Mutants of ETS domain PU.1 and GGAA/T recognition: Free energies and kinetics

Protein Science

Volumn 8, Issue 10, 1999, Pages 2098-2109

  Pio, Frederic ^a   Assa Munt, N ^a   Yguerabide, J ^b   Maki, R A ^a,c  

^a BURNHAM INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c NEUROCRINE BIOSCIENCES INC   (United States)

Author keywords

ETS domain; Free energy of dissociation; Kinetics; Modeling; Mutagenesis; Protein DNA interaction; Surface plasmon resonance

Indexed keywords

AMINO ACID; DNA;

ARTICLE; BINDING AFFINITY; BINDING KINETICS; DNA BINDING; DNA SEQUENCE; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; SEQUENCE ANALYSIS; SITE DIRECTED MUTAGENESIS; SURFACE PLASMON RESONANCE; THERMODYNAMICS;

EID: 0032884399     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.10.2098     Document Type: Article

References (46)

1. Alber T. 1989. Mutational effects on protein stability. Annu Rev Biochem 58:765-798.
2. Batchelor AH, Piper DE, De la Brousse FC, McKnight SL, Wolberger C. 1998. The structure of GABPα/β: An ETS domain ankyrin repeat heterodimer bound to DNA. Science 279:1037-1040.
3. Bosselut R, Levin J, Adjadj E, Ghysdael J. 1993. A single amino acid substitution in the ETS domain alters core DNA binding specificity of ETS-1 to that of the related transcription factors ELF-1 and E74. Nucleic Acids Res 21:5184-5191.
4. Brass LA, Kehrli E, Eisenbeis CF, Storb U, Singh H. 1996. PIP, a lymphoid-restricted IRF, contains a regulatory domain that is important for auto inhibition and ternary complex formation with the ETS factor PU. 1. Genes Dev 10:2335-2347.
5. Brown LA, Amores A, Schilling TF, Jowett T, Baert JL, De Launoit Y, Sharrocks AD. 1998. Molecular characterization of the zebrafish PEA3 ETS domain transcription factor. Oncogene 17:93-104.
6. Choo Y, Klug A. 1997. Physical basis of a protein-DNA recognition code. Curr Opin Struct Biol 7:117-125.
7. Donaldson LW, Petersen JM, Graves BJ, McIntosh LP. 1996. Solution structure of the ETS domain from murine ETS-1: A winged helix-turn-helix DNA binding motif. EMBO J 15:125-134.
8. Erman B, Sen R. 1996. Context dependent transactivation domains activate the immunoglobulin mu heavy chain gene enhancer. EMBO J 15:4565-4575.
9. Fisher RJ, Fivash M, Casas-Finet J, Erickson JW, Kondoh A. Bladen SV, Fisher C, Watson DK, Papas T. 1994a. Real-time binding measurements of the ETS-1 recombinant oncoproteins reveal significant kinetic differences between the p42 and p51 isoforms. Protein Sci 3:257-266.
10. Fisher RJ, Fivash M, Finet JC, Bladen S, McNitt KL. 1994b. Real-time BIAcore measurements of Escherichia coli single-stranded DNA binding (SSB) protein to polydeoxythymidylic acid reveal single-state kinetics with steric cooperativity. Methods 6:121-133.
11. Frankel AD, Kim PS. 1991. Modular structure of transcription factors: Implication for gene regulation. Cell 65:717-719.
12. Galson DL, Hensold JO, Bishop TR, Schalling M, D'Andrea AD, Jones C, Auron PE, Housman DE. 1993. Mouse beta-globin DNA binding protein B1 is identical to a proto-oncogene, the transcription factor Spi-1/PU.1, and is restricted in expression to hematopoietic cells and the testis. Mol Cell Biol 13:2929-2941.
13. Goodrich JA, Cutler G, Tjian R. 1996. Contacts in context: Promoter specificity and macromolecular interactions in transcription. Cell 84:825-830.
14. Graves BJ, Gillespie ME, McIntosh LP. 1996. DNA binding by the ETS domain. Nature 384:322.
15. Gross P, Yee AA, Arrowsmith CH, Macgregor RB Jr. 1998. Quantitative hydroxyl radical footprinting reveals cooperative interactions between DNA binding subdomains of PU.1 and IRF4. Biochemistry 37:9802-9811.
16. Joachimiak A, Haran TE, Sigler PB. 1994. Mutagenesis support water mediated recognition in the trp represser-operator system. EMBO J 13:367-372.
17. Karlsson R, Roos H, Fagerstam L, Persson B. 1994. Kinetics and concentration analysis using BIA Technology. Methods 6:99-110.
18. Kelley RF, O'Connell MP. 1993. Thermodynamic analysis of an antibody functional epitope. Biochemistry 32:6828-6835.
19. Klemsz MJ, McKercher SR. Celada A, Van Beveren C, Maki RA. 1990. The macrophage and B Cell-specific transcription factor PU.1 is related to the ETS oncogene. Cell 61:113-124.
20. Kodandapani R, Pio F, Ni CZ, Piccialli G, Klemsz M, McKercher S, Maki RA, Ely KR. 1996. A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS domain DNA complex. Nature 380:456-460.
