Heteronuclear (1H, 13C, 15N) NMR assignments and secondary structure of the basic region-helix-loop-helix domain of E47

Protein Science

Volumn 6, Issue 1, 1997, Pages 175-184

  Fairman, Robert ^a,b   Beran Steed, Rita K ^a,d   Handel, Tracy M ^a,c  

^a DUPONT COMPANY   (United States)

^b BRISTOL MYERS SQUIBB   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d Amersham Biosciences   (United States)

Author keywords

E47; helix loop helix; homodimers; NMR; transcription factor

Indexed keywords

DNA BINDING PROTEIN; TRANSCRIPTION FACTOR; CARBON; NITROGEN; PROTON; RECOMBINANT PROTEIN; T CELL FACTOR 3; T CELL FACTOR PROTEIN;

ALPHA HELIX; ARTICLE; DIMERIZATION; DNA BINDING; ENHANCER REGION; GENETIC REGULATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; TRANSCRIPTION REGULATION; AMINO ACID SEQUENCE; CHEMISTRY; MOLECULAR GENETICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

AMINO ACID SEQUENCE; CARBON ISOTOPES; DNA-BINDING PROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR SEQUENCE DATA; NITROGEN ISOTOPES; PROTEIN STRUCTURE, SECONDARY; PROTONS; RECOMBINANT PROTEINS; TCF TRANSCRIPTION FACTORS; TRANSCRIPTION FACTORS;

EID: 0030614748     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560060120     Document Type: Article

References (54)

