A Raman spectroscopic study of the interaction between nucleotides and the DNA binding protein gp32 of bacteriophage T4

Cornelis Otto, F.F.M. de Mul, Jan Greve

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Abstract

Raman spectra of the bacteriophage T4 denaturing protein gp32, its complex with the polynucleotides poly(rA), poly(dA), poly(dT), poly(rU), and poly(rC), and with the oligonucleotides (dA)8 and (dA)2, were recorded and interpreted. According to an analysis of the gp32 spectra with the reference intensity profiles of Alix and co-workers [M. Berjot, L. Marx, and A.J.P. Alix (1985) J. Ramanspectrosc., submitted; A.J.P. Alix, M. Berjot, and J. Marx (1985) in Spectroscopy of Biological Molecules, A. J. P. Alix, L. Bernard, and M. Manfait, Eds., pp. 149-154], 1 gp32 contains ≈ 45% helix, ≈ 40% β-sheet, and 15% undefined structure. Aggregation of gp32 at concentrations higher than 40 mg/mL leads to a coordination of the phenolic OH groups of 4-6 tyrosines and of all the sulfhydryl (SH) groups present in the protein with the COO- groups of protein. The latter coordination persists even at concentrations as low as 1 mg/mL. In polynucleotide-protein complexes the nucleotide shields the 4-6 tyrosine residues from coordination by the COO- groups even at high protein concentration. The presence of the nucleotide causes no shielding of the SH groups. With Raman difference spectroscopy it is shown that binding of the protein to a single-stranded nucleotide involves both tyrosine and trytophan residues. A change in the secondary structure of the protein upon binding is observed. In the complex, gp32 contains more -sheet structure than when uncomplexed. A comparison of the spectra of complexed poly(rA) and poly(dA) with the spectra of their solution conformations at 15°C reveals that in both polynucleotides the phosphodiester vibration changes upon complex formation in the same way as upon a transition from a regular to a more disordered conformation. Distortion of the phosphate-sugar-base conformation occurs upon complex formation, so that the spectra of poly(rA) and poly(dA) are more alike in the complex than they are in the free polynucleotides. The decrease in intensity of the Raman bands at 1304 cm-1 in poly(rA), at 1230 cm-1 in poly(rU), and at 1240 and 1378 cm-1 of poly(dT) may be indicative of increased stacking interactions in the complex. No influence of the nucleotide chain length upon the Raman spectrum of gp322 in the complex was detected. Both the nucleotide lines and the protein lines in the spectrum of a complex are identical in poly(dA) and (dA)8.
Original languageUndefined
Pages (from-to)1667-1689
JournalBiopolymers
Volume26
Issue number10
DOIs
Publication statusPublished - 1987

Keywords

  • IR-70834

Cite this

@article{dab574996a5a4d388c242e4fad416bee,
title = "A Raman spectroscopic study of the interaction between nucleotides and the DNA binding protein gp32 of bacteriophage T4",
abstract = "Raman spectra of the bacteriophage T4 denaturing protein gp32, its complex with the polynucleotides poly(rA), poly(dA), poly(dT), poly(rU), and poly(rC), and with the oligonucleotides (dA)8 and (dA)2, were recorded and interpreted. According to an analysis of the gp32 spectra with the reference intensity profiles of Alix and co-workers [M. Berjot, L. Marx, and A.J.P. Alix (1985) J. Ramanspectrosc., submitted; A.J.P. Alix, M. Berjot, and J. Marx (1985) in Spectroscopy of Biological Molecules, A. J. P. Alix, L. Bernard, and M. Manfait, Eds., pp. 149-154], 1 gp32 contains ≈ 45{\%} helix, ≈ 40{\%} β-sheet, and 15{\%} undefined structure. Aggregation of gp32 at concentrations higher than 40 mg/mL leads to a coordination of the phenolic OH groups of 4-6 tyrosines and of all the sulfhydryl (SH) groups present in the protein with the COO- groups of protein. The latter coordination persists even at concentrations as low as 1 mg/mL. In polynucleotide-protein complexes the nucleotide shields the 4-6 tyrosine residues from coordination by the COO- groups even at high protein concentration. The presence of the nucleotide causes no shielding of the SH groups. With Raman difference spectroscopy it is shown that binding of the protein to a single-stranded nucleotide involves both tyrosine and trytophan residues. A change in the secondary structure of the protein upon binding is observed. In the complex, gp32 contains more -sheet structure than when uncomplexed. A comparison of the spectra of complexed poly(rA) and poly(dA) with the spectra of their solution conformations at 15°C reveals that in both polynucleotides the phosphodiester vibration changes upon complex formation in the same way as upon a transition from a regular to a more disordered conformation. Distortion of the phosphate-sugar-base conformation occurs upon complex formation, so that the spectra of poly(rA) and poly(dA) are more alike in the complex than they are in the free polynucleotides. The decrease in intensity of the Raman bands at 1304 cm-1 in poly(rA), at 1230 cm-1 in poly(rU), and at 1240 and 1378 cm-1 of poly(dT) may be indicative of increased stacking interactions in the complex. No influence of the nucleotide chain length upon the Raman spectrum of gp322 in the complex was detected. Both the nucleotide lines and the protein lines in the spectrum of a complex are identical in poly(dA) and (dA)8.",
keywords = "IR-70834",
author = "Cornelis Otto and {de Mul}, F.F.M. and Jan Greve",
year = "1987",
doi = "10.1002/bip.360261003",
language = "Undefined",
volume = "26",
pages = "1667--1689",
journal = "Biopolymers",
issn = "0006-3525",
publisher = "Wiley",
number = "10",

}

A Raman spectroscopic study of the interaction between nucleotides and the DNA binding protein gp32 of bacteriophage T4. / Otto, Cornelis; de Mul, F.F.M.; Greve, Jan.

