Tags

Type your tag names separated by a space and hit enter

Thermodynamics of DNA binding and distortion by the hyperthermophile chromatin protein Sac7d.
J Mol Biol. 2004 Oct 15; 343(2):339-60.JM

Abstract

Sac7d is a hyperthermophile chromatin protein which binds non-specifically to the minor groove of duplex DNA and induces a sharp kink of 66 degrees with intercalation of valine and methionine side-chains. We have utilized the thermal stability of Sac7d and the lack of sequence specificity to define the thermodynamics of DNA binding over a wide temperature range. The binding affinity for poly(dGdC) was moderate at 25 degrees C (Ka = 3.5(+/-1.6) x 10(6) M(-1)) and increased by nearly an order of magnitude from 10 degrees C to 80 degrees C. The enthalpy of binding was unfavorable at 25 degrees C, and decreased linearly from 5 degrees C to 60 degrees C. A positive binding heat at 25 degrees C is attributed in part to the energy of distorting DNA, and ensures that the temperature of maximal binding affinity (75.1+/-5.6 degrees C) is near the growth temperature of Sulfolobus acidocaldarius. Truncation of the two intercalating residues to alanine led to a decreased ability to bend and unwind DNA at 25 degrees C with a small decrease in binding affinity. The energy gained from intercalation is slightly greater than the free energy penalty of bending duplex DNA. Surprisingly, reduced distortion from the double alanine substitution did not lead to a significant decrease in the heat of binding at 25 degrees C. In addition, an anomalous positive DeltaCp of binding was observed for the double alanine mutant protein which could not be explained by the change in polar and apolar accessible surface areas. Both the larger than expected binding enthalpy and the positive heat capacity can be explained by a temperature dependent structural transition in the protein-DNA complex with a Tm of 15-20 degrees C and a DeltaH of 15 kcal/mol. Data are discussed which indicate that the endothermic transition in the complex is consistent with DNA distortion.

Authors+Show Affiliations

Laboratory for Structural Biology, Graduate Program in Biotechnology Science and Engineering, Department of Chemistry, Materials Science Building, John Wright Drive University of Alabama in Huntsville, 35899, USA.No affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, P.H.S.

Language

eng

PubMed ID

15451665

Citation

Peters, William B., et al. "Thermodynamics of DNA Binding and Distortion By the Hyperthermophile Chromatin Protein Sac7d." Journal of Molecular Biology, vol. 343, no. 2, 2004, pp. 339-60.
Peters WB, Edmondson SP, Shriver JW. Thermodynamics of DNA binding and distortion by the hyperthermophile chromatin protein Sac7d. J Mol Biol. 2004;343(2):339-60.
Peters, W. B., Edmondson, S. P., & Shriver, J. W. (2004). Thermodynamics of DNA binding and distortion by the hyperthermophile chromatin protein Sac7d. Journal of Molecular Biology, 343(2), 339-60.
Peters WB, Edmondson SP, Shriver JW. Thermodynamics of DNA Binding and Distortion By the Hyperthermophile Chromatin Protein Sac7d. J Mol Biol. 2004 Oct 15;343(2):339-60. PubMed PMID: 15451665.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Thermodynamics of DNA binding and distortion by the hyperthermophile chromatin protein Sac7d. AU - Peters,William B, AU - Edmondson,Stephen P, AU - Shriver,John W, PY - 2004/07/08/received PY - 2004/08/10/revised PY - 2004/08/12/accepted PY - 2004/9/29/pubmed PY - 2004/11/16/medline PY - 2004/9/29/entrez SP - 339 EP - 60 JF - Journal of molecular biology JO - J Mol Biol VL - 343 IS - 2 N2 - Sac7d is a hyperthermophile chromatin protein which binds non-specifically to the minor groove of duplex DNA and induces a sharp kink of 66 degrees with intercalation of valine and methionine side-chains. We have utilized the thermal stability of Sac7d and the lack of sequence specificity to define the thermodynamics of DNA binding over a wide temperature range. The binding affinity for poly(dGdC) was moderate at 25 degrees C (Ka = 3.5(+/-1.6) x 10(6) M(-1)) and increased by nearly an order of magnitude from 10 degrees C to 80 degrees C. The enthalpy of binding was unfavorable at 25 degrees C, and decreased linearly from 5 degrees C to 60 degrees C. A positive binding heat at 25 degrees C is attributed in part to the energy of distorting DNA, and ensures that the temperature of maximal binding affinity (75.1+/-5.6 degrees C) is near the growth temperature of Sulfolobus acidocaldarius. Truncation of the two intercalating residues to alanine led to a decreased ability to bend and unwind DNA at 25 degrees C with a small decrease in binding affinity. The energy gained from intercalation is slightly greater than the free energy penalty of bending duplex DNA. Surprisingly, reduced distortion from the double alanine substitution did not lead to a significant decrease in the heat of binding at 25 degrees C. In addition, an anomalous positive DeltaCp of binding was observed for the double alanine mutant protein which could not be explained by the change in polar and apolar accessible surface areas. Both the larger than expected binding enthalpy and the positive heat capacity can be explained by a temperature dependent structural transition in the protein-DNA complex with a Tm of 15-20 degrees C and a DeltaH of 15 kcal/mol. Data are discussed which indicate that the endothermic transition in the complex is consistent with DNA distortion. SN - 0022-2836 UR - https://www.unboundmedicine.com/medline/citation/15451665/Thermodynamics_of_DNA_binding_and_distortion_by_the_hyperthermophile_chromatin_protein_Sac7d_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0022-2836(04)01022-8 DB - PRIME DP - Unbound Medicine ER -