Study of a noncovalent trp repressor: DNA operator complex by electrospray ionization time-of-flight mass spectrometry

Protein Science

Volumn 7, Issue 6, 1998, Pages 1388-1395

  Potier, Noelle ^a,c   Donald, Lynda J ^a   Chernushevich, Igor ^a,d   Ayed, Ayeda ^a   Ens, Werner ^a   Arrowsmith, Cheryl H ^b   Standing, Kenneth G ^a   Duckworth, Harry W ^a  

^a UNIVERSITY OF MANITOBA   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c Polymers and Materials   (France)

^d MDS SCIEX   (Canada)

Author keywords

Electrospray ionization; Noncovalent; Protein DNA interaction; Time of flight mass spectrometry; trp repressor

Indexed keywords

5 METHYLTRYPTOPHAN; AMMONIUM ACETATE; APOPROTEIN; DIMER; DNA; DOUBLE STRANDED DNA; REPRESSOR PROTEIN; TRYPTOPHAN; WATER;

ARTICLE; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA PROTEIN COMPLEX; MASS SPECTROMETRY; OPERATOR GENE; PRIORITY JOURNAL; PROTEIN ANALYSIS;

EID: 0031777368     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560070615     Document Type: Article

References (48)

1. 1H NMR assignments and secondary structure in solution of Escherichia coli trp repressor. Biochemistry 29:6332-6341.
2. Arvidson DN, Bruce C, Gunsalus RP. 1986. Interaction of the Escherichia coli trp aporepressor with its ligand, L-tryptophan. J Biol Chem 261:238-243.
3. Baca M, Kent SBH. 1992. Direct observation of a ternary complex between the dimeric enzyme HIV-1 protease and a substrate-based inhibitor. J Am Chem Soc 114:3992-3993.
4. Carey J. 1988. Gel retardation at low pH resolves trp repressor-DNA complexes for quantitative study. Proc Natl Acad Sci USA 85:975-979.
5. Carey J, Lewis DEA, Lavoie TA, Yang J. 1991. How does trp repressor bind to its operator? J Biol Chem 266:24509-24513.
6. Cheng X, Harms AC, Goudreau PN, Terwilliger TC, Smith RD. 1996a. Direct measurement of oligonucleotide binding stoichiometry of gene V protein by mass spectrometry. Proc Natl Acad Sci USA 93:7022-7027.
7. Cheng X, Morin PE, Harms AC, Bruce JE, Ben-David Y, Smith RD. 1996b. Mass spectrometric characterization of sequence-specific complexes of DNA and transcription factor PU.1 DNA binding domain. Anal Biochem 239: 35-40.
8. Chowdhury SK, Katta V, Chait BT. 1990. Probing conformational changes in proteins by mass spectrometry. J Am Chem Soc 112:9012-9013.
9. Chung EW, Rostom A, Robinson CV. 1997. Investigating non-covalent protein-ligand interactions using nanoflow electrospray. In: Proceedings of the 45th ASMS Conference on Mass Spectrometry and Allied Topics. Palm Springs, CA: ASMS. p 359.
10. Czernik PJ, Shin DS, Hurlburt BK. 1994. Functional selection and characterization of DNA binding sites for trp repressor of Escherichia coli. J Biol Chem 269:27869-27875.
11. Denisov VP, Halle B. 1994. Dynamics of the internal and external hydration of globular proteins. J Am Chem Soc 116:10324-10325.
12. Dötsch V, Wider G. 1995. Exchange rates of internal water molecules in proteins measured using pulsed field gradients. J Am Chem Soc 117:6064-6070.
13. Feng R. 1995. Unusually strong binding of a noncovalent gas-phase sperminepeptide complex and its dramatic temperature dependence. In: Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics. Atlanta, GA: ASMS. p 1264.
14. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM. 1990. Electrospray ionization for mass spectrometry of large biomolecules. Mass Spectrom Rev 9:37-70.
15. Fitzgerald MC, Chemushevich I, Standing KG, Whitman CP, Kent SBH. 1996. Probing the oligomeric structure of an enzyme by electrospray ionization time-of-flight mass spectrometry. Proc Natl Acad Sci USA 93:6851-6856.
16. Gale DC, Smith RD. 1995. Characterization of noncovalent complexes formed between minor groove binding molecules and duplex DNA by electrospray ionization-mass spectrometry. J Am Soc Mass Spectrom 6:1154-1164.
17. Ganem B, Li YT, Henion JD. 1991. Observation of non-covalent enzyme-substrate and enzyme-product complexes by ion-spray mass spectrometry. J Am Chem Soc 113:7818-7819.
18. Joachimiak A, Kelly RL, Gunsalus RP, Yanofsky C, Sigler PB. 1983. Purification and characterization of Trp aporepressor. Proc Natl Acad Sci USA 80:668-672.
19. Kodandapani R, Pio F, Ni C-Z, 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.
20. Krutchinsky AN, Chernushevich IV, Spicer V, Ens W, Standing KG. 1995. Collisional focusing of ions in the electrospray TOF mass spectrometer. In: Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics. Atlanta, GA:ASMS. p 126.
21. Lawson CL, Carey J. 1993. Tandem binding in crystals of a trp repressor/ operator half-site complex. Nature 366:178-182.
22. 15N]-L-tryptophan. J Biomolec NMR 5:367-375.
