A Code Controlling Specific Binding of Proteins to Double-Helical DNA and RNA

Gursky, G. V.; Tumanyan, V. G.; Заседателев, А. С.; Zhuze, A. L.; Grokhovsky, S. L.; Gottikh, B. P.

doi:10.1016/b978-0-12-722560-9.50016-0

Cited by 38 publications

(12 citation statements)

References 50 publications

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“…dT base pairs of the octanucleotide (Scheme 2) for this resonance at this time. The adenine C-2 proton is located in the minor groove and our results support proposals that require netropsin to complex with the nucleic acid in the minor groove [1,3,7]. The second adenine C-2 proton resonance in the complex can only be monitored between 80°C and 100°C (Fig.8B).…”

Section: Interactions In the Minor Groovesupporting

confidence: 74%

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Netropsin · dG‐dG‐dA‐dA‐dT‐dT‐dC‐dC Complex

Patel¹

1979

European Journal of Biochemistry

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The structure of the netropsin . dG-dG-dA-dA-dT-dT-dC-dC complex (one antibiotic molecule/ self-complementary octanucleotide duplex) and its dynamics as a function of temperature have been monitored by the nuclear magnetic resonances of the Watson-Crick protons, the nonexchangeable base and sugar protons and the backbone phosphates. The antibiotic forms a complex with the nucleic acid duplex at the dA . dT-containing tetranucleotide segment dA-dA-dT-dT, with slow migration amongst potential binding sites at low temperature. The downfield shifts in the exchangeable protons of netropsin on complex formation demonstrate the contributions of hydrogen-bonding interactions between the antibiotic and the nucleic acid to the stability of the complex. Complex formation results in changes in the glycosidic torsion angles of both thymidine residues and one deoxyadenosine residue as monitored by chemical shift changes in the thymine C-6 and adenine C-8 protons. The close proximity of the pyrrole rings of the antibiotic and the base-pair edges in the minor groove is manifested in the downfield shifts (0.3-0.5 ppm) of the pyrrole C-3 protons of netropsin and one adenine C-2 proton and one thymine N-3 base-pair proton on complex formation. The internucleotide phosphates of the octanucleotide undergo 31P chemical shift changes on addition of netropsin and these may reflect, in part, contributions from electrostatic interactions between the charged ends of the antibiotic and the backbone phosphates of the nucleic acid.The oligopeptide antibiotic netropsin (Scheme 1) isolated from Streptomyces netropsis exhibits a wide range of activities against bacteria, fungi and viruses [l -31. The complexes formed between netropsin and nucleic acids in solution have been extensively investigated by spectroscopic techniques [4-91. The antibiotic forms a complex with double-stranded DNA and stabilizes the thermal melting transition of the nucleic acid while no stabilization is observed for double-stranded RNA, D N A . RNA hybrids or singlestranded DNA [1,7]. The antibiotic exhibits a specificity for dA . dT and dI . dC base pairs but not for dG . dC base pairs, with binding unaffected by halogen atoms at the C-5 position of the pyrimidine ring [7]. These data suggest that netropsin binds in the minor groove of double-helical DNA and that the amino group at C-2 of guanosine sterically hinders binding at the dG . dC site. The complex between netropsin and dA . dT regions of DNA is stabilized by hydrogenbonding interactions between the antibiotic amide protons and acceptor groups on the base-pair edges facing the minor groove, as well as by electrostatic interactions between the charged ends of the antibiotic and the backbone phosphates. It has been demonstrated that the closest distance between bound netropsins on a DNA double helix is three base pairs and that netropsin and actinomycin can bind adjacent to each other on the DNA double helix [7,8].The three-dimensional structure of netropsin has recently been solved by X-ray analysis [lo]. The a...

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Section: Interactions In the Minor Groovesupporting

confidence: 74%

“…nucleicacid hydrogen-bonding interactions. It has been proposed that the netropsin amide protons hydrogen bond to the thymine carbonyl oxygen at C-2 or the adenine nitrogen N-3, while the charged ends form electrostatic interactions with the backbone phosphates [I, 3,7,10].…”

Section: Antibiotic Nucleic-acid Hydrogen Bondingmentioning

confidence: 99%

Netropsin · dG‐dG‐dA‐dA‐dT‐dT‐dC‐dC Complex

Patel¹

1979

European Journal of Biochemistry

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“…Our analysis suggests that, in the main, these workers (6) were very close to the truth, even though their ideas concerning the role ofthe four subunits of lac need modification. The structure we propose for the DNA-binding region of lac repressor is not consistent with models in which the operator-binding region adopts an extended 3-strand conformation (35,39) or a left-handed 8-helix (40,41). However, as can be seen in Fig.…”

mentioning

confidence: 57%

Structure of the DNA-binding region of lac repressor inferred from its homology with cro repressor.

Matthews¹,

Ohlendorf²,

Anderson³

et al. 1982

Proc. Natl. Acad. Sci. U.S.A.

