DOI: 10.1002/pro.5560030706. Interaction of the DNA‐binding domain of <i>Drosophila</i> heat shock factor with its cognate DNA site: A thermodynamic analysis using analytical ultracentrifugation

Interaction of the DNA‐binding domain of Drosophila heat shock factor with its cognate DNA site: A thermodynamic analysis using analytical ultracentrifugation

10.1002/pro.5560030706

Crossref journal-article

Wiley

Protein Science (311)

Abstract

AbstractHeat shock transcription factor (HSF) mediates the activation of heat shock genes by binding to its cognate sites with high affinity and specificity. The high‐affinity binding of HSF is dependent on the formation of an HSF homotrimer, which interacts specifically with the heat shock response element (HSE), comprised of 3 inverted repeats of the 5‐bp sequence NGAAN. In order to investigate the thermodynamic basis of the interaction between HSF and HSE, we have overexpressed and purified a polypeptide (dHSF(33–163)) encompassing only the DNA‐binding domain of HSF from Drosophila and analyzed its binding to DNA by equilibrium analytical ultracentrifugation using a multiwavelength scan technique. We demonstrate that dHSF(33–163) can bind as a monomer with 1:1 stoichiometry to a synthetic 13‐bp DNA containing a single NGAAN sequence. The values of the thermodynamic parameters obtained from the temperature dependence of the equilibrium binding constants indicate that the changes of free energy for the binding of dHSF(33–163) to the wild‐type site and a mutant DNA site are predominantly characterized by substantial negative changes of enthalpy. Binding to the wild‐type DNA is characterized by a significant positive change of entropy, whereas binding to the mutant DNA is distinguished by a negative change of entropy of comparable magnitude. The binding to the mutant DNA was also highly sensitive to increasing salt concentrations, indicating a dominance of ionic interactions. The sequence‐specific, 1:1 binding of dHSF(33–163) to the NGAAN sequence provides a basis for the analysis of higher order interactions between HSF trimers and the HSE.

Bibliography

Kim, S., Tsukiyama, T., Lewis, M. S., & Wu, C. (1994). Interaction of the DNAâbinding domain of Drosophila heat shock factor with its cognate DNA site: A thermodynamic analysis using analytical ultracentrifugation. Protein Science, 3(7), 1040â1051. Portico.

Authors 4

Soon‐Jong Kim (first)
Toshio Tsukiyama (additional)
Marc S. Lewis (additional)
Carl Wu (additional)

References 40 Referenced 41

10.1126/science.3187531
10.1002/bip.1972.360110410
10.1016/0968-0004(88)90085-0
10.1126/science.1411504
10.1038/364412a0
10.1039/tf9666200539
10.1016/0092-8674(90)90511-C
{'key': 'e_1_2_1_9_1', 'first-page': '46', 'volume-title': 'Thermodynamic data for biochemistry and biotechnology.', 'author': 'Durchschlag H', 'year': '1986'} / Thermodynamic data for biochemistry and biotechnology. by Durchschlag H (1986)
10.1093/nar/22.2.167
10.1016/0003-2697(89)90602-7
10.1016/0022-2836(89)90608-6
10.1126/science.8284672
10.1021/bi00079a029
{'key': 'e_1_2_1_15_1', 'first-page': '11716', 'article-title': 'Ultracentrifugal analysis of a mixed association', 'volume': '30', 'author': 'Lewis MS', 'year': '1991', 'journal-title': 'Biochemistry'} / Biochemistry / Ultracentrifugal analysis of a mixed association by Lewis MS (1991)
{'key': 'e_1_2_1_16_1', 'volume-title': 'Modern analytical ultracentrifugation: Acquisition and interpretation of data for biological and synthetic polymer systems.', 'author': 'Lewis MS', 'year': '1994'} / Modern analytical ultracentrifugation: Acquisition and interpretation of data for biological and synthetic polymer systems. by Lewis MS (1994)
10.1016/0092-8674(93)90286-Y
{'key': 'e_1_2_1_18_1', 'first-page': '411', 'volume-title': 'Stress proteins in biology and medicine.', 'author': 'Lis JT', 'year': '1990'} / Stress proteins in biology and medicine. by Lis JT (1990)
10.1021/bi00231a019
10.1021/bi00070a015
10.1021/bi00152a033
10.1021/bi00163a042
10.1016/0092-8674(89)90603-X
10.1016/0022-2836(74)90188-0
10.1016/0076-6879(89)80108-9
10.1073/pnas.88.16.6906
10.1017/S003358350000202X
10.1016/0076-6879(91)08018-D
{'key': 'e_1_2_1_29_1', 'first-page': '121', 'volume-title': 'Plant promoters and transcription factors.', 'author': 'Scharf KD', 'year': '1993'} / Plant promoters and transcription factors. by Scharf KD (1993)
10.1016/0092-8674(89)90604-1
10.1073/pnas.86.21.8382
10.1126/science.8303294
{'key': 'e_1_2_1_33_1', 'first-page': '138', 'volume-title': 'Introduction to applied mathematics.', 'author': 'Strang G', 'year': '1986'} / Introduction to applied mathematics. by Strang G (1986)
10.1016/0092-8674(85)90110-2
10.1038/367525a0
10.1021/bi00167a002
10.1038/353822a0
10.1128/MCB.13.6.3481
10.1126/science.3685975
10.1126/science.3125608
10.1016/0092-8674(91)90242-Q

Dates

Type	When
Created	16 years, 6 months ago (Feb. 9, 2009, 8:43 p.m.)
Deposited	1 year, 10 months ago (Oct. 23, 2023, 7:17 p.m.)
Indexed	2 weeks, 5 days ago (Aug. 7, 2025, 4:24 p.m.)
Issued	31 years, 1 month ago (July 1, 1994)
Published	31 years, 1 month ago (July 1, 1994)
Published Online	16 years, 7 months ago (Dec. 31, 2008)
Published Print	31 years, 1 month ago (July 1, 1994)

Funders 0

None

BibTeX

@article{Kim_1994, title={Interaction of the DNA‐binding domain of Drosophila heat shock factor with its cognate DNA site: A thermodynamic analysis using analytical ultracentrifugation}, volume={3}, ISSN={1469-896X}, url={http://dx.doi.org/10.1002/pro.5560030706}, DOI={10.1002/pro.5560030706}, number={7}, journal={Protein Science}, publisher={Wiley}, author={Kim, Soon‐Jong and Tsukiyama, Toshio and Lewis, Marc S. and Wu, Carl}, year={1994}, month=jul, pages={1040–1051} }

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