21. Macleod K, Leprince D, Stehelin D. 1992. The ETS gene family. Trends Biochem Sci 17:251-256.
22. Mo Y, Vaessen B, Johnson K, Marmorstein R. 1998. Structures of SAP-1 bound to DNA targets from the E74 and c-fos promoters: Insights into DNA sequence discrimination by ETS proteins. Mol Cell 2:201-212.
23. Moreau-Gachelin F. 1994. Spi-1/PU.1: An oncogene of the ETS family. Biochim Biophys Acta 1198:149-163.
24. Nikolajczyk BS, Nelsen B, Sen R. 1996. Precise alignment of sites required from enhancer activation in B cells. Mol Cell Biol 16:4544-4554.
25. Pace NC. 1997. Evaluating contribution of hydrogen bonding and hydrophobic bonding to protein folding. Methods Enzymol 259:538-554.
26. Pahl HL, Scheibe RJ, Zhang DE, Chen HM, Galson DL, Maki RA, Tenen DG. 1993. The proto-oncogene PU.1 regulates expression of the myeloid-specific CD1lb promoter. J Biol Chem 268:5014-5020.
27. Pio F, Kodandapani R, Ni CZ, Shepard W, Klemsz M, McKercher SR, Maki RA, Ely KR. 1996. New insights on the DNA recognition by ETS proteins from the crystal structure of the PU.1 ETS domain DNA complex. J Biol Chem 271:23329-23337.
28. Pio F, Ni CZ, Mitchell RS, Knight J, McKercher SR, Klemsz M, Lombardo A, Maki RA, Ely KR. 1995. Cocrystallization of an ETS domain (PU.1) in complex with DNA. Engineering the length of both protein and oligonucleotide. J Biol Chem 270:24258-24263.
29. Pongubala JM, Nagulapalli S, Klemsz MJ, McKercher SR, Maki RA, Atchison ML. 1992. PU.1 recruits a second nuclear factor to a site important for immunoglobulin kappa 3′ enhancer activity. Mol Cell Biol 12:368-378.
30. Pongubala JM, Van Beveren C, Nagulapalli S, Klemsz MJ, McKercher SR, Maki RA, Atchison ML. 1993. Effect of PU.1 phosphorylation on interaction with NF-EM5 and transcriptional activation. Science 259:1622-1625.
31. Ptashne M, Gann A. 1997. Transcriptional activation by recruitment. Nature 386:569-577.
32. Puglisi JD, Tinoco IJ. 1989. Absorhance melting curve of RNA. Methods Enzymol 180:304-325.
33. Ray-Gallet D, Mao C, Tavitian A, Moreau-Gachelin F. 1995. DNA binding specificities of Spi-1/PU.1 and Spi-B transcription factors and identification of a Spi-1/Spi-B binding site in the c-fes/c-fps promoter. Oncogene 11:303-313.
34. Schuck P. 1997. Use of surface plasmon resonance to probe the equilibrium and dynamic aspects of interactions between biological macromolecules. Annu Rev Biophys Biomol Struct 26:541-566.
35. Schuck P, Minton AP. 1996a. Analysis of mass transport-limited binding kinetics in evanescent wave biosensors. Analytical Biochem 240:262-272.
36. Schuck P, Minton AP. 1996b. Kinetics analysis of biosensor data: Elementary tests for self consistency. Trends Biochem Sci 21:458-460.
37. Schwabe JW. 1997. The role of water in Protein-DNA interactions. Curr Opin Struct Biol 7:126-134.
38. Seimiya M, Kurosawa Y. 1996. Kinetics of binding of Antp homeodomain to DNA analysed by measurements of surface plasmon resonance. FEBS Lett 398:279-284.
39. Shin MK, Koshland ME. 1993. ETS-related protein PU.1 regulates expression of the immunoglobulin J-chain gene through a novel ETS binding element. Genes Dev 7:2006-2015.
40. Spolar RS, Record MT Jr. 1994. Coupling of local folding to site specific binding of proteins to DNA. Science 263:777-784.
41. Urness LD, Thummel CS. 1990. Molecular interactions within the ecdysone regulatory hierarchy: DNA binding properties of the Drosophila ecdysone-inducible E74A protein. Cell 63:47-61.
42. Wang CY, Petryniak B, Ho IC, Thompson CB, Leiden JM. 1992. Evolutionarily conserved ETS family members display distinct DNA binding specificities. J Exp Med 175:1391-1399.
43. Werner MH, Clore GM, Fisher CL, Fisher RJ, Trinh L, Shiloach J, Gronenborn AM. 1995. The solution structure of the human ETS-1 DNA complex reveals a novel mode of binding and true side chain intercalation. Cell 83:761-771.
44. Werner MH, Clore GM, Fisher CL, Fisher RJ, Trinh L, Shiloach J, Gronenborn AM. 1996. Erratum. Cell 87.
45. Wintjens R, Rooman M. 1996. Structural classification of helix-turn-helix DNA binding domains and protein-DNA interaction modes. J Mol Biol 262:294-313.
46. Zhang L, Lemarchandel V, Romeo PH, Ben-David Y, Greer P, Bernstein A. 1993. The Fli-1 proto-oncogene, involved in erythroleukemia and Ewing's sarcoma, encodes a transcriptional activator with DNA binding specificities distinct from other ETS family members. Oncogene 8:1621-1630.