DOI: 10.1002/prot.340060203. An NMR‐based molecular dynamics simulation of the interaction of the <i>lac</i> repressor headpiece and its operator in aqueous solution

An NMR‐based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution

10.1002/prot.340060203

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractThe results of a 125 psec molecular dynamics simulation of a lac headpiece–operator complex in aqueous solution are reported. The complexsatisfies essentially all experimental distance information derived from two‐dimensional nuclear magnetic resonance (2‐D‐NMR) studies. The interaction between lac repressor headpiece and its operator based on many direct‐ and water‐mediated hydrogenbonds and nonpolar contacts which allow the formation of a tight complex. Nostable hydrogen bonds between side chains and bases and found, while specific contacts occur between both nonpolar groups and, to a lesserextent, through water‐mediated hydrogen bonds. The simulated complex structure in water is intrinsically stable without application of nuclear Overhauser effect (NOE) distance restraints, while being compatible with most of the available biochemical, genetic, andchemically induced dynamic nuclear polarization (CIDNP) data.

Bibliography

de Vlieg, J., Berendsen, H. J. C., & van Gunsteren, W. F. (1989). An NMRâbased molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution. Proteins: Structure, Function, and Bioinformatics, 6(2), 104â127. Portico.

Authors 3

J. de Vlieg (first)
H. J. C Berendsen (additional)
W. F. van Gunsteren (additional)

References 64 Referenced 56

10.1038/298447a0
10.1073/pnas.79.5.1428
10.1038/290754a0
10.1038/298718a0
10.1038/317782a0
10.1073/pnas.81.13.3973
10.1038/298443a0
10.1038/290744a0
10.1093/nar/10.16.5085
10.1146/annurev.bi.53.070184.001453
10.1038/326846a0
10.1126/science.3187531
10.1126/science.3187530
10.1038/335321a0
10.1073/pnas.73.3.804
10.1016/0079-6107(76)90011-0
{'key': 'e_1_2_1_18_2', 'first-page': '155', 'volume-title': 'The Operon', 'author': 'Weber K.', 'year': '1978'} / The Operon by Weber K. (1978)
10.1016/0022-2836(79)90384-X / J. Mol. Biol. / DNA‐binding site of lac repressor probed by dimethylsulfate methylation of lac operator by Ogata R. T.
10.1073/pnas.80.19.5837
10.1002/bip.360241208
10.1016/0022-2836(85)90036-1
10.1016/S0300-9084(85)80158-9
{'key': 'e_1_2_1_24_2', 'first-page': '181', 'article-title': "Restrained molecular dynamics procedure for protein tertiary structure determination from NMR data: A lac repressor headpiece structure based on information on J‐coupling and from presence and absence of NOE's. Isr", 'volume': '27', 'author': 'de Vlieg J.', 'year': '1986', 'journal-title': 'J. Chem.'} / J. Chem. / Restrained molecular dynamics procedure for protein tertiary structure determination from NMR data: A lac repressor headpiece structure based on information on J‐coupling and from presence and absence of NOE's. Isr by de Vlieg J. (1986)
10.1002/prot.340030402
de Vlieg J. Kaptein R. van Gunsteren W. F.Molecular dynamics simulation in aqueous solution using NMR data: Application to the DNA binding domain oflacrepressor fromEscherichia coli. In preparation.
10.1007/978-1-4684-5383-6_14
10.1016/0022-2836(87)90638-3
Boelens R. Lamerichs R. M. N. J. Rullmann J. A. C. van Boom J. H. Kaptein R.The interaction oflacrepressor headpiece and its operator:A NMR view. Protein Sequence Data Anal. in press.
Rullmann J. A. C. Boelens R. Kaptein R.NMR based docking studies oflacrepressor headpiece on alacoperator fragment.UCLA Symp. in press.
