A Thermodynamic Basis of DNA Sequence Selectivity by the ETS Domain of Murine PU.1

Poon, Gregory M.K.; Macgregor, Robert B.

doi:10.1016/j.jmb.2003.09.046

Cited by 19DNA and Nucleic Acid ChemistryDiffusion and Search DynamicsProtein Structure and Dynamics

A Thermodynamic Basis of DNA Sequence Selectivity by the ETS Domain of Murine PU.1

Poon, Gregory M.K., Macgregor, Robert B.·2004·Journal of Molecular Biology

DOI 10.1016/j.jmb.2003.09.046

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Abstract

The ETS domain of the transcription factor PU.1 tolerates a large number of DNA cognate variants that differ exclusively in the sequences flanking a critical central consensus, 5'-GGAA-3'. We investigated the thermodynamics of site selection by the DNA-binding domain by following the PU.1 ETS/DNA equilibrium with a large set of cognate variants under various temperature and salt conditions by filter binding. Our results indicate that the stability of the ETS/DNA complex is quantitatively tied to variations in the change in heat capacity. Thermodynamic effects induced by changing Na(+) concentrations from 150 mM to 250 mM are complex and not readily interpreted by polyelectrolyte theory. We also extended our understanding of data from our previous investigation on energetic base-neighbour coupling, by dissecting the thermodynamic contributions underlying the observed free-energy coupling. In conjunction with available structural and biochemical data, we propose that site selectivity by the PU.1 ETS domain arises from differential protein/DNA contacts in the flanking sequences that modulate the orientation of the ETS recognition helix and trigger a coupled reduction in the flexibility observed in the unbound ETS domain.

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The Sequence-Specific Association of the ETS Domain of Murine PU.1 with DNA Exhibits Unusual Energetics
Poon, G. M. K., Gross, P., & Macgregor, R. B. (2002) · Biochemistry · doi:10.1021/bi015572q · Cited by 16 · see citing works
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Base Coupling in Sequence-specific Site Recognition by the ETS Domain of Murine PU.1
Poon, G. M. K., & Macgregor, R. B. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00362-0 · Cited by 29 · see citing works
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DNA Binding Regulates the Self-Association of the ETS Domain of PU.1 in a Sequence-Dependent Manner
Poon, G. M. K. (2012) · Biochemistry · doi:10.1021/bi300331v · Cited by 23 · see citing works
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Sequence Discrimination by DNA-binding Domain of ETS Family Transcription Factor PU.1 Is Linked to Specific Hydration of Protein-DNA Interface
Poon, G. M. K. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.342345 · Cited by 28 · see citing works
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Hydrational Control of ETS-Family Transcription Factors: A Possible Resolution of the “Specificity Conundrum”
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Authors: Poon, G. M. K., & Macgregor, R. B.
Affiliations: University of Toronto (CA)
Corresponding author: Macgregor, Robert B.
ORCID: Poon, Gregory M.K.
Macgregor, Robert B.
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 2004-01
Volume: 335
Issue: 1
Pages: 113-127
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1016/j.jmb.2003.09.046
OpenAlex: W2164569166
Cited by: 19
References: 46
Citations by year: 2023: 3 · 2021: 1 · 2019: 1 · 2018: 1 · 2017: 1 · 2016: 1 · 2015: 1 · 2014: 2 · 2013: 1 · 2012: 2
FWCI: 0.35
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Funders: Canadian Institutes of Health Research
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords: PU.1, ETS domain, heat capacity change, salt concentration dependence, free energy coupling, protein-DNA contacts, transcription factor-DNA binding
MeSH terms: Proto-Oncogene Protein Spi-1, Animals, Base Sequence, Binding Sites, DNA, DNA-Binding Proteins, Osmolar Concentration, Protein Binding, Proto-Oncogene Proteins, Sodium, Temperature, Thermodynamics, Transcription Factors, Trans-Activators, Protein Structure, Tertiary, Pliability, Proto-Oncogene Proteins c-ets, Mice

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A Thermodynamic Basis of DNA Sequence Selectivity by the ETS Domain of Murine PU.1

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