In: Biopolymers, Vol. 26, No. 10, 1987, p. 1667-1689.

Research output: Contribution to journalArticleAcademic

TY - JOUR

T1 - A Raman spectroscopic study of the interaction between nucleotides and the DNA binding protein gp32 of bacteriophage T4

AU - Otto, Cornelis

AU - de Mul, F.F.M.

AU - Greve, Jan

PY - 1987

Y1 - 1987

N2 - Raman spectra of the bacteriophage T4 denaturing protein gp32, its complex with the polynucleotides poly(rA), poly(dA), poly(dT), poly(rU), and poly(rC), and with the oligonucleotides (dA)8 and (dA)2, were recorded and interpreted. According to an analysis of the gp32 spectra with the reference intensity profiles of Alix and co-workers [M. Berjot, L. Marx, and A.J.P. Alix (1985) J. Ramanspectrosc., submitted; A.J.P. Alix, M. Berjot, and J. Marx (1985) in Spectroscopy of Biological Molecules, A. J. P. Alix, L. Bernard, and M. Manfait, Eds., pp. 149-154], 1 gp32 contains ≈ 45% helix, ≈ 40% β-sheet, and 15% undefined structure. Aggregation of gp32 at concentrations higher than 40 mg/mL leads to a coordination of the phenolic OH groups of 4-6 tyrosines and of all the sulfhydryl (SH) groups present in the protein with the COO- groups of protein. The latter coordination persists even at concentrations as low as 1 mg/mL. In polynucleotide-protein complexes the nucleotide shields the 4-6 tyrosine residues from coordination by the COO- groups even at high protein concentration. The presence of the nucleotide causes no shielding of the SH groups. With Raman difference spectroscopy it is shown that binding of the protein to a single-stranded nucleotide involves both tyrosine and trytophan residues. A change in the secondary structure of the protein upon binding is observed. In the complex, gp32 contains more -sheet structure than when uncomplexed. A comparison of the spectra of complexed poly(rA) and poly(dA) with the spectra of their solution conformations at 15°C reveals that in both polynucleotides the phosphodiester vibration changes upon complex formation in the same way as upon a transition from a regular to a more disordered conformation. Distortion of the phosphate-sugar-base conformation occurs upon complex formation, so that the spectra of poly(rA) and poly(dA) are more alike in the complex than they are in the free polynucleotides. The decrease in intensity of the Raman bands at 1304 cm-1 in poly(rA), at 1230 cm-1 in poly(rU), and at 1240 and 1378 cm-1 of poly(dT) may be indicative of increased stacking interactions in the complex. No influence of the nucleotide chain length upon the Raman spectrum of gp322 in the complex was detected. Both the nucleotide lines and the protein lines in the spectrum of a complex are identical in poly(dA) and (dA)8.

AB - Raman spectra of the bacteriophage T4 denaturing protein gp32, its complex with the polynucleotides poly(rA), poly(dA), poly(dT), poly(rU), and poly(rC), and with the oligonucleotides (dA)8 and (dA)2, were recorded and interpreted. According to an analysis of the gp32 spectra with the reference intensity profiles of Alix and co-workers [M. Berjot, L. Marx, and A.J.P. Alix (1985) J. Ramanspectrosc., submitted; A.J.P. Alix, M. Berjot, and J. Marx (1985) in Spectroscopy of Biological Molecules, A. J. P. Alix, L. Bernard, and M. Manfait, Eds., pp. 149-154], 1 gp32 contains ≈ 45% helix, ≈ 40% β-sheet, and 15% undefined structure. Aggregation of gp32 at concentrations higher than 40 mg/mL leads to a coordination of the phenolic OH groups of 4-6 tyrosines and of all the sulfhydryl (SH) groups present in the protein with the COO- groups of protein. The latter coordination persists even at concentrations as low as 1 mg/mL. In polynucleotide-protein complexes the nucleotide shields the 4-6 tyrosine residues from coordination by the COO- groups even at high protein concentration. The presence of the nucleotide causes no shielding of the SH groups. With Raman difference spectroscopy it is shown that binding of the protein to a single-stranded nucleotide involves both tyrosine and trytophan residues. A change in the secondary structure of the protein upon binding is observed. In the complex, gp32 contains more -sheet structure than when uncomplexed. A comparison of the spectra of complexed poly(rA) and poly(dA) with the spectra of their solution conformations at 15°C reveals that in both polynucleotides the phosphodiester vibration changes upon complex formation in the same way as upon a transition from a regular to a more disordered conformation. Distortion of the phosphate-sugar-base conformation occurs upon complex formation, so that the spectra of poly(rA) and poly(dA) are more alike in the complex than they are in the free polynucleotides. The decrease in intensity of the Raman bands at 1304 cm-1 in poly(rA), at 1230 cm-1 in poly(rU), and at 1240 and 1378 cm-1 of poly(dT) may be indicative of increased stacking interactions in the complex. No influence of the nucleotide chain length upon the Raman spectrum of gp322 in the complex was detected. Both the nucleotide lines and the protein lines in the spectrum of a complex are identical in poly(dA) and (dA)8.

KW - IR-70834

U2 - 10.1002/bip.360261003

DO - 10.1002/bip.360261003

M3 - Article

VL - 26

SP - 1667

EP - 1689

JO - Biopolymers

JF - Biopolymers

SN - 0006-3525

IS - 10

ER -