the American Chemical Society
Volume136
Issue number9
DOIs
StatePublished - Mar 5 2014

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DNA-Directed DNA Polymerase
Metal ions
DNA
Metals
Ions
Energy barriers
Catalytic Domain
Enzymes
DNA Repair Enzymes
Sampling

ASJC Scopus subject areas

  • Chemistry(all)
  • Catalysis
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

Optimal and variant metal-ion routes in DNA polymerase β's conformational pathways. / Li, Yunlang; Freudenthal, Bret D.; Beard, William A.; Wilson, Samuel H.; Schlick, Tamar.

In: Journal of the American Chemical Society, Vol. 136, No. 9, 05.03.2014, p. 3630-3639.

Research output: Contribution to journalArticle

Li, Yunlang ; Freudenthal, Bret D. ; Beard, William A. ; Wilson, Samuel H. ; Schlick, Tamar. / Optimal and variant metal-ion routes in DNA polymerase β's conformational pathways. In: Journal of the American Chemical Society. 2014 ; Vol. 136, No. 9. pp. 3630-3639.
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