Evidence from thermodynamics that DNA photolyase recognizes a solvent-exposed CPD lesion

Thomas J. Wilson, Matthew A. Crystal, Meredith C. Rohrbaugh, Kathleen P. Sokolowsky, Yvonne Gindt

Research output: Contribution to journalArticleResearchpeer-review

8 Citations (Scopus)

Abstract

Binding of a cis,syn-cyclobutane pyrimidine dimer (CPD) to Escherichia coli DNA photolyase was examined as a function of temperature, enzyme oxidation state, salt, and substrate conformation using isothermal titration calorimetry. While the overall ΔG° of binding was relatively insensitive to most of the conditions examined, the enthalpic and entropic terms that make up the free energy of binding are sensitive to the conditions of the experiment. Substrate binding to DNA photolyase is generally driven by a negative change in enthalpy. Electrostatic interactions and protonation are affected by the oxidation state of the required FAD cofactor and substrate conformation. The fully reduced enzyme appears to bind approximately two additional water molecules as part of substrate binding. More significantly, the experimental change in heat capacity strongly suggests that the CPD lesion must be flipped out of the intrahelical base stacking prior to binding to the protein; the DNA repair enzyme appears to recognize a solvent-exposed CPD as part of its damage recognition mechanism.

Original languageEnglish
Pages (from-to)13746-13754
Number of pages9
JournalJournal of Physical Chemistry B
Volume115
Issue number46
DOIs
StatePublished - 24 Nov 2011

Fingerprint

Deoxyribodipyrimidine Photo-Lyase
Pyrimidine Dimers
cyclobutane
pyrimidines
Dimers
lesions
DNA
deoxyribonucleic acid
dimers
Thermodynamics
thermodynamics
Substrates
Conformations
enzymes
Enzymes
DNA Repair Enzymes
Oxidation
Flavin-Adenine Dinucleotide
Protonation
Calorimetry

Cite this

Wilson, Thomas J. ; Crystal, Matthew A. ; Rohrbaugh, Meredith C. ; Sokolowsky, Kathleen P. ; Gindt, Yvonne. / Evidence from thermodynamics that DNA photolyase recognizes a solvent-exposed CPD lesion. In: Journal of Physical Chemistry B. 2011 ; Vol. 115, No. 46. pp. 13746-13754.
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abstract = "Binding of a cis,syn-cyclobutane pyrimidine dimer (CPD) to Escherichia coli DNA photolyase was examined as a function of temperature, enzyme oxidation state, salt, and substrate conformation using isothermal titration calorimetry. While the overall ΔG° of binding was relatively insensitive to most of the conditions examined, the enthalpic and entropic terms that make up the free energy of binding are sensitive to the conditions of the experiment. Substrate binding to DNA photolyase is generally driven by a negative change in enthalpy. Electrostatic interactions and protonation are affected by the oxidation state of the required FAD cofactor and substrate conformation. The fully reduced enzyme appears to bind approximately two additional water molecules as part of substrate binding. More significantly, the experimental change in heat capacity strongly suggests that the CPD lesion must be flipped out of the intrahelical base stacking prior to binding to the protein; the DNA repair enzyme appears to recognize a solvent-exposed CPD as part of its damage recognition mechanism.",
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Evidence from thermodynamics that DNA photolyase recognizes a solvent-exposed CPD lesion. / Wilson, Thomas J.; Crystal, Matthew A.; Rohrbaugh, Meredith C.; Sokolowsky, Kathleen P.; Gindt, Yvonne.

In: Journal of Physical Chemistry B, Vol. 115, No. 46, 24.11.2011, p. 13746-13754.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Evidence from thermodynamics that DNA photolyase recognizes a solvent-exposed CPD lesion

AU - Wilson, Thomas J.

AU - Crystal, Matthew A.

AU - Rohrbaugh, Meredith C.

AU - Sokolowsky, Kathleen P.

AU - Gindt, Yvonne

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AB - Binding of a cis,syn-cyclobutane pyrimidine dimer (CPD) to Escherichia coli DNA photolyase was examined as a function of temperature, enzyme oxidation state, salt, and substrate conformation using isothermal titration calorimetry. While the overall ΔG° of binding was relatively insensitive to most of the conditions examined, the enthalpic and entropic terms that make up the free energy of binding are sensitive to the conditions of the experiment. Substrate binding to DNA photolyase is generally driven by a negative change in enthalpy. Electrostatic interactions and protonation are affected by the oxidation state of the required FAD cofactor and substrate conformation. The fully reduced enzyme appears to bind approximately two additional water molecules as part of substrate binding. More significantly, the experimental change in heat capacity strongly suggests that the CPD lesion must be flipped out of the intrahelical base stacking prior to binding to the protein; the DNA repair enzyme appears to recognize a solvent-exposed CPD as part of its damage recognition mechanism.

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