Specific DNA binding by the homeodomain Nkx2.5(C56S): Detection of impaired DNA or unfolded protein by isothermal titration calorimetry

Proteins: Structure, Function and Genetics

Volumn 64, Issue 1, 2006, Pages 13-18

  Fodor, Elfrieda ^a   Ginsburg, Ann ^a  

^a NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

Author keywords

Duplex DNA stability; Heat capacity change; Homeodomain; Protein

Indexed keywords

BIOPOLYMER; DOUBLE STRANDED DNA; HOMEODOMAIN PROTEIN; SOLVENT; TRANSCRIPTION FACTOR NKX2.5; UNCLASSIFIED DRUG;

ARTICLE; CALORIMETER; DNA DAMAGE; DNA STRAND; ENTHALPY; ISOTHERMAL TITRATION CALORIMETRY; LOW TEMPERATURE; MOLECULAR STABILITY; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN FOLDING; SURFACE PROPERTY; TEMPERATURE DEPENDENCE; THERMODYNAMICS;

ANIMALS; BINDING SITES; CALORIMETRY; CALORIMETRY, DIFFERENTIAL SCANNING; DNA; HOMEODOMAIN PROTEINS; KINETICS; MICE; NUCLEIC ACID DENATURATION; PROTEIN FOLDING;

EID: 33744826233     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20960     Document Type: Article

References (31)

