Preparation and properties of pure, full-length IclR protein of Escherichia coli. Use of time-of-flight mass spectrometry to investigate the problems encountered

Protein Science

Volumn 5, Issue 8, 1996, Pages 1613-1624

  Donald, Lynda J ^a   Chernushevich, Igor V ^a,b   Zhou, Jie ^a,c   Verentchikov, Anatoli ^a,d   Poppe Schriemer, Nancy ^a   Hosfield, David J ^a   Westmore, John B ^a   Ens, Werner ^a   Duckworth, Harry W ^a   Standing, Kenneth G ^a  

^a UNIVERSITY OF MANITOBA   (Canada)

^b SEMENOV INSTITUTE OF CHEMICAL PHYSICS   (Russian Federation)

^c CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

^d PERKINELMER INC   (United States)

Author keywords

DNA binding protein; electrospray; glyoxylate cycle operon; IclR; matrix assisted laser desorption ionization (MALDI); time of flight mass spectrometry

Indexed keywords

DNA BINDING PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; ESCHERICHIA COLI; MASS SPECTROMETRY; NONHUMAN; OPERON; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PURIFICATION;

ESCHERICHIA COLI;

EID: 9344246840     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560050815     Document Type: Article

References (58)

1. Akiyama Y, Ito K. 1990. SecY protein, a membrane-embedded secretion factor of E. coli, is cleaved by the ompT protease in vitro. Biochem Biophys Res Commun 167:711-715.
2. Axelsson J, Reimann CT, Sundqvist BUR. 1994. Secondary electron resolved mass spectrometry of electrosprayed ions. Int J Mass Spectrom Ion Processes 133:141.
3. Bradford MM. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein using the principle of protein-dye binding. Anal Biochem 72:248-254.
4. Brenowitz M, Jamison E, Majumdar A, Adhya S. 1990. Interaction of the Escherichia coli Gal repressor protein with its DNA operators in vitro. Biochemistry 29:3374-3383.
5. Brenowitz M, Senear DF, Kingston RE. 1989. DNase I footprint analysis of protein-DNA binding. In: Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K, eds. Current protocols in molecular biology. New York: Wiley.
6. Brice CD, Kornberg HL. 1968. Genetic control of isocitrate lyase activity in Escherichia coli. J Bacteriol 96:2185-2186.
7. Brown RS, Lennon JJ. 1995. Mass resolution improvement by incorporation of pulsed ion extraction in a matrix-assisted laser desorption/ionization linear time-of-flight mass spectrometer. Anal Chem 67:1998-2003.
8. Byrne C, Stokes HW, Ward KA. 1988. Nucleotide sequence of the aceB gene encoding malate synthase A in Escherichia coli. Nucleic Acids Res 16: 9342.
9. Carey J. 1988. Gel retardation at low pH resolves trp-repressor-DNA complexes for quantitative study. Proc Natl Acad Sci USA 85:975-979.
10. Carey J. 1991. Gel retardation. Methods Enzymol 208:103-117.
11. Chait BT, Kent SBH. 1992. Weighing naked proteins; practical, high accuracy mass measurement of peptides and proteins. Science 257:1885-1894.
12. Chung T, Klumpp DJ, Laporte DC. 1988. Glyoxylate bypass operon of Escherichia coli: Cloning and determination of the functional map. J Bacteriol 170:386-392.
13. Cortay JC, Bleicher F, Rieul C, Reeves HC, Cozzone AJ. 1988. Nucleotide sequence and expression of the aceK gene coding for isocitrate dehydrogenase kinase/phosphatase in Escherichia coli. J Bacteriol 170:89-97.
14. Cortay JC, Nègre D, Galinier A, Duclos B, Perrière G, Cozzone AJ. 1991. Regulation of the acetate operon in Escherichia coli: Purification and functional characterization of the IclR repressor. EMBO J 10:675-679.
15. DiRusso CC, Heimert TL, Metzger AK. 1992. Characterization of FadR, a global transcription regulator of fatty acid metabolism in Escherichia coli. J Biol Chem 267:8685-8691.
16. Edelhoch H. 1967. Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry 6:1948-1954.
17. El-Mansi EM, MacKintosh C, Duncan K, Holms WH, Nimmo HG. 1987. Molecular cloning and over-expression of the glyoxylate bypass operon from Escherichia coli ML308. Biochem J 242:661-665.
18. Ens W, Dworschak RG, Spicer V, Standing KG. 1995. Delayed extraction in matrix-assisted laser desorption. Atlanta, Georgia: Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics. p 684.
19. Feng JA, Johnson RC, Dickerson RE. 1994. Hin recombinase bound to DNA. The origin of specificity in major and minor groove interactions. Science 262:348-354.
20. Gross E, Witkop B. 1961. Selective cleavage of the methionyl peptide bonds in ribonuclease with cyanogen bromide. J Am Chem Soc 83:1510-1511.
21. Hedrick JL, Smith AJ. 1968. Size and charge isomer separation and estimation of molecular weights of proteins by disc gel electrophoresis. Arch Biochem Biophys 126:155-164.
22. Hill AV. 1910. A new mathematical treatment of changes of ionic concentration in muscle and nerve under the action of electric currents with a theory as to their mode of excitation. J Physiol (Lond) 40:190-224.
23. Jordan SR, Pabo CO. 1988. Structure of the lambda complex at 2.5 Å resolution: Details of the repressor-operator interactions. Science 242: 893-899.
24. Klumpp DJ, Plank DW, Bowdin LJ, Stueland CS, Chung T, LaPorte DC. 1988. Nucleotide sequence of aceK, the gene encoding isocitrate dehydrogenase kinase/phosphatase. J Bacteriol 170:2763-2769.