132

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It is shown that the amino acid sequence and the DNA gene sequence of the 25 amino-terminal residues of the lac repressor protein of Escherichia coli are homologous with the sequences of five DNA-binding proteins: the cro repressor proteins from phage A and phage 434, the cI and cdi proteins from phage A, and the repressor protein from Salmonella phage P22. The region of homology between lac repressor and the other proteins coincides with the principal DNA-binding region ofcro repressor. In particular, residues Tyr-17 through Gln-26 oflac repressor correspond to the a-helix Gln-27 through Ala-36 of cro repressor, which we have postulated to bind within the major groove of the DNA Fig. 1 shows a comparison of the amino-terminal sequences of a series of proteins that bind to sequence-specific regions of double-stranded DNA (5). cro and 434-cro are small repressor proteins from bacteriophage A and bacteriophage 434, respectively (10-13). "cI" (often referred to as A repressor) and "P22" are larger repressor proteins from phage A and from Salmonella phage P22, respectively, that, under different circumstances, can mediate positive or negative control of gene transcription (14-18). "clI" is also larger than cro and, in conjunction with another protein (cIII), acts as a positive regulator of transcription in bacteriophage A (16,17,19,20). With the exception of cro and cI, these five proteins all recognize different sequences on the DNA.As can be seen in Fig. 1, there is extensive amino acid sequence homology between the five DNA-binding proteins. The correspondence between the five proteins can also be seen in the DNA gene sequences that code for the respective polypeptides, and, on the basis of this sequence homology, we have argued (5) that these proteins all have in common a region of tertiary structure corresponding to the segments labeled al, a2, and a3. In the cro structure, al and a2 are "structural" a-helices, whereas a3 is the "DNA recognition" a-helix, which we have postulated to lie within the major groove of B-form DNA and to be primarily responsible for the specific recognition of the DNA by the protein (4).A series ofcomparisons ofboth the amino acid sequence . (21,22) and the DNA coding sequence (23) indicates that the lac repressor protein from E. coli ("lac") may also have structural features in common with the other DNA-binding proteins. In Fig. 1 we have included the first 38 amino acids of lac, aligned to maximize the homology with the other proteins. The homology is most striking in the region 19-32 of cro (9-22 of lac), where Gly-24 is invariant and Ala-20 and Val-25. of cro, which are conserved in four of the five proteins, also occur in lac.The homology between lac and the other proteins can also be seen at the level of the DNA sequences that code for the respective polypeptides. The publication costs ofthis article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U. S. C. §1734 solely to indicate this f...

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“…The drug molecule attaches to clusters of four or more A'T or ITC, but not to G-C, base pairs (3,10,11). Alternating A-T-A-T regions bind netropsin less well than continuous runs of A or T (12,13). Binding involves both an electrostatic component from the two cationic ends and hydrogen bonds from the central three amide NH groups, although neither aspect is absolute-FIG.…”

mentioning

confidence: 99%

The molecular origin of DNA-drug specificity in netropsin and distamycin.

Kopka¹,

Yoon²,

Goodsell³

et al. 1985

Proc. Natl. Acad. Sci. U.S.A.

800

577

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X-ray analysis of the complex of netropsin with the B-DNA dodecamer of sequence C-G-C-G-A-A-T-TBrC-G-C-G reveals that the antitumor antibiotic binds within the minor groove by displacing the water molecules of the spine of hydration. Netropsin amide NH furnish hydrogen bonds to bridge DNA adenine N-3 and thymine 0-2 atoms occurring on adjacent base pairs and opposite helix strands, exactly as with the spine of hydration. The narrowness of the groove forces the netropsin molecule to sit symmetrically in the center, with its two pyrrole rings slightly non-coplanar so that each ring is parallel to the walls of its respective region of the groove. Drug binding neither unwinds nor elongates the double helix, but it does force open the minor groove by 0.5-2.0 A, and it bends back the helix axis by 8°across the region of attachment. The netropsin molecule has an intrinsic twist that favors insertion into the minor groove of B-DNA, and it is given a small additional twist upon binding. The base specificity that makes netropsin bind preferentially to runs of four or more ACT base pairs is provided not by hydrogen bonding but by close van der Waals contacts between adenine C-2 hydrogens and CH groups on the pyrrole rings of the drug molecule. Substitution of one or more pyrroles by imidazole could permit recognition of G'C base pairs as well, and it could lead to a class of synthetic "lexitropsins," capable of reading any desired short sequence of DNA base pairs.Netropsin and its close relative distamycin ( Fig. 1) are antiviral antitumor antibiotics that, although too toxic for clinical use, have received extensive study as the paradigms of base-specific yet non-intercalative DNA-binding drug molecules. First isolated from Streptomyces netropsis in 1951 (1, 2), netropsin exerts its biological activity by binding tightly to double-helical B-DNA, interfering with both replication and transcription (3, 4). It shows little or no affinity for single-stranded DNA or RNA or for double-stranded RNA or DNA-RNA hybrids (3-5), suggesting that it does not bind to the A helix. It also fails to bind to left-handed Z-DNA; in fact, binding of netropsin to DNA favors A-to-B and Z-to-B helix transitions (6, 7).Chemical protection studies (3,4,8) and Overhauser NMR experiments (9) indicate that netropsin does not intercalate between base pairs, but it binds within the minor groove of the intact double helix, using hydrogen bonds between netropsin amide NH and exposed adenine N-3 and thymine 0-2 on the floor of the minor groove. The drug molecule attaches to clusters of four or more A'T or ITC, but not to G-C, base pairs (3, 10, 11). Alternating A-T-A-T regions bind netropsin less well than continuous runs of A or T (12, 13). Binding involves both an electrostatic component from the two cationic ends and hydrogen bonds from the central three amide NH groups, although neither aspect is absolute- FIG. 1. The netropsin molecule can be regarded as being assembled from (left to right): guanidinium, amide, methylpyrrole, amide, methylpyrr...

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A Code Controlling Specific Binding of Proteins to Double-Helical DNA and RNA

Cited by 38 publications

References 50 publications

Netropsin · dG‐dG‐dA‐dA‐dT‐dT‐dC‐dC Complex

Netropsin · dG‐dG‐dA‐dA‐dT‐dT‐dC‐dC Complex

Structure of the DNA-binding region of lac repressor inferred from its homology with cro repressor.

The molecular origin of DNA-drug specificity in netropsin and distamycin.

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