1. Ghering WJ, Affolter M, Bürglin T. Homeodomain proteins. Annu Rev Biochem 1994;63:487-526.
2. Carra JH, Privalov PL. Energetics of folding and DNA binding of the MAT alpha 2 homeodomain. Biochemistry 1997;36:526-535.
3. Gonzalez M, Weiler S, Ferretti JA, Ginsburg A. The vnd/NK-2 homeodomain: thermodynamics of reversible unfolding and DNA binding for wild-type and with residue replacements H52R and H52R/T56W in helix III. Biochemistry 2001;40:4923-4931.
4. Damante G, Tell G, Leonardi A, Fogolari F, Bortolotti N, Di Lauro R, Formisano S. Analysis of the conformation and stability of rat TTF-1 homeodomain by circular dichroism. FEBS Lett 1994;354: 293-296.
5. Subramaniam V, Jovin TM, Rivera-Pomar RV. Aromatic amino acids are critical for stability of the bicoid homeodomain. J Biol Chem 2001;276:21506-21511.
6. Weiler S, Gruschus JM, Tsao DHH, Yu L, Wang LH, Nirenberg M, Ferretti JA. Site-directed mutations in the vnd/NK-2 homeodomain. Basis of variations in structure and sequence-specific DNA binding. J Biol Chem 1998;273:10994-11000.
7. Frasch M, Warrior R, Tugwood J, Levine M. Molecular analysis of even-skipped mutants in Drosophila development. Genes Dev 1988;2:1824-1838.
8. Heberlein U, Penton A, Falsafi S, Hackett D, Rubin GM. The C-terminus of the homeodomain is required for functional specificity of the Drosophila rough gene. Mech Dev 1994;48:35-49.
9. Laughon A, Scott MP. Sequence of a Drosophila segmentation gene: protein structure homology with DNA-binding proteins. Nature 1984;310:25-31.
10. Hirsch JA, Aggarwal AK. Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity. EMBO J 1995;14:6280-6291.
11. Komuro I, Izumo S. Csx: a murine homeobox-containing gene specifically expressed in the developing heart. Proc Natl Acad Sci USA 1993;90:8145-8149.
12. Turbay D, Wechsler SB, Blanchard KM, Izumo S. Molecular cloning, chromosomal mapping, and characterization of the human cardiac-specific homeobox gene hCsx. Mol Med 1996;2:86-96.
13. Schott JJ, Benson DW, Basson CT, Pease W, Silberbach GM, Moak JP, Maron BJ, Seidman CE, Seidman JG. Congenital heart disease caused by mutations in the transcription factor NKX2.5. Science 1998;281:108-111.
14. Benson DW, Silberbach GM, Kavanaugh-McHugh A, Cottrill, C, Zhang Y, Riggs S, Smalls O, Johnson MC, Watson MS, Seidman JG, Seidman CE, Plowden J, Kugler JD. Mutations in the cardiac transcription factor NKX2.5 affect diverse cardiac developmental pathways. J Clin Invest 1999;104:1567-1573.
15. Goldmuntz E, Geiger E, Benson DW. NKX2.5 mutations in patients with tetralogy of fallot. Circulation 2001;104:2565-2568.
16. Kasahara H, Benson DW. Biochemical analyses of eight NKX2.5 homeodomain missense mutations causing atrioventricular block and cardiac anomalies. Cardiovasc Res 2004;64:40-51.
17. Kim Y, Nirenberg M. Drosophila NK-homeobox genes. Proc Natl Acad Sci USA 1989;86:7716-7720.
18. Wang LH, Chmelik R, Nirenberg M. Sequence-specific DNA binding by the vnd/NK-2 homeodomain of Drosophila. Proc Natl Acad Sci USA 2002;99:12721-12726.
19. Chen CY, Schwartz RJ. Identification of novel DNA binding targets and regulatory domains of a murine tinman homeodomain factor, Nkx2.5. J Biol Chem 1995;270:15628-15633.
20. Damante G, Fabbro D, Pellizzari L, Civitareale D, Guazzi S, Polycarpou-Schwartz M, Caucci S, Quadrifoglio F, Formisano S, Di Lauro R. Sequence-specific DNA recognition by the thyroid transcription factor-1 homeodomain. Nucleic Acids Res 1994;22: 3075-3083.
21. Gruschus JM, Tsao DHH, Wang LH, Nirenberg M, Ferretti JA. The three-dimensional structure of the vnd/NK-2 homeodomain-DNA complex by NMR spectroscopy. J Mol Biol 1999;289:529-545.
22. Fodor E, Mack JW, Maeng J-S, Ju J-H, Lee, HS, Gruschus JM, Ferretti JA, Ginsburg A. The cardiac-specific homeodomain Nkx2.5: conformational stability and specific DNA binding of Nkx2.5(C56S). Biochemistry 2005;44:12480-12490.
23. Ladbury JE. Application of isothermal titration calorimetry in the biological sciences: things are heating upBioTechniques 2004;37: 885-887.
24. Perkins SJ. Protein volumes and hydration effects. The calculations of partial specific volumes, neutron scattering matchpoints and 280-nm absorption coefficients for proteins and glycoproteins from amino acid sequences. Eur J Biochem 1986;157:169-180.
25. Plotnikov VV, Brandts JM, Lin LN, Brandts JF. A new ultra sensitive scanning calorimeter. Anal Biochem 1997;250:237-244.
26. Spolar RS, Ha JH, Record MT. Hydrophobic effect in protein folding and other noncovalent processes involving proteins. Proc Natl Acad Sci USA 1989;86:8382-8385.
27. Spolar RS, Record MT. Coupling of local folding to site-specific binding of proteins to DNA. Science 1994;263:777-784.
28. Gruschus JM, Ferretti JA. Quantitative measurement of water diffusion lifetimes at a protein/DNA interface by NMR. J Biomolecular NMR 2001;20:111-126.
29. Privalov PL, Jelesarov L, Read CM, Dragan AI, Crane-Robinson C. The energetics of HMG box interactions with DNA. Thermodynamics of the DNA binding of the HMG box from mouse Sox-5. J Mol Biol 1999;294:997-1013.
30. Dragan AI, Klass J, Read C, Churchill MEA, Crane-Robinson C, Privalov PL. DNA binding of a non-sequence-specific HMG-D protein is entropy driven with a substantial non-electrostatic contribution. J Mol Biol 2003;331:795-813.
31. Milev S, Gorfe AA, Karshikoff A, Clubb RT, Bosshard HR, Jelesarov I. Energetics of sequence-specific protein-DNA association: Binding of Integrase Tn916 to its target DNA. Biochemistry 2003;42:3481-3491.