Energetics of the specific binding interaction of the first three zinc fingers of the transcription factor TFIIIA with its cognate DNA sequence

Irene Luque, Ernesto I Freire

Research output: Contribution to journalArticle

Abstract

The energetics of the specific interaction of a protein fragment (zf1-3) containing the three N-terminal zinc fingers of the Xenopus laevis transcription factor TFIIIA with its cognate DNA sequence, contained in a 15 bp DNA duplex were studied using isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC) and fluorescence titration. The use of both ITC and DSC is necessary to provide values for the thermodynamic parameters that have been corrected for thermal fluctuations of the interacting molecules. In the temperature range from 13°C to 45°C (where all the binding reaction components are folded), formation of the complex is enthalpically driven with a negative heat capacity effect (ΔC(p)). In this respect, the binding reaction of zf1-3 is similar to those of other proteins that bind in the major groove of DNA. It is dissimilar to the association reactions of proteins, however, that bind in the minor groove of DNA and that are driven by a dominating entropy factor. Comparison of the experimental values of ΔH(ass) and ΔC(p) with expected values of these parameters, calculated from the burial of polar and nonpolar molecular surfaces, indicates that the polar groups at the protein/DNA interface are not completely dehydrated upon formation of the complex. It also seems that the expected large positive entropy of dehydration upon forming the zf1-3/DNA complex (~1900 J · K-1 · mol-1) cannot be balanced by the reduction in translational/rotational and configurational freedom of the protein to the level of the observed entropy of binding (38 J · K-1 · mol-1). It is suggested that the additional negative entropy contribution comes from a damping of torsional motions in the DNA duplex. (C) 2000 Wiley-Liss, Inc.

Original languageEnglish (US)
Pages (from-to)50-62
Number of pages13
JournalProteins
Volume41
Issue numberSUPPL. 4
DOIs
StatePublished - 2000

Fingerprint

Transcription Factor TFIIIA
DNA sequences
Zinc Fingers
Zinc
Entropy
DNA
Titration
Calorimetry
Differential Scanning Calorimetry
Proteins
Differential scanning calorimetry
Hot Temperature
Burial
Equidae
Xenopus laevis
Dehydration
Thermodynamics
Specific heat
Damping
Fluorescence

Keywords

  • Calorimetry
  • Dehydration
  • Enthalpically driven
  • Isothermal titration calorimetry
  • Major groove
  • Negative heat capacity
  • Protein-DNA association

ASJC Scopus subject areas

  • Genetics
  • Structural Biology
  • Biochemistry

Cite this

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title = "Energetics of the specific binding interaction of the first three zinc fingers of the transcription factor TFIIIA with its cognate DNA sequence",
abstract = "The energetics of the specific interaction of a protein fragment (zf1-3) containing the three N-terminal zinc fingers of the Xenopus laevis transcription factor TFIIIA with its cognate DNA sequence, contained in a 15 bp DNA duplex were studied using isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC) and fluorescence titration. The use of both ITC and DSC is necessary to provide values for the thermodynamic parameters that have been corrected for thermal fluctuations of the interacting molecules. In the temperature range from 13°C to 45°C (where all the binding reaction components are folded), formation of the complex is enthalpically driven with a negative heat capacity effect (ΔC(p)). In this respect, the binding reaction of zf1-3 is similar to those of other proteins that bind in the major groove of DNA. It is dissimilar to the association reactions of proteins, however, that bind in the minor groove of DNA and that are driven by a dominating entropy factor. Comparison of the experimental values of ΔH(ass) and ΔC(p) with expected values of these parameters, calculated from the burial of polar and nonpolar molecular surfaces, indicates that the polar groups at the protein/DNA interface are not completely dehydrated upon formation of the complex. It also seems that the expected large positive entropy of dehydration upon forming the zf1-3/DNA complex (~1900 J · K-1 · mol-1) cannot be balanced by the reduction in translational/rotational and configurational freedom of the protein to the level of the observed entropy of binding (38 J · K-1 · mol-1). It is suggested that the additional negative entropy contribution comes from a damping of torsional motions in the DNA duplex. (C) 2000 Wiley-Liss, Inc.",
keywords = "Calorimetry, Dehydration, Enthalpically driven, Isothermal titration calorimetry, Major groove, Negative heat capacity, Protein-DNA association",
author = "Irene Luque and Freire, {Ernesto I}",
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TY - JOUR