{'key': 'e_1_2_1_31_2', 'volume-title': 'Computer Simulation Using Particles', 'author': 'Hockney R. W.', 'year': '1981'} / Computer Simulation Using Particles by Hockney R. W. (1981)
{'key': 'e_1_2_1_32_2', 'first-page': '5', 'volume-title': 'Molecular Dynamics and Protein Structure', 'author': 'van Gunsteren W. F.', 'year': '1985'} / Molecular Dynamics and Protein Structure by van Gunsteren W. F. (1985)
{'key': 'e_1_2_1_33_2', 'first-page': '1', 'volume-title': '“Enrico Fermi,” course 97', 'author': 'Ciccotti G.', 'year': '1986'} / “Enrico Fermi,” course 97 by Ciccotti G. (1986)
McCammon J. A. C. Harvey S. C.“Dynamics of Proteins and Nucleric Acids.” London: Cambridge University Press 1987:1–234. (10.1017/CBO9781139167864)
{'key': 'e_1_2_1_35_2', 'series-title': 'American Chemical Society Symposium Series 353, Supercomputer Research in Chemistry and Chemical Engineering', 'first-page': '106', 'author': 'Berendsen H. J. C.', 'year': '1987'} / American Chemical Society Symposium Series 353, Supercomputer Research in Chemistry and Chemical Engineering by Berendsen H. J. C. (1987)
{'key': 'e_1_2_1_36_2', 'first-page': '92', 'volume-title': 'Molecular Dynamics and Protein Structure', 'author': 'van Gunsteren W. F.', 'year': '1985'} / Molecular Dynamics and Protein Structure by van Gunsteren W. F. (1985)
10.1016/0006-291X(72)90243-4
10.1111/j.1749-6632.1986.tb20962.x
10.1016/S0022-2836(83)80144-2
10.1002/jcc.540080205
10.1002/bip.360260602
van Gunsteren W. F. Berendsen H. J. C.Groningen Molecular Simulation (GROMOS) library manual. Biomos B. V. Nijenborgh 16 Groningen The Netherlands 1987:1–229.
10.1002/bip.360230807
10.1016/0021-9991(77)90098-5
10.1080/00268977700102571
10.1007/978-94-015-7658-1_21
10.1111/j.1749-6632.1986.tb20961.x
10.1063/1.448118
10.1016/0014-5793(88)80553-2
10.1016/0079-6107(84)90007-5
Lamerichs R. M. N. J. Boelens R. Kaptein R.In: preparation.
10.1073/pnas.78.4.2179
10.1038/273443a0
10.1016/0022-2836(84)90438-8
{'key': 'e_1_2_1_55_2', 'first-page': '228', 'article-title': 'Lac repressor headpiece binds specifically to half of the Lac operator', 'volume': '22', 'author': 'Scheek R. M.', 'year': '1983', 'journal-title': 'A proton nuclear magnetic resonance study. Biochemistry'} / A proton nuclear magnetic resonance study. Biochemistry / Lac repressor headpiece binds specifically to half of the Lac operator by Scheek R. M. (1983)
10.1073/pnas.79.8.2427
10.1021/ar50149a005
10.1002/j.1460-2075.1987.tb02625.x
10.1016/0301-4622(74)80050-5
10.1021/bi00527a028
10.1021/bi00527a030
10.1038/314235a0
10.1073/pnas.83.2.303
10.1126/science.3140377
{'key': 'e_1_2_1_65_2', 'volume-title': 'Computer Simulation of Biomolecular System', 'author': 'van Gunsteren W. F.', 'year': '1989'} / Computer Simulation of Biomolecular System by van Gunsteren W. F. (1989)

Dates

Type	When
Created	20 years, 3 months ago (May 28, 2005, 9:04 p.m.)
Deposited	1 year, 10 months ago (Oct. 22, 2023, 6:29 a.m.)
Indexed	1 year, 6 months ago (Feb. 5, 2024, 7:58 p.m.)
Issued	36 years, 7 months ago (Jan. 1, 1989)
Published	36 years, 7 months ago (Jan. 1, 1989)
Published Online	21 years, 6 months ago (Feb. 3, 2004)
Published Print	36 years, 7 months ago (Jan. 1, 1989)

Funders 0

None

BibTeX

@article{de_Vlieg_1989, title={An NMR‐based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution}, volume={6}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.340060203}, DOI={10.1002/prot.340060203}, number={2}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={de Vlieg, J. and Berendsen, H. J. C and van Gunsteren, W. F.}, year={1989}, month=jan, pages={104–127} }

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