1. Anthony-Cahill SJ, Benfield PA, Fairman R, Wasserman ZR, Brenner SL, Altenbach C, Hubbell WL, Stafford WF III, DeGrado WF. 1992. Molecular characterization of helix-loop-helix peptides. Science 255:979-983.
2. Archer SJ, Ikura M, Torchia DA, Bax A. 1991. An alternative 3D-NMR technique for correlating backbone N-15 with side chain H-beta resonances in larger proteins. J Magn Reson 95:636-641.
3. Bain G, Maandag ECR, Izon DJ, Amsen D, Kruisbeek AM, Weintraub BC, Krop I, Schlissel MS, Feeney AJ, van Roon M, van der Valk M, te Riele HPJ, Berns A, Murre C. 1994. E2A proteins are required for proper B cell development and initiation of immunoglobulin gene rearrangements. Cell 79:885-892.
4. Bax A, Clore GM, Gronenborn AM. 1990a. 1H-1H correlation via isotropic mixing of 13C magnetization, a new 3-dimensional approach for assigning 1H and 13C spectra of 13C-enriched proteins. J Magn Reson 88:425-431.
5. Bax A, Ikura M, Kay LE, Torchia DA, Tschudin R. 1990b. Comparison of different modes of 2-dimensional reverse-correlation NMR for the study of proteins. J Magn Reson 86:304-318.
6. 1H COSY experiments. J Biomol NMR 2:257-274.
7. Bishop P, Jones C, Ghosh I, Chmielewski J. 1995. Synthesis of the basic-helix-loop-helix region of the immunoglobulin enhancer binding protein E47 and evaluation of its structural and DNA binding properties. Int J Pept Prot Res 46:149-154.
8. Blackwood E, Eisenman RN. 1991. MAX - A helix-loop-helix protein that forms a sequence specific DNA-binding complex with myc. Science 251: 1211-1217.
9. Boucher W, Laue ED, Campbell-Burk S, Domaille PJ. 1992a. 4-Dimensional heteronuclear triple resonance NMR methods for the assignment of backbone nuclei in proteins. J Am Chem Soc 114:2262-2264.
10. Boucher W, Laue ED, Campbell-Burk SL, Domaille PJ. 1992b. Improved 4D-NMR experiments for the assignment of backbone nuclei in C-13/N-15 labelled proteins. J Biomol NMR 2:631-637.
11. Burley SK. 1994. Plus ça change, plus c'est la même chose. Nature Struct Biol 1:207-208.
12. Chou PY, Fasman GD. 1978. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol 47:45-148.
13. Clowes RT, Boucher W, Hardman CH, Domaille PJ, Laue ED. 1993. A 4D HC-C(CO)NNH experiment for the correlation of aliphatic side chain and backbone resonances in C-13/N-15 labelled proteins. J Biomol NMR 3:349-354.
14. Ellenberger T, Fass D, Arnaud M, Harrison SC. 1994. Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer. Genes & Dev 8:970-980.
15. Fairman R, Beran-Steed RK, Anthony-Cahill SJ, Lear JD, Stafford WF, DeGrado WF, Benfield PA, Brenner SL. 1993. Multiple oligomeric states regulate the DNA-binding of helix-loop-hehx peptides. Proc Natl Acad Sci USA 90:10429-10433.
16. Farmer K, Catala F, Wright WE. 1992. Alternative multimeric structures affect myogenin DNA binding activity. J Biol Chem 267:5631-5636.
17. Ferré-D'Amaré AR, Pognonec P, Roeder RG, Burley SK. 1994. Structure and function of the b/HLH/Z domain of USF. EMBO J 13:180-189.
18. Ferré-D'Amaré AR, Prendergast GC, Ziff EB, Burley SK. 1993. Recognition by MAX of its cognate DNA through a dimeric b/HLH/Z domain. Nature 363:18-45.
19. Fisher DE, Carr CS, Parent LA, Sharp PA. 1991. TFEB has DNA-binding and oligomerization properties of a unique helix-loop-helix/leucine-zipper family. Genes & Dev 5:2342-2352.
20. Gibson TJ, Thompson JD, Abagyan RA. 1993. Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins. Protein Eng 6:41-50.
21. Halazonetis TD, Kandil AN. 1992. Predicted structural similarities of the DNA binding domains of c-Myc and endonuclease Eco RI. Science 255:464-466.
22. Handel TM, Williams SA, DeGrado WF. 1993. Metal ion-dependent modulation of the dynamics of a designed protein. Science 261:879-885.
23. Hsu HL, Wadman I, Tsan JT, Baer R. 1994. Positive and negative transcriptional control by the TAL1 helix-loop-helix protein. Proc Natl Acad Sci USA 91:5947-5951.
24. Jones N. 1990. Transcriptional regulation by dimerization: Two sides to an incestuous relationship. Cell 61:9-11.
25. Kadesch T. 1993. Consequences of heteromeric interactions among helix-loop-helix proteins. Cell Growth Differ 4:49-55.
26. Lamb P, McKnight SL. 1991. Diversity and specificity in transcriptional regulation: The benefits of heterotypic dimerization. Trends Biochem Sci 16:417-422.