T1 - Energetics of the specific binding interaction of the first three zinc fingers of the transcription factor TFIIIA with its cognate DNA sequence

AU - Luque, Irene

AU - Freire, Ernesto I

PY - 2000

Y1 - 2000

N2 - The energetics of the specific interaction of a protein fragment (zf1-3) containing the three N-terminal zinc fingers of the Xenopus laevis transcription factor TFIIIA with its cognate DNA sequence, contained in a 15 bp DNA duplex were studied using isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC) and fluorescence titration. The use of both ITC and DSC is necessary to provide values for the thermodynamic parameters that have been corrected for thermal fluctuations of the interacting molecules. In the temperature range from 13°C to 45°C (where all the binding reaction components are folded), formation of the complex is enthalpically driven with a negative heat capacity effect (ΔC(p)). In this respect, the binding reaction of zf1-3 is similar to those of other proteins that bind in the major groove of DNA. It is dissimilar to the association reactions of proteins, however, that bind in the minor groove of DNA and that are driven by a dominating entropy factor. Comparison of the experimental values of ΔH(ass) and ΔC(p) with expected values of these parameters, calculated from the burial of polar and nonpolar molecular surfaces, indicates that the polar groups at the protein/DNA interface are not completely dehydrated upon formation of the complex. It also seems that the expected large positive entropy of dehydration upon forming the zf1-3/DNA complex (~1900 J · K-1 · mol-1) cannot be balanced by the reduction in translational/rotational and configurational freedom of the protein to the level of the observed entropy of binding (38 J · K-1 · mol-1). It is suggested that the additional negative entropy contribution comes from a damping of torsional motions in the DNA duplex. (C) 2000 Wiley-Liss, Inc.

AB - The energetics of the specific interaction of a protein fragment (zf1-3) containing the three N-terminal zinc fingers of the Xenopus laevis transcription factor TFIIIA with its cognate DNA sequence, contained in a 15 bp DNA duplex were studied using isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC) and fluorescence titration. The use of both ITC and DSC is necessary to provide values for the thermodynamic parameters that have been corrected for thermal fluctuations of the interacting molecules. In the temperature range from 13°C to 45°C (where all the binding reaction components are folded), formation of the complex is enthalpically driven with a negative heat capacity effect (ΔC(p)). In this respect, the binding reaction of zf1-3 is similar to those of other proteins that bind in the major groove of DNA. It is dissimilar to the association reactions of proteins, however, that bind in the minor groove of DNA and that are driven by a dominating entropy factor. Comparison of the experimental values of ΔH(ass) and ΔC(p) with expected values of these parameters, calculated from the burial of polar and nonpolar molecular surfaces, indicates that the polar groups at the protein/DNA interface are not completely dehydrated upon formation of the complex. It also seems that the expected large positive entropy of dehydration upon forming the zf1-3/DNA complex (~1900 J · K-1 · mol-1) cannot be balanced by the reduction in translational/rotational and configurational freedom of the protein to the level of the observed entropy of binding (38 J · K-1 · mol-1). It is suggested that the additional negative entropy contribution comes from a damping of torsional motions in the DNA duplex. (C) 2000 Wiley-Liss, Inc.

KW - Calorimetry

KW - Dehydration

KW - Enthalpically driven

KW - Isothermal titration calorimetry

KW - Major groove

KW - Negative heat capacity

KW - Protein-DNA association

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DO - 10.1002/1097-0134(2000)41:4+<50::AID-PROT50>3.0.CO;2-H

M3 - Article

VL - 41

SP - 50

EP - 62

JO - Proteins: Structure, Function and Genetics

JF - Proteins: Structure, Function and Genetics

SN - 0887-3585

IS - SUPPL. 4

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