23. Li YT, Hsieh YL, Henion JD, Ocain TD, Schiehser GA, Ganem B. 1994. Analysis of the energetics of gas-phase immunophilin ligand complexes by ion spray mass spectrometry. J Am Chem Soc 116:7487-7493.
24. Li YT, Hsieh YL, Henion JD, Senko MW, McLafferty FW, Ganem B. 1993. Mass spectrometric studies on noncovalent dimers of leucine zipper peptides. J Am Chem Soc 115:8409-8413.
25. Light-Wahl KJ, Schwartz BL, Smith RD. 1994. Observation of the noncovalent quaternary associations of proteins by electrospray ionization mass spectrometry. J Am Chem Soc 116:5271-5278.
26. Light-Wahl KJ, Springer DL, Winger BE, Edmonds CG, Camp DG II, Thrall BD, Smith RD. 1993. Observation of a small oligonucleotide duplex by electrospray ionization mass spectrometry. J Am Chem Soc 15:803-804.
27. Loo JA. 1995. Observation of large subunit protein complexes by electrospray ionization mass spectrometry. J Mass Spectrom 30:180-183.
28. Loo JA. 1997. Studying noncovalent protein complexes by electrospray ionization mass spectrometry. Mass Spectrom Rev 16:1-23.
29. Loo JA, Hu P, McConnell P, Mueller WT, Sawyer TK, Thanabal V. 1997. A study of Src SH2 domain protein-phosphopeptide binding interactions by electrospray ionization mass spectrometry. J Am Soc Mass Spectrom 8:234-243.
30. Loo JA, Ogorzalek-Loo RR, Udseth HR, Edmonds CG, Smith RD. 1991. Solvent-induced conformational changes of polypeptides probed by electrospray-ionisation mass spectrometry. Rapid Commun Mass Spectrom 5:101-105.
31. Mann M, Wilm M. 1995. Electrospray mass spectrometry for protein characterization. Trends Biochem Sci 20:219-224.
32. Marmorstein RQ, Joachimiak A, Sprinzl M, Sigler PB. 1987. The structural basis for the interaction between L-tryptophan and the Escherichia coli trp aporepressor. J Biol Chem 262:4922-4927.
33. Orr A, Ivanova VS, Bonner WM. 1995. "Waterbug" dialysis. Biotechniques 19:204-206.
34. Otwinowski Z, Schevitz RW, Zhang RG, Lawson CL, Joachimiak A, Marmorstein RQ, Luisi BF, Sigler PB. 1988. Crystal structure of trp repressor/ operator complex at atomic resolution. Nature 335:321-329.
35. Paluh JL, Yanofsky C. 1986. High level production and rapid purification of the E. coli trp repressor. Nucleic Acids Res 14:7851-7860.
36. Potier N, Barth P, Tritsch D, Biellmann JF, Van Dorsselaer A. 1997. Study of non-covalent enzyme-inhibitor complexes of aldose reductase by electrospray mass spectrometry. Eur J Biochem 243:274-282.
37. Potier N, Van Dorsselaer A, Cordier Y, Roch O, Bischoff R. 1994. Negative electrospray ionization mass spectrometry of synthetic and chemically modified oligonucleotides. Nucleic Acids Res 22:3895-3903.
38. Ramesh V, Frederick RO, Syed SEH, Gibson CF, Yang J-C, Roberts GCK. 1994. The interactions of Escherichia coli trp repressor with tryptophan and with an operator oligonucleotide. Eur J Biochem 225:601-608.
39. Robinson CV, Chung EW, Kragelund BB, Knudsen J, Aplin RT, Poulsen FM, Dobson CM. 1996. Probing the nature of noncovalent interactions by mass spectrometry. A study of protein-CoA ligand binding and assembly. J Am Chem Soc 118:8646-8653.
40. Schwartz BL, Bruce JE, Anderson GA, Hofstadler SA, Rockwood AL, Smith RD, Chilkoti A, Stayton PS. 1995. Dissociation of letrameric ions of non-covalent streptavidin complexes formed by electrospray ionization. J Am Soc Mass Spectrom 6:459-465.
41. Smith DL, Zhang Z. 1994. Probing nonocovalent structural features of proteins by mass spectrometry. Mass Spectrom Rev 13:411-429.
42. Stults JT, Marsters JC. 1991. Improved electrospray ionization of synthetic oligodeoxynucleotides. Rapid Commun Mass Spectrom 5:359-363.
43. Verentchikov AN, Ens W, Standing KG. 1994. Reflecting time-of-flight mass spectrometer with an electrospray ion source and orthogonal extraction. Anal Chem 66:126-133.
44. Wu Q, Gao J, Joseph-McCarthy D, Sigal GB, Bruce JE, Whitesides GM, Smith RD. 1997. Carbonic anhydrase-inhibitor binding: From solution to the gas phase. J Am Chem Soc 119:1157-1158.
45. Youderian P, Arvidson DN. 1994. Direct recognition of the trp operator by the trp holorepressor - A review. Gene 150:1-8.
46. Zhang H, Zhao D, Revington M, Lee W, Jia X, Arrowsmith C, Jardetzky O. 1994. The solution structures of the trp repressor-operator DNA complex.. J Mol Biol 238:592-614.
47. Zhang RG, Joachimiak A, Lawson CL, Schevitz RW, Otwinowski Z, Sigler PB. 1987. The crystal structure of trp aporepressor at 1.8 Å shows how binding tryptophan enhances DNA affinity. Nature 327:591-596.
48. Zhao D, Arrowsmith CH, Jardetzky O. 1993. Refined solution structures of the Escherichia coli trp holo-and aporepressor. J Mol Biol 229:735-746.