27. Lassar AB, Davis RL, Wright WE, Kadesch T, Murre C, Voronova A, Baltimore D, Weintraub H. 1991. Functional activity of myogenic HLH proteins requires hetero-oligomerization with E12/E47-like proteins in vivo. Cell 66:305-315.
28. Laue ED, Mayger MR, Skilling J, Staunton J. 1986. Reconstruction of phase sensitive two-dimensional NMR spectra by maximum entropy. J Magn Reson 68:14-29.
29. Laue TM, Starovasnik MA, Weintraub H, Sun XH, Snider L, Klevitt R. 1995. MyoD forms micelles which can dissociate to form heterodimers with E47: Implications of micellization on function. Proc Natl Acad Sci USA 92:11824-11828.
30. Live DH, Davis DG, Agosta WC, Cowburn D. 1984. Long-range hydrogen bond mediated effects in peptides: 15N NMR study of gramacidin S in water and organic solvents. J Am Chem Soc 106:1934-1941.
31. Lumb KJ, Kim PS. 1995. A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil. Biochemistry 34:8642-8648.
32. Ma PCM, Rould MA, Weintraub H, Pabo CO. 1994. Crystal structure of MyoD b/HLH domain-DNA complex: Perspectives on DNA recognition and implications for transcriptional activation. Cell 77:451-459.
33. Marion D, Driscoll PC, Kay LE, Wingfield PT, Bax A, Gronenbom AM, Clore GM. 1989. Overcoming the overlap problem in the assignment of H-1 NMR spectra of larger proteins by use of 3-dimensional heteronuclear 1H-15N Hartmann-Hahn multiple quantum coherence and nuclear Overhauser multiple quantum coherence spectroscopy - Application to interleukin-1-beta. Biochemistry 28:6150-6156.
34. 2O solutions. J Magn Reson 85:608-613.
35. Moffatt BA, Studier FW. 1987. T7 lysozyme inhibits transcription by T7 RNA polymerase. Cell 49:221-227.
36. Murre C, McCaw PS, Baltimore D. 1989. A new DNA binding and dimerization motif in immunoglobulin enhancer binding, daughterless, MyoD, and myc proteins. Cell 56:777-783.
37. Norwood TJ, Boyd J, Heritage J, Soffe N, Campbell ID. 1990. Comparison of techniques for 1H-detected heteronuclear 1H-15N spectroscopy J Magn Reson 87:488-501.
38. O'Shea EK, Klemm JD, Kim PS, Alber T. 1991. X-ray structure of the GCN4 leucine zipper, a 2-stranded, parallel coiled coil. Science 254:539-544.
39. Phillips SEV. 1994. Built by association: Structure and function of helix-loop-helix DNA-binding proteins. Structure 2:1-4.
40. Prendergast GC, Lawe D, Ziff E. 1991. Association of MYN, the murine homolog of MAX, with C-MYC stimulates methylation sensitive DNA-binding and ras cotransformation. Cell 65:395-407.
41. Raleigh DP, Betz SE, Degrade WF. 1995. A de novo designed protein mimics the native state of natural proteins. J Am Chem Soc 117:7558-7559.
42. Regan L, DeGrado WF. 1988. Characterization of a helical protein designed from first principles. Science 241:976-978.
43. Richardson JS, Richardson DC. 1988. Amino acid preferences for specific locations at the ends of α-helices. Science 240:1648-1652.
44. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487-491.
45. Shen CP, Kadesch T. 1995. B-cell-specific DNA binding by an E47 homodimer. Mol Cell Biol 15:4518-4524.
46. Shirataka M, Friedman FK, Wei Q, Paterson BM. 1993. Dimerization specificity of myogenic helix-loop-helix DNA-binding factors directed by nonconserved hydrophilic residues. Genes & Dev 7:2456-2470.
47. Spera S, Bax A. 1991. Empirical correlation between protein backbone conformation and C-alpha and C-beta C-13 nuclear magnetic resonance chemical shifts. J Am Chem Soc 113:5490-5492.
48. Spolar RS, Record TR. 1994. Coupling of local folding to site-specific binding of proteins to DNA. Science 263:777-783.
49. Starovasnik MA, Blackwell TK, Laue TM, Weintraub H, Klevit RE. 1992. Folding topology of the disulfide-bonded dimeric DNA-binding domain of the myogenic determination factor MyoD. Biochemists 31:9891-9903.
50. Studier FW, Moffatt BA. 1986. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol 189:113-130.
51. Sun XH, Baltimore D. 1991. An inhibitory domain of E12 transcription factor prevents DNA binding in E12 homodimers but not in E12 heterodimers. Cell 64:459-470.
52. Vinson CR, Garcia C. 1992. Molecular model for DNA recognition by the family of basic-helix-loop-helix-zipper proteins. New Biol 4:396-403.
53. Wishart DS, Sykes BD. 1994. The 13C chemical-shift index: A simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 4:171-180.
54. Wolberger C. 1994. b/HLH without the zip. Nature Struct Biol 1:413-416.