25. Knight KL, Sauer RT. 1989. Identification of functionally important residues in the DNA binding region of the Mnt repressor. J Biol Chem 264:13706-13710,
26. Kornberg HL. 1963. The role of acetate in isocitrate lyase induction. Biochim Biophys Acta 73:517-519.
27. Kornberg HL. 1966. The role and control of the glyoxylate cycle in Escherichia coli. Biochem J 99:1-11.
28. Kunkel TA, Roberts JD, Zakour RA. 1987. Rapid and efficient site-directed mutagenesis without phenotypic selection. Methods Enzymol 154:367-382.
29. Laemmli UK. 1970. Cleavage of structural proteins during assembly of bacteriophage T4. Nature 227:280-285.
30. Laine B, Kmiecik D, Sautière P, Biserte G, Cohen-Solal M. 1980. Complete amino acid sequence of DNA-binding proteins HU-1 and HU-2 from Escherichia coli. Eur J Biochem 103:447-461.
31. LaPorte DC, Chung T. 1985. A single gene codes for the kinase and phosphatase which regulate isocitrate dehydrogenase. J Biol Chem 260:15291-15297.
32. Maniatis T, Fritsch EF, Sambrook J. 1982. Molecular cloning. A laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory.
33. Mann M, Meng CK, Fenn JB. 1989. Interpreting mass spectra of multiply charged ions. Anal Chem 61:1702-1708.
34. Maxam A, Gilbert W. 1980. Sequencing end-labelled DNA with base-specific chemical cleavages. Methods Enzymol 65:499-560.
35. Mende L, Timm B, Subramaniam AR. 1978. Primary structure of two homologous ribosome-associated DNA-binding proteins of Escherichia coli. FEBS Lett 96:395-398.
36. Miller JH. 1972. Experiments in molecular genetics. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory.
37. Nègre D, Cortay JC, Galinier A, Sauve P, Cozzone AJ. 1992. Specific interactions between the IclR repressor of the acetate operon of Escherichia coli and its operator. J Mol Biol 228:23-29.
38. Nègre D, Cortay JC, Old IG, Galinier A, Richaud C, Saint Girons I, Cozzone AJ. 1991. Overproduction and characterization of the iclR gene product of Escherichia coli K-12 and comparison with that of Salmonella typhimurium LT2. Gene 97:29-37.
39. Orchard K, May GE. 1993. An EMSA-based method for determining the molecular weight of a protein-DNA complex. Nucleic Acids Res 21: 3335-3336.
40. Pabo CO, Krovatin W, Jeffrey A, Sauer RT. 1982. The N-terminal arms of λ repressor wrap around the operator DNA. Nature 298:441-443.
41. Perczel A, Park K, Fasman GD. 1992. Analysis of the circular dichroism spectrum of proteins using the convex constraint algorithm: A practical guide. Anal Biochem 203:83-93.
42. Rieul C, Bleicher F, Duclos B, Cortay JC, Cozzone AJ. 1988. Nucleotide sequence of the aceA gen coding for isocitrate lyase in Escherichia coli. Nucleic Acids Res 16:5689.
43. 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.
44. Sanger F, Nicklen S, Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463-5467.
45. Schultz SC, Shields GC, Steitz TA. 1991. Crystal structure of a CAP-DNA complex: The DNA is bent by 90 degrees. Science 253:1001-1007.
46. Standing KG, Chernushevich IV, Ens W, Verentchikov AN. 1994. Time-of-flight methods for analysing large molecules. Chicago, Illinois: Proceedings of the 42nd ASMS Conference on Mass Spectrometry and Allied Topics. p 1148.
47. Sugimura K, Nishihara T. 1988. Purification, characterization and primary structure of Escherichia coli protease VII with specificity for paired basic residues: Identity of protease VII with ompT. J Bacteriol 170:5625-5632.
48. Sunnarborg A, Klumpp D, Chung T, Lapone DC. 1990. Regulation of the glyoxylate bypass operon: Cloning and characterization of iclR. J Bacteriol 172:2642-2649.
49. Tang X, Beavis R, Ens W, Lafortune F, Schueler B, Standing KG. 1988. A secondary ion time-of-flight mass spectrometer with an ion mirror. Int J Mass Spectrom Ion Processes 85:43-67.
50. Tong EK, Duckworth HW. 1975. The quaternary structure of citrate synthase from Escherichia coli K12. Biochemistry 14:235-241.
51. Vanderwinkel E, DeVlieghere M. 1968. Physiologie et génétique de l'isocitratase et des malate synthases chez Escherichia coli. Eur J Biochem 5:81-90.
52. Verentchikov A, Ens W, Standing KG. 1994. A reflecting time-of-flight mass spectrometer with an electrospray ion source and orthogonal injection. Anal Chem 56:126-133.
53. Vershon KA, Liao SA, McClure WR, Sauer RT. 1987. Bacteriophage P22 Mnt repressor. DNA binding and effects on transcription in vitro. J Mol Biol 195:311-322.
54. Vestal ML, Juhasz P, Martin SA. 1995. Delayed extraction matrix-assisted laser desorption time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 9:1044-1050.
55. Wiley WC, McLaren IH. 1955. Time-of-flight mass spectrometer with improved resolution. Rev Sci Instrum 26:1150-1157.
56. Wolberger C, Vershon AK, Liu B, Johnson AD, Pabo CO. 1991. Crystal structure of a MATα2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. Cell 67:517-528.
57. Wood WB. 1966. Host specificity of DNA produced by Escherichia coli: Bacterial mutations affecting the restriction and modification of DNA. J Mol Biol 16:118-133.
58. Zhou J. 1994. Investigations of matrix-assisted laser desorption with a reflecting time-of-flight mass spectrometer [thesis, part 2]. Winnipeg, Manitoba, Canada: